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Shehaj A, Khristov V, Mareboina M, Tufano E, Abdeen A, Rizk E, Connor J. Genetic Biomarkers in Astrocytoma: Diagnostic, Prognostic, and Therapeutic Potential. World Neurosurg 2024; 189:339-350.e1. [PMID: 38857866 DOI: 10.1016/j.wneu.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Astrocytoma is the most common adult brain tumor, with glioblastoma being the deadliest neuro-related malignancy. Despite advances in oncology, the prognosis for astrocytoma, especially glioblastoma, remains poor, and tracking disease progression is challenging due to a lack of robust biomarkers. Genetic biomarkers, including microRNAs, cell-free DNA, circulating tumor DNA, circular RNA, and long noncoding RNA, can serve as potential diagnostic and therapeutic targets. In this review, we examine the existing literature, analyzing the various less established liquid and tumor genetic biomarkers and their potential to act as diagnostic, prognostic, and therapeutic targets. We highlight the clinical challenges and limitations in implementing liquid biopsy strategies in clinical practice. The article discusses the potential of liquid biopsies as valuable tools for personalized astrocytoma management while emphasizing the need for standardized protocols and further advancements to establish their clinical utility and therapeutic application.
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Affiliation(s)
- Andrea Shehaj
- Department of Neurosurgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA.
| | - Vladimir Khristov
- Department of Neurosurgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - Manvita Mareboina
- Department of Neurosurgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - Emily Tufano
- Department of Neurosurgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - Ahmed Abdeen
- Department of Neurosurgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - Elias Rizk
- Department of Neurosurgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - James Connor
- Department of Neurosurgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
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Zhang J, Luo Z, Zheng Y, Duan M, Qiu Z, Huang C. CircRNA as an Achilles heel of cancer: characterization, biomarker and therapeutic modalities. J Transl Med 2024; 22:752. [PMID: 39127679 DOI: 10.1186/s12967-024-05562-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Circular RNAs (circRNAs) are a class of endogenous noncoding RNAs characterized by their lack of 5' caps and 3' poly(A) tails. These molecules have garnered substantial attention from the scientific community. A wide range of circRNA types has been found to be expressed in various tissues of the human body, exhibiting unique characteristics such as high abundance, remarkable stability, and tissue-specific expression patterns. These attributes, along with their detectability in liquid biopsy samples such as plasma, position circRNAs an ideal choice as cancer diagnostic and prognostic biomarkers. Additionally, several studies have reported that the functions of circRNAs are associated with tumor proliferation, metastasis, and drug resistance. They achieve this through various mechanisms, including modulation of parental gene expression, regulation of gene transcription, acting as microRNA (miRNA) sponges, and encoding functional proteins. In recent years, a large number of studies have focused on synthesizing circRNAs in vitro and delivering them to tumor tissue to exert its effects in inhibit tumor progression. Herein, we briefly discuss the biogenesis, characteristics, functions, and detection of circRNAs, emphasizing their clinical potential as biomarkers for cancer diagnosis and prognosis. We also provide an overview the recent techniques for synthesizing circRNAs and delivery strategies, and outline the application of engineered circRNAs in clinical cancer therapy.
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Affiliation(s)
- Jun Zhang
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Zai Luo
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China.
| | - Yang Zheng
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Mingyu Duan
- Department of Education, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 650 Xinsongjiang Road, Songjiang District, Shanghai, 201600, China
| | - Zhengjun Qiu
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China.
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Wang A, Chen P. Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure. BMC Med Genomics 2024; 17:193. [PMID: 39080700 PMCID: PMC11290139 DOI: 10.1186/s12920-024-01944-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/21/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Abnormal endometrial blood flow causes a decrease in endometrial receptivity and is considered a relatively independent risk factor for recurrent implantation failure (RIF). This study aimed to explore the potentially functional circRNA-miRNA-mRNA network in RIF, and further explore its mechanism. METHODS Datasets were downloaded from the GEO database to identify differentially expressed circRNAs, miRNAs and mRNAs. The circRNA-miRNA-mRNA and PPI networks were constructed using Cytoscape 3.6.0 and the STRING database, the hub genes were identified with the cytoHubba plug-in, and a circRNA-miRNA-hub mRNA regulatory sub-network was constructed. Then, GO and KEGG pathway enrichment analyses of the hub genes were performed to comprehensively analyze the mechanism of hub mRNAs in RIF. Due to the results of circRNAs-miRNAs-hub mRNAs regulatory network, we verified the expression of circRNA_0001721, circRNA_0000714, miR-17-5p, miR-29b-3p, HIF1A and VEGFA in the RIF mouse model by qRT‒PCR and western blotting. RESULTS We initially identified 175 DEmRNAs, 48 DEmiRNAs and 56 DEcircRNAs in RIF associated with angiogenesis and constructed a circRNA-miRNA‒mRNA network and PPI network. We further identified six hub genes in the acquired network. Based on these genes, functional enrichment analysis revealed that the HIF-1 signaling pathway plays a vital role in endometrial angiogenesis in RIF. In addition, the interaction networks of circRNA_0001721/miR-17-5p/HIF1A and the circRNA_0000714/miR-29b-3p/VEGFA axis were predicted. In the RIF mouse model, circRNA_0001721, circRNA_0000714, HIF1A and VEGFA were down-regulated, whereas miR-17-5p and miR-29b-3p were up-regulated according to qRT‒PCR and western blotting. CONCLUSION This study revealed that the HIF-1 signaling pathway plays a vital role in endometrial angiogenesis in RIF. The circRNA_0001721/miR-17-5p/HIF1A and circRNA_0000714/miR-29b-3p/VEGFA axes might play a role in the pathogenesis of endometrial angiogenesis in RIF.
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Affiliation(s)
- Anran Wang
- Department of Adult Chinese Medicine, Qingdao Women and Children's Hospital, Tongfu Road, Qingdao, Shandong, 266034, China.
| | - Piaopiao Chen
- Department of Orthopedics 1, Qingdao Huangdao District Second Traditional Chinese Medicine Hospital, Zhongyuan Street, Qingdao, Shandong, 266427, China
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Zhang Y, Wang Z, Wei H, Chen M. Exploring potential circRNA biomarkers for cancers based on double-line heterogeneous graph representation learning. BMC Med Inform Decis Mak 2024; 24:159. [PMID: 38844961 PMCID: PMC11157868 DOI: 10.1186/s12911-024-02564-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Compared with the time-consuming and labor-intensive for biological validation in vitro or in vivo, the computational models can provide high-quality and purposeful candidates in an instant. Existing computational models face limitations in effectively utilizing sparse local structural information for accurate predictions in circRNA-disease associations. This study addresses this challenge with a proposed method, CDA-DGRL (Prediction of CircRNA-Disease Association based on Double-line Graph Representation Learning), which employs a deep learning framework leveraging graph networks and a dual-line representation model integrating graph node features. METHOD CDA-DGRL comprises several key steps: initially, the integration of diverse biological information to compute integrated similarities among circRNAs and diseases, leading to the construction of a heterogeneous network specific to circRNA-disease associations. Subsequently, circRNA and disease node features are derived using sparse autoencoders. Thirdly, a graph convolutional neural network is employed to capture the local graph network structure by inputting the circRNA-disease heterogeneous network alongside node features. Fourthly, the utilization of node2vec facilitates depth-first sampling of the circRNA-disease heterogeneous network to grasp the global graph network structure, addressing issues associated with sparse raw data. Finally, the fusion of local and global graph network structures is inputted into an extra trees classifier to identify potential circRNA-disease associations. RESULTS The results, obtained through a rigorous five-fold cross-validation on the circR2Disease dataset, demonstrate the superiority of CDA-DGRL with an AUC value of 0.9866 and an AUPR value of 0.9897 compared to existing state-of-the-art models. Notably, the hyper-random tree classifier employed in this model outperforms other machine learning classifiers. CONCLUSION Thus, CDA-DGRL stands as a promising methodology for reliably identifying circRNA-disease associations, offering potential avenues to alleviate the necessity for extensive traditional biological experiments. The source code and data for this study are available at https://github.com/zywait/CDA-DGRL .
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Affiliation(s)
- Yi Zhang
- School of Computer Science and Engineering, Guilin University of Technology, Guilin, 541004, China
- Guangxi Key Laboratory of Embedded Technology and Intelligent System, Guilin University of Technology, Guilin, 541004, China
| | - ZhenMei Wang
- School of Big Data, Guangxi Vocational and Technical College, Nanning, 530003, China.
| | - Hanyan Wei
- Pharmacy School, Guilin Medical University, Guilin, 541004, China
| | - Min Chen
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, 421010, China
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Digby B, Finn S, Ó Broin P. Computational approaches and challenges in the analysis of circRNA data. BMC Genomics 2024; 25:527. [PMID: 38807085 PMCID: PMC11134749 DOI: 10.1186/s12864-024-10420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Circular RNAs (circRNA) are a class of non-coding RNA, forming a single-stranded covalently closed loop structure generated via back-splicing. Advancements in sequencing methods and technologies in conjunction with algorithmic developments of bioinformatics tools have enabled researchers to characterise the origin and function of circRNAs, with practical applications as a biomarker of diseases becoming increasingly relevant. Computational methods developed for circRNA analysis are predicated on detecting the chimeric back-splice junction of circRNAs whilst mitigating false-positive sequencing artefacts. In this review, we discuss in detail the computational strategies developed for circRNA identification, highlighting a selection of tool strengths, weaknesses and assumptions. In addition to circRNA identification tools, we describe methods for characterising the role of circRNAs within the competing endogenous RNA (ceRNA) network, their interactions with RNA-binding proteins, and publicly available databases for rich circRNA annotation.
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Affiliation(s)
- Barry Digby
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland.
| | - Stephen Finn
- Discipline of Histopathology, School of Medicine, Trinity College Dublin and Cancer Molecular Diagnostic Laboratory, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
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Matos AGDM, Silva GEB, Barbosa EDS, de Andrade MS, Santos Lages J, Corrêa RDGCF, Oliveira AGC, Teixeira EB, da Silva MGDOP, da Fonseca SSS, Teixeira-Júnior AAL, Alves MS, Alencar Junior AM, Khayat AS, Pinho JD. What is the role of circRNAs in the pathogenesis of cervical cancer? A systematic literature review. Front Genet 2024; 15:1287869. [PMID: 38859935 PMCID: PMC11163134 DOI: 10.3389/fgene.2024.1287869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 04/29/2024] [Indexed: 06/12/2024] Open
Abstract
Cervical Cancer (CC) is one of the most prevalent neoplasms among women, considered the leading cause of gynecological death worldwide, and the fourth most common type of cancer. Regional metastasis is closely related to the low effectiveness of treatment, and validating biomarkers can optimize accuracy in diagnosis and prognosis. Among the potential biomarkers associated with disease metastasis are circular RNAs (circRNAs), whose altered expression has been linked to CC progression. In this context, this systematic review aims to compile information on the clinical-pathological significance and describe the biological function of circRNAs. Inclusion and exclusion criteria were used to include relevant literature, followed by in silico analysis. Additionally, we employed the UALCAN tools to search for host genes of circRNAs and expression data, miRTargetLink 2.0 to predict interactions of microRNA target genes and the Cytoscape software to predict possible interactions of microRNA target genes. According to the research, most circRNAs were found to be overexpressed and described as regulators of processes such as invasion, cell proliferation, apoptosis and migration. They were also implicated in clinical significance, including metastasis, TNM staging and microRNA interactions. CircRNAs may participate in critical processes in tumorigenesis; therefore, understanding the underlying molecular mechanisms of gene regulation in CC can contribute to the accuracy of diagnosis, prognosis and therapy.
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Affiliation(s)
| | - Gyl Eanes Barros Silva
- Postgraduate Program in Adult Health, Federal University of Maranhão, São Luís, Brazil
- Laboratory of Immunofluorescence and Electron Microscopy, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- Molecular Pathology Study Group, University Hospital of the Federal University of Maranhão, São Luís, Brazil
| | | | | | - Joyce Santos Lages
- University Hospital of the Federal University of Maranhão, São Luís, Brazil
| | - Rita da Graça Carvalhal Frazão Corrêa
- Laboratory of Immunofluorescence and Electron Microscopy, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- University Hospital of the Federal University of Maranhão, São Luís, Brazil
| | | | | | | | | | - Antonio Augusto Lima Teixeira-Júnior
- Laboratory of Immunofluorescence and Electron Microscopy, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- Molecular Pathology Study Group, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Matheus Silva Alves
- State University of the Tocantina Region of Maranhão, Department of Health Sciences, Imperatriz, Maranhão, Brazil
| | - Antonio Machado Alencar Junior
- Molecular Pathology Study Group, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- University Hospital of the Federal University of Maranhão, São Luís, Brazil
| | - André Salim Khayat
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
| | - Jaqueline Diniz Pinho
- Laboratory of Immunofluorescence and Electron Microscopy, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- Molecular Pathology Study Group, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- State University of Maranhão, Zé Doca, Maranhão, Brazil
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
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Zhang D, Dong X, Li X, Yang Y, Li H, Hong Y, Yang G, Kong X, Wang X, Ma X. Moxibustion ameliorates chronic inflammatory visceral pain via spinal circRNA-miRNA-mRNA networks: a central mechanism study. Mol Brain 2024; 17:23. [PMID: 38750560 PMCID: PMC11097453 DOI: 10.1186/s13041-024-01093-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
This study aimed to unveil the central mechanism of moxibustion treating chronic inflammatory visceral pain (CIVP) from the angle of circRNA-miRNA-mRNA networks in the spinal cord. The rat CIVP model was established using a mixture of 5% (w/v) 2,4,6-trinitrobenzene sulfonic acid and 50% ethanol at a volume ratio of 2:1 via enema. Rats in the moxibustion group received herb-partitioned moxibustion at Tianshu (ST25, bilateral) and Qihai (CV6) points. The abdominal withdrawal reflex (AWR), mechanical withdrawal threshold (MWT), and thermal withdrawal latency (TWL) were adopted for pain behavior observation and pain sensitivity assessment. The circRNA, miRNA, and mRNA expression profiles were detected using the high-throughput sequencing technique. Relevant databases and bioinformatics analysis methods were used to screen for differentially expressed (DE) RNAs and build a circRNA-miRNA-mRNA (competing endogenous RNA) ceRNA regulatory network. The real-time quantitative PCR was employed to verify the sequencing result. CIVP rat models had a significantly higher AWR and lower TWL and MWT than normal rats. Between normal and model rats, there were 103 DE-circRNAs, 16 DE-miRNAs, and 397 DE-mRNAs in the spinal cord. Compared with the model group, the moxibustion group had a lower AWR and higher TWL and MWT; between these two groups, there were 118 DE-circRNAs, 15 DE-miRNAs, and 804 DE-mRNAs in the spinal cord. Two ceRNA networks were chosen to be verified. As a result, moxibustion's analgesic effect on visceral pain in CIVP rats may be associated with regulating the circRNA_02767/rno-miR-483-3p/Gfap network in the spinal cord and improving central sensitization.
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Affiliation(s)
- Dan Zhang
- Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Xiaoqing Dong
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Department of Acupuncture and Moxibustion, Xi'an Hospital of Encephalopathy, Shaanxi University of Chinese Medicine, Shaanxi, 710032, China
| | - Xiaoying Li
- Department of Acupuncture and Moxibustion, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Yanting Yang
- Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Hongna Li
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yue Hong
- Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Guang Yang
- Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Xiehe Kong
- Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Xuejun Wang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
| | - Xiaopeng Ma
- Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China.
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
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Yan S, Wang Z, Lan D, Niu J, Jian X, He F, Tang W, Hu C, Liu W. Circ_PABPC1 promotes the malignancy of gastric cancer through interacting with ILK to activate NF-κB pathway. Exp Cell Res 2024; 438:114058. [PMID: 38688434 DOI: 10.1016/j.yexcr.2024.114058] [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: 02/17/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Gastric cancer (GC) is a common cancer type with both high incidence and mortality. Recent studies have revealed an important role of circRNA in the development of GC. However, more experiments are needed to reveal the precise molecular mechanisms of circRNA in GC development. METHODS Bioinformatics analysis was conducted to predict the potential role of circ_PABPC1 in GC and the target proteins of circ_PABPC1. Quantitative RT-PCR, Western blot and immunohistochemistry assays were conducted to detect the levels of circ_PABPC1, NF-κB p65, NF-κB p65 (Ser536) and ILK. MTT, Edu staining, cell scratch-wound and trans-well assays were carried out to detect cell proliferation, migration and invasion. The interaction between ILK and circ_PABPC1 was confirmed by RNA immunoprecipitation (RIP), RNA pull-down and fluorescence in situ hybridization assays. Genetically modified GC cells were injected into mice to evaluate the tumor growth performance. RESULTS This study found that the high expression of circ_PABPC1 was associated with a poor prognosis of GC. The up-regulation of circ_PABPC1 promoted the proliferation, migration and invasion of GC cells. Circ_PABPC1 bound to ILK protein, thereby preventing the degradation of ILK. ILK mediated the effect of circ_PABPC1 on GC cells through activating NF-κB. CONCLUSION circ_PABPC1 promotes the malignancy of GC cells through binding to ILK to activate NF-κB signaling pathway.
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Affiliation(s)
- Siqi Yan
- Departments of Oncology, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, 410011, China; Departments of Radiotherapy, Hunan Provincial Hospital of Integrated Chinese and Western Medicine, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan, 410006, China
| | - Zhu Wang
- Departments of Radiotherapy, Hunan Provincial Hospital of Integrated Chinese and Western Medicine, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan, 410006, China
| | - Dongqiang Lan
- Departments of Radiotherapy, Hunan Provincial Hospital of Integrated Chinese and Western Medicine, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan, 410006, China
| | - Junjie Niu
- Departments of Radiotherapy, Hunan Provincial Hospital of Integrated Chinese and Western Medicine, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan, 410006, China
| | - Xiaolan Jian
- Departments of Radiotherapy, Hunan Provincial Hospital of Integrated Chinese and Western Medicine, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan, 410006, China
| | - Fengjiao He
- Departments of Radiotherapy, Hunan Provincial Hospital of Integrated Chinese and Western Medicine, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan, 410006, China; Departments of Oncology, Xiangya Hospital of Central-South University, Changsha, Hunan, 410008, China
| | - Weizhi Tang
- Departments of Radiotherapy, Hunan Provincial Hospital of Integrated Chinese and Western Medicine, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan, 410006, China
| | - Chunhong Hu
- Departments of Oncology, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, 410011, China.
| | - Wei Liu
- Departments of Radiotherapy, Hunan Provincial Hospital of Integrated Chinese and Western Medicine, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan, 410006, China.
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Ashrafizadeh M, Dai J, Torabian P, Nabavi N, Aref AR, Aljabali AAA, Tambuwala M, Zhu M. Circular RNAs in EMT-driven metastasis regulation: modulation of cancer cell plasticity, tumorigenesis and therapy resistance. Cell Mol Life Sci 2024; 81:214. [PMID: 38733529 PMCID: PMC11088560 DOI: 10.1007/s00018-024-05236-w] [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: 12/05/2023] [Revised: 03/05/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024]
Abstract
The non-coding RNAs comprise a large part of human genome lack of capacity in encoding functional proteins. Among various members of non-coding RNAs, the circular RNAs (circRNAs) have been of importance in the pathogenesis of human diseases, especially cancer. The circRNAs have a unique closed loop structure and due to their stability, they are potential diagnostic and prognostic factors in cancer. The increasing evidences have highlighted the role of circRNAs in the modulation of proliferation and metastasis of cancer cells. On the other hand, metastasis has been responsible for up to 90% of cancer-related deaths in patients, requiring more investigation regarding the underlying mechanisms modulating this mechanism. EMT enhances metastasis and invasion of tumor cells, and can trigger resistance to therapy. The cells demonstrate dynamic changes during EMT including transformation from epithelial phenotype into mesenchymal phenotype and increase in N-cadherin and vimentin levels. The process of EMT is reversible and its reprogramming can disrupt the progression of tumor cells. The aim of current review is to understanding the interaction of circRNAs and EMT in human cancers and such interaction is beyond the regulation of cancer metastasis and can affect the response of tumor cells to chemotherapy and radiotherapy. The onco-suppressor circRNAs inhibit EMT, while the tumor-promoting circRNAs mediate EMT for acceleration of carcinogenesis. Moreover, the EMT-inducing transcription factors can be controlled by circRNAs in different human tumors.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Radiation Oncology, Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jingyuan Dai
- School of computer science and information systems, Northwest Missouri State University, Maryville, MO, 64468, USA.
| | - Pedram Torabian
- Cumming School of Medicine, Arnie Charbonneau Cancer Research Institute, University of Calgary, Calgary, AB, T2N 4Z6, Canada
- Department of Medical Sciences, University of Calgary, Calgary, AB, T2N 4Z6, Canada
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, V6H3Z6, Canada
| | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Translational Sciences, Xsphera Biosciences Inc. Boston, Boston, MA, USA
| | - Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Irbid, Jordan
| | - Murtaza Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln, LN6 7TS, UK.
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Minglin Zhu
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, Hubei, 430071, China.
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Bakinowska E, Kiełbowski K, Skórka P, Dach A, Olejnik-Wojciechowska J, Szwedkowicz A, Pawlik A. Non-Coding RNA as Biomarkers and Their Role in the Pathogenesis of Gastric Cancer-A Narrative Review. Int J Mol Sci 2024; 25:5144. [PMID: 38791187 PMCID: PMC11121563 DOI: 10.3390/ijms25105144] [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: 04/08/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Non-coding RNAs (ncRNAs) represent a broad family of molecules that regulate gene expression, including microRNAs, long non-coding RNAs and circular RNAs, amongst others. Dysregulated expression of ncRNAs alters gene expression, which is implicated in the pathogenesis of several malignancies and inflammatory diseases. Gastric cancer is the fifth most frequently diagnosed cancer and the fourth most common cause of cancer-related death. Studies have found that altered expression of ncRNAs may contribute to tumourigenesis through regulating proliferation, apoptosis, drug resistance and metastasis. This review describes the potential use of ncRNAs as diagnostic and prognostic biomarkers. Moreover, we discuss the involvement of ncRNAs in the pathogenesis of gastric cancer, including their interactions with the members of major signalling pathways.
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Affiliation(s)
| | | | | | | | | | | | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (E.B.); (K.K.); (P.S.); (A.D.); (J.O.-W.); (A.S.)
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11
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Deng LQ, Shi CJ, Zhou ST, Zeng WQ, Xian YF, Wang YY, Fu WM, Lin HL, Liu W, Zhang JF. EIF4A3-negatively driven circular RNA β-catenin (circβ-catenin) promotes colorectal cancer progression via miR-197-3p/CTNND1 regulatory axis. Br J Cancer 2024; 130:1517-1528. [PMID: 38459187 PMCID: PMC11058807 DOI: 10.1038/s41416-024-02612-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Circβ-catenin, our first reported circRNA, has been reported to mediate tumorigenesis in various cancers. However, its biological functions and underlying mechanisms in colorectal cancer (CRC) remain unknown. METHODS The qRT-PCR examination was used to detect the expression of circβ-catenin, miR-197-3p, and CTNND1 in cells and human tissues. Western blot was conducted to detect the protein expression levels. The biological function of circβ-catenin was verified by MTT, colony formation, wound healing, and transwell assays. The in vivo effects of circβ-catenin were verified by nude mice xenograft and metastasis models. The regulatory network of circβ-catenin/miR-197-3p/CTNND1 was confirmed via dual-luciferase reporter and RIP assays. RESULTS In the present study, circβ-catenin was found to promote CRC cell proliferation and metastasis in vitro and in vivo. Mechanistically, circβ-catenin served as miRNA decoy to directly bind to miR-197-3p, then antagonized the repression of the target gene CTNND1, and eventually promoted the malignant phenotype of CRC. More interestingly, the inverted repeated Alu pairs termed AluJb1/2 and AluY facilitated the biogenesis of circβ-catenin, which could be partially reversed by EIF4A3 binding to Alu element AluJb2. CONCLUSIONS Our findings illustrated a novel mechanism of circβ-catenin in modulating CRC tumorigenesis and metastasis, which provides a potential therapeutic target for CRC patients.
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Affiliation(s)
- Li-Qiang Deng
- Cancer center, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
| | - Chuan-Jian Shi
- Cancer center, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
| | - Shu-Ting Zhou
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Wei-Qiang Zeng
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Yan-Fang Xian
- School of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yu-Yan Wang
- Cancer center, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
| | - Wei-Ming Fu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Han-Li Lin
- Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China.
| | - Wei Liu
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China.
| | - Jin-Fang Zhang
- Cancer center, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China.
- Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China.
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China.
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12
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Fang R, Yuan W, Mao C, Cao J, Chen H, Shi X, Cong H. Human circular RNA hsa_circ_0000231 clinical diagnostic effectiveness as a new tumor marker in gastric cancer. Cancer Rep (Hoboken) 2024; 7:e2081. [PMID: 38703060 PMCID: PMC11069127 DOI: 10.1002/cnr2.2081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Owing to the subtlety of initial symptoms associated with gastric cancer (GC), the majority of patients are diagnosed at later stages. Given the absence of reliable diagnostic markers, it is imperative to identify novel markers that exhibit high sensitivity and specificity. Circular RNA, a non-coding RNA, plays an important role in tumorigenesis and development and is well expressed in body fluids. AIMS In this study, we aimed to identify hsa_circ_0000231 as a new biomarker for the diagnosis of GC and to assess its clinical diagnostic value in serum. METHODS AND RESULTS The stability and correctness of hsa_circ_0000231 was determined by agarose gel electrophoresis, Rnase R assay and Sanger sequencing. Real-time quantitative polymerase chain reaction (qRT-PCR) was designed to discover the expression level of hsa_circ_0000231 and whether it has dynamic serum monitoring capability. The correlation between hsa_circ_0000231 and clinicopathological parameters was analyzed by collecting clinical and pathological data from GC patients. In addition, diagnostic efficacy was assessed by constructing receiver operating characteristic curves (ROC). Hsa_circ_0000231 exhibits a stable and consistently expressed structure. In GC serum, cells, and tissues, it demonstrates reduced expression levels. Elevated expression levels observed postoperatively suggest its potential for dynamic monitoring. Additionally its expression level correlates with TNM staging and neuro/vascular differentiation. The area under ROC curve (AUC) for hsa_circ_0000231 is 0.781, indicating its superior diagnostic value compared to CEA, CA19-9, and CA72-4. The combination of these four indicators enhances diagnostic accuracy, with an AUC of 0.833. CONCLUSIONS The stable expression of hsa_circ_0000231 in the serum of gastric cancer patients holds promise as a novel biomarker for both the diagnosis and dynamic monitoring of GC.
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Affiliation(s)
- Ronghua Fang
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
- Department of Clinical MedicineMedical School of Nantong UniversityNantongChina
| | - Wentao Yuan
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
- Department of Clinical MedicineMedical School of Nantong UniversityNantongChina
| | - Chunyan Mao
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
- Department of Clinical MedicineMedical School of Nantong UniversityNantongChina
| | - Jing Cao
- Department of Blood TransfusionAffiliated Hospital of Nantong UniversityNantongChina
| | - Hongmei Chen
- Vip WardAffiliated Hospital of Nantong UniversityNantongChina
| | - Xiuying Shi
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
| | - Hui Cong
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
- Department of Blood TransfusionAffiliated Hospital of Nantong UniversityNantongChina
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13
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Tang Z, Li J, Lu B, Zhang X, Yang L, Qi Y, Jiang S, Wu Q, Wang Y, Cheng T, Xu M, Sun P, Wang X, Miao K, Wu H, Huang J. CircBIRC6 facilitates the malignant progression via miR-488/GRIN2D-mediated CAV1-autophagy signal axis in gastric cancer. Pharmacol Res 2024; 202:107127. [PMID: 38438090 DOI: 10.1016/j.phrs.2024.107127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Circular RNAs (circRNAs) represent a novel class of non-coding RNAs that play significant roles in tumorigenesis and tumor progression. High-throughput sequencing of gastric cancer (GC) tissues has identified circRNA BIRC6 (circBIRC6) as a potential circRNA derived from the BIRC6 gene, exhibiting significant upregulation in GC tissues. The expression of circBIRC6 is notably elevated in GC patients. Functionally, it acts as a molecular sponge for miR-488, consequently upregulating GRIN2D expression and promoting GC proliferation, migration, and invasion. Moreover, overexpression of circBIRC6 leads to increased GRIN2D expression, which in turn enhances caveolin-1 (CAV1) expression, resulting in autophagy deficiency due to miR-488 sequestration. This cascade of events significantly influences tumorigenesis in vivo. Our findings collectively illustrate that the CircBIRC6-miR-488-GRIN2D axis fosters CAV1 expression in GC cells, thereby reducing autophagy levels. Both circBIRC6 and GRIN2D emerge as potential targets for treatment and independent prognostic factors for GC patients.
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Affiliation(s)
- Zhiyuan Tang
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Jieying Li
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Bing Lu
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Xiaojing Zhang
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Lei Yang
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Yue Qi
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Sutian Jiang
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Qianqian Wu
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Yingjing Wang
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Tong Cheng
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Manyu Xu
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Pingping Sun
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China
| | - Xudong Wang
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Kai Miao
- MOE Frontier Science Centre for Precision Oncology, University of Macau, Macau.
| | - Han Wu
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China.
| | - Jianfei Huang
- Department of Clinical Biobank, Department of Pharmacy, Affiliated Hospital of Nantong University & Department of Pathology, Medical School of Nantong University, Nantong 226001, China.
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14
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Mou X, Peng Z, Yin T, Sun X. Non-endoscopic Screening for Esophageal Squamous Cell Carcinoma: Recent Advances. J Gastrointest Cancer 2024; 55:118-128. [PMID: 37924487 DOI: 10.1007/s12029-023-00980-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most common tumors in the gastrointestinal tract, and China has a high incidence area with a high burden on the disease. As early symptoms of ESCC are not obvious, the mortality rate is high, and it is often diagnosed in the intermediate and advanced stages. However, early screening and treatment may reduce morbidity and mortality. METHODS Screening methods are divided into endoscopic and non-endoscopic screening. RESULTS Endoscopic screening cannot be widely used because of its invasive nature and high cost. Currently, non-endoscopic screening consists primarily of tumor biomarkers and cytology, and tumor biomarkers including autoantibodies, circulating tumor cells, circulating tumor DNA, exosomes and serum metabolomics are more likely to be effective. But the efficiency of early diagnosis of esophageal cancer is low and the accuracy of screening needs to be improved. The aim of this study is to summarize advances in non-endoscopic esophageal cancer screening and strategies to provide a scientific basis and research idea for esophageal cancer prevention and control. CONCLUSIONS Non-endoscopic screening is better than endoscopic screening. And the application of tumor biomarkers is much better than other non-endoscopic screening methods.
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Affiliation(s)
- Xiao Mou
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, China.
| | - Zhenglin Peng
- College of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Tao Yin
- College of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
- Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Xingwang Sun
- College of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
- Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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15
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Samare-Najaf M, Kouchaki H, Moein Mahini S, Saberi Rounkian M, Tavakoli Y, Samareh A, Karim Azadbakht M, Jamali N. Prostate cancer: Novel genetic and immunologic biomarkers. Clin Chim Acta 2024; 555:117824. [PMID: 38316287 DOI: 10.1016/j.cca.2024.117824] [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: 10/29/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024]
Abstract
Prostate cancer (PCa) is considered one of the most prevalent male malignancies worldwide with a global burden estimated to increase over the next two decades. Due to significant mortality and debilitation of survival, early diagnosis has been described as key. Unfortunately, current diagnostic serum-based strategies have low specificity and sensitivity. Histologic examination is invasive and not useful for treatment and monitoring purposes. Hence, a plethora of studies have been conducted to identify and validate an efficient noninvasive approach in the diagnosis, staging, and prognosis of PCa. These investigations may be categorized as genetic (non-coding biomarkers and gene markers), immunologic (immune cells, interleukins, cytokines, antibodies, and auto-antibodies), and heterogenous (PSA-related markers, PHI-related indices, and urinary biomarkers) subgroups. This review examines current approaches and potential strategies using biomarker panels in PCa.
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Affiliation(s)
- Mohammad Samare-Najaf
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Hosein Kouchaki
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Moein Mahini
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Masoumeh Saberi Rounkian
- Student Research Committee, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Yasaman Tavakoli
- Department of Medicine, Mazandaran University of Medical Sciences, Sari, Mazandaran, Iran
| | - Ali Samareh
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Navid Jamali
- Department of Laboratory Sciences, Sirjan School of Medical Sciences, Sirjan, Iran.
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16
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Yang Z, Chen JQ, Liu TJ, Chen YL, Ma ZK, Fan YZ, Wang ZX, Xu S, Wang K, Wang XY, Li L, Xie HJ. Knocking down AR promotes osteoblasts to recruit prostate cancer cells by altering exosomal circ-DHPS/miR-214-3p/CCL5 pathway. Asian J Androl 2024; 26:195-204. [PMID: 37966336 PMCID: PMC10919426 DOI: 10.4103/aja202351] [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: 04/25/2023] [Accepted: 09/04/2023] [Indexed: 11/16/2023] Open
Abstract
Tumor-derived exosomes have been shown to play a key role in organ-specific metastasis, and the androgen receptor regulates prostate cancer (PCa) progression. It is unclear whether the androgen receptor regulates the recruitment of prostate cancer cells to the bone microenvironment, even bone metastases, through exosomes. Here, we found that exosomes isolated from PCa cells after knocking down androgen receptor (AR) or enzalutamide treatment can facilitate the migration of prostate cancer cells to osteoblasts. In addition, AR silencing or treatment with the AR antagonist enzalutamide may increase the expression of circular RNA-deoxyhypusine synthase (circ-DHPS) in PCa cells, which can be transported to osteoblasts by exosomes. Circ-DHPS acts as a competitive endogenous RNA (ceRNA) against endogenous miR-214-3p to promote C-C chemokine ligand 5 ( CCL5 ) levels in osteoblasts. Increasing the level of CCL5 in osteoblasts could recruit more PCa cells into the bone microenvironment. Thus, blocking the circ-DHPS/miR-214-3p/CCL5 signal may decrease exosome-mediated migration of prostate cancer cells to osteoblasts.
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Affiliation(s)
- Zhao Yang
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Jia-Qi Chen
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Tian-Jie Liu
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yu-Le Chen
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Zhen-Kun Ma
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yi-Zeng Fan
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Zi-Xi Wang
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Shan Xu
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Ke Wang
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Xin-Yang Wang
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Hong-Jun Xie
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
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Yoshitomi R, Kumazoe M, Lee KW, Marugame Y, Fujimura Y, Tachibana H. Regulatory effect of Epigallocatechin-3-O-gallate on circular RNA expression in mouse liver. J Nutr Biochem 2024; 124:109506. [PMID: 37890708 DOI: 10.1016/j.jnutbio.2023.109506] [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: 02/03/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
There are few studies on the connection between food components and circular RNA (circRNA), a type of noncoding RNA that is significant for living organisms. (-)-Epigallocatechin-3-O-gallate (EGCG) has been reported to have various biological effects, and elucidation of the molecular mechanism is important for clarifying the functionality of EGCG. In the current study, we looked at how EGCG regulates the expression of circRNA in the liver, which expresses a lot of circRNAs. Mice were given EGCG (10 mg/kg b.w.) orally for one week before circRNA microarray testing was done on their livers. The microarray analysis revealed that mice treated with EGCG had altered expression of 35 circRNAs in their livers. To clarify the function of mmu_circRNA_011775, one of the circRNAs upregulated by EGCG, mouse liver cells after the mmu_circRNA_011775 expression vector was transfected into NMuLi cells, next-generation sequencing (NGS) was used to analyze the gene expression. NGS analysis shows that the expression of the genes responsible for liver fibrosis and inflammation. Gene ontology (GO) analysis showed that mmu_circRNA_011775 changed the meaning of GO terms associated with the cardiovascular system. In the microarray, EGCG altered 35 genes expression. Among them, pre-ribosomal RNA-derived circRNA mmu_circRNA_011775 regulated the expression of various genes related to liver fibrosis and cardiovascular system.
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Affiliation(s)
- Ren Yoshitomi
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Motofumi Kumazoe
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kwan-Woo Lee
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yuki Marugame
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yoshinori Fujimura
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Hirofumi Tachibana
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.
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18
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Bai Z, Wu Y, Cai W, Zheng Y, Hui T, Yue C, Sun J, Wang Y, Xu Z, Wang Z. High-throughput analysis of CircRNA in cows with naturally infected Staphylococcus aureus mammary gland. Anim Biotechnol 2023; 34:4236-4246. [PMID: 36576137 DOI: 10.1080/10495398.2022.2140056] [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] [Indexed: 12/29/2022]
Abstract
Circular RNAs (CircRNA) are a special type of non-coding RNA molecule with a closed ring structure and are not affected by RNA exonucases. It has stable expression, is not easy to degrade, and exists in most eukaryotes. However, circRNA regulation of cow mastitis has not been widely recognized. Mammary epithelial tissues were collected from healthy Holstein cows (HCN) and mastitis Holstein cows (HCU). RNA sequencing (RNA SEQ) was performed for the differentially expressed circRNAs, and analysis results showed that 19 differentially expressed circRNAs were identified in HCN and HCU, among which 6 circRNAs were up-regulated and 13 circRNAs were down-regulated. We randomly selected nine circRNAs for Q-PCR verification, and the results showed consistent expression. Three circRNAs: circRNA2860, circRNA5323 and circRNA4027 were confirmed to be significantly differentially expressed circRNAs in cow mastitis. Also, their host genes TRPS1, SLC12A2 and MYH11 might be directly or indirectly play a role in cow mastitis. Furthermore, RNA polymerase transcription factor binding and tight junction are most enriched in GO and KEGG pathways, respectively. In addition, the regulatory network of circRNA-miRNA has been inferred from a bioinformatics perspective, which may help to understand the underlying molecular mechanism of circRNAs involved in regulating mastitis in cows.
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Affiliation(s)
- Zhixian Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuanyuan Zheng
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Taiyu Hui
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chang Yue
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jiaming Sun
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanru Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhiguo Xu
- Dalian Modern Agricultural Production Development Service Center, Dalian, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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19
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Derakhshan Z, Bahmanpour S, Alaee S, Fallahi J, Tabei SMB. The Role of Circular RNAs in Male Infertility and Reproductive Cancers: A Narrative Review. IRANIAN JOURNAL OF MEDICAL SCIENCES 2023; 48:527-541. [PMID: 38094281 PMCID: PMC10715113 DOI: 10.30476/ijms.2022.95302.2661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/01/2022] [Accepted: 08/28/2022] [Indexed: 12/18/2023]
Abstract
Infertility is a global health problem affecting about 15% of all couples, of which 50% are due to male infertility. Although the etiology of infertility is known in most infertile men, idiopathic male infertility remains a challenge. Therefore, there is a need for novel diagnostic methods to detect the underlying mechanisms and develop appropriate therapies. Recent studies have focused on the role of non-coding RNAs (ncRNAs) in male infertility. Circular RNAs (CircRNAs), a type of ncRNAs, are found to play a key role in the development of some pathological conditions, including cardiovascular diseases, diabetes, cancers, autoimmune diseases, etc. Several studies have reported the presence of CircRNAs and their target genes in the human reproductive system. In addition, their expression in testicular tissues, sperm cells, and seminal fluid has been identified. Abnormal expression of CircRNAs has been associated with azoospermia and asthenozoospermia in infertile men. The present narrative review provides a brief description of the role of CircRNAs in spermatogenic cells, male infertility, and reproductive cancers. In addition, some CircRNAs have been identified as potential biomarkers for disease detection and treatment.
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Affiliation(s)
- Zahra Derakhshan
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soghra Bahmanpour
- Department of Anatomy and Reproductive Biology, School of Medical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sanaz Alaee
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Bagher Tabei
- Department of Medical Genetics, School of Medical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
- Maternal-Fetal Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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20
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Feng XY, Zhu SX, Pu KJ, Huang HJ, Chen YQ, Wang WT. New insight into circRNAs: characterization, strategies, and biomedical applications. Exp Hematol Oncol 2023; 12:91. [PMID: 37828589 PMCID: PMC10568798 DOI: 10.1186/s40164-023-00451-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed, endogenous ncRNAs. Most circRNAs are derived from exonic or intronic sequences by precursor RNA back-splicing. Advanced high-throughput RNA sequencing and experimental technologies have enabled the extensive identification and characterization of circRNAs, such as novel types of biogenesis, tissue-specific and cell-specific expression patterns, epigenetic regulation, translation potential, localization and metabolism. Increasing evidence has revealed that circRNAs participate in diverse cellular processes, and their dysregulation is involved in the pathogenesis of various diseases, particularly cancer. In this review, we systematically discuss the characterization of circRNAs, databases, challenges for circRNA discovery, new insight into strategies used in circRNA studies and biomedical applications. Although recent studies have advanced the understanding of circRNAs, advanced knowledge and approaches for circRNA annotation, functional characterization and biomedical applications are continuously needed to provide new insights into circRNAs. The emergence of circRNA-based protein translation strategy will be a promising direction in the field of biomedicine.
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Affiliation(s)
- Xin-Yi Feng
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shun-Xin Zhu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ke-Jia Pu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Heng-Jing Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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21
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Zhou Z, Chen C, Han B, Wang Y, Liu Y, Liu Q, Xu X, Yin Y, Sun B. Circular RNA in cholangiocarcinoma: A systematic review and bibliometric analysis. Pathol Res Pract 2023; 249:154755. [PMID: 37651837 DOI: 10.1016/j.prp.2023.154755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is a common primary liver malignancy with a poor prognosis. Many studies have demonstrated the involvement of circular RNAs (circRNAs) in tumorigenesis and progression. METHODS Four online databases (PubMed, Web of Science, Embase, and Scopus) were searched on May 04, 2023, for original papers regarding CCA and circRNAs. Bibliometric analysis of included studies was performed on R Studio and GraphPad Prism. RESULTS Thirty studies were included in the systematic review and bibliometric analysis. The systematic review showed that circRNAs were involved in CCA proliferation, invasion, metastasis, chemotherapy resistance, and other biological processes and were related to the prognosis of patients and many clinicopathological features. Exosomal circRNAs provide a new idea for the early diagnosis of CCA. The bibliometric analysis showed a significant upward trend in the number of studies on CCA and circRNAs. The 30 included papers had 201 authors and were published in 22 English journals. The first paper was published in 2018, and the second paper was the most cited (148 citations). CONCLUSION This systematic review and bibliometric analysis demonstrates that circRNAs in CCA have not been studied enough. CircRNAs play an important role in the occurrence and progression of CCA. They may become new targets for the diagnosis, treatment, and prognostic monitoring of CCA.
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Affiliation(s)
- Zheyu Zhou
- Department of General Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing 210008, China
| | - Chaobo Chen
- Department of General Surgery, Xishan People's Hospital of Wuxi City, Wuxi 214105, China; Department of Hepatobiliary and Transplantation Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Bing Han
- Department of Hepatobiliary and Transplantation Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yinyu Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Yang Liu
- Department of Hepatobiliary and Transplantation Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Qiaoyu Liu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Xiaoliang Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.
| | - Yin Yin
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.
| | - Beicheng Sun
- Department of General Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing 210008, China; Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.
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22
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Theron D, Hopkins LN, Sutherland HG, Griffiths LR, Fernandez F. Can Genetic Markers Predict the Sporadic Form of Alzheimer's Disease? An Updated Review on Genetic Peripheral Markers. Int J Mol Sci 2023; 24:13480. [PMID: 37686283 PMCID: PMC10488021 DOI: 10.3390/ijms241713480] [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: 08/04/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia that affects millions of individuals worldwide. Although the research over the last decades has provided new insight into AD pathophysiology, there is currently no cure for the disease. AD is often only diagnosed once the symptoms have become prominent, particularly in the late-onset (sporadic) form of AD. Consequently, it is essential to further new avenues for early diagnosis. With recent advances in genomic analysis and a lower cost of use, the exploration of genetic markers alongside RNA molecules can offer a key avenue for early diagnosis. We have here provided a brief overview of potential genetic markers differentially expressed in peripheral tissues in AD cases compared to controls, as well as considering the changes to the dynamics of RNA molecules. By integrating both genotype and RNA changes reported in AD, biomarker profiling can be key for developing reliable AD diagnostic tools.
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Affiliation(s)
- Danelda Theron
- School of Behavioural and Health Sciences, Faculty of Heath Sciences, Australian Catholic University, Banyo, QLD 4014, Australia;
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
| | - Lloyd N. Hopkins
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
| | - Heidi G. Sutherland
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
| | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
| | - Francesca Fernandez
- School of Behavioural and Health Sciences, Faculty of Heath Sciences, Australian Catholic University, Banyo, QLD 4014, Australia;
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
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23
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Molaei P, Savari M, Mahdavinezhad A, Najafi R, Afshar S, Esfandiari N, Khorrami R, Hashemi M. Highlighting functions of apoptosis and circular RNAs in colorectal cancer. Pathol Res Pract 2023; 248:154592. [PMID: 37295258 DOI: 10.1016/j.prp.2023.154592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Colorectal cancer (CRC) is known as one of the global problems that endangers the lives of thousands of people every year. Various treatments have been used to deal with this disease, but in some cases, they are not effective. Circular RNAs, as a novel class of noncoding RNAs, have different expression levels and various functions in cancer cells, such as gene regulation through microRNA sponging. They play an important role in various cellular processes, including differentiation, proliferation, invasion, and apoptosis. Changes in the process of apoptosis are closely related to the progression or inhibition of various malignancies. Induction of apoptosis in cancer cells is a promising target for tumor therapy. In this study, circRNAs were investigated as being central to the induction or inhibition of apoptosis in CRC. It is hoped that through targeted changes in the function of these biomolecules, better outcomes will be achieved in cancer treatment. Perhaps better outcomes for cancer treatment can be achieved by using new methods and modifying the expression of these nucleic acids. However, using this method may come with challenges and limitations.
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Affiliation(s)
- Pejman Molaei
- Department of Molecular Medicine and Genetics, Research Center for Molecular Medicine, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Marzieh Savari
- Department of Molecular Medicine and Genetics, Research Center for Molecular Medicine, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Mahdavinezhad
- Department of Molecular Medicine and Genetics, Research Center for Molecular Medicine, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rezvan Najafi
- Department of Molecular Medicine and Genetics, Research Center for Molecular Medicine, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeid Afshar
- Department of Molecular Medicine and Genetics, Research Center for Molecular Medicine, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Negin Esfandiari
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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24
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Malviya A, Bhuyan R. The recent advancements in circRNA research: From biogenesis to therapeutic interventions. Pathol Res Pract 2023; 248:154697. [PMID: 37506629 DOI: 10.1016/j.prp.2023.154697] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023]
Abstract
Circular RNAs (circRNAs) belong to the genre of long non-coding RNAs that are formed by special back-splicing events and are currently the molecule of interest for studies globally due their involvement in various ailments like diabetes, neurodegenerative disorders, cardio-vascular diseases and cancers. These class of highly stable RNAs participate in diverse cellular functionalities including microRNA (miRNA) sponging, ceRNA (competing endogenous RNA) activity or via exhibiting RNA binding protein (RBP) interactions. They are also known to regulate cancer progression both positively and negatively through various biological pathways such as, modulating the cell cycle and apoptotic pathways, epigenetic regulation, and translational and/or transcriptional regulations etc. Given its significance, a variety of computational tools and dedicated databases have been created for the identification, quantification, and differential expression of such RNAs in combination with sequencing approaches. In this review, we provide a comprehensive analysis of the numerous computational tools, pipelines, and online resources developed in recent years for the detection and annotation of circRNAs. We also summarise the most recent findings regarding the characteristics, functions, biological processes, and involvement of circRNAs in diseases. The review emphasises the significance of circRNAs as potential disease biomarkers and new treatment targets.
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Affiliation(s)
- Ayushi Malviya
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Tonk, Rajasthan 304022, India
| | - Rajabrata Bhuyan
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Tonk, Rajasthan 304022, India.
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25
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Yuan H, Liu F, Long J, Duan G, Yang H. A review on circular RNAs and bacterial infections. Int J Biol Macromol 2023:125391. [PMID: 37321437 DOI: 10.1016/j.ijbiomac.2023.125391] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
Bacterial infections and related diseases have been a major burden on social public health and economic stability around the world. However, the effective diagnostic methods and therapeutic approaches to treat bacterial infections are still limited. As a group of non-coding RNA, circular RNAs (circRNAs) that were expressed specifically in host cells and played a key regulatory role have the potential to be of diagnostic and therapeutic value. In this review, we systematically summarize the role of circRNAs in common bacterial infections and their potential roles as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Haitao Yuan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fang Liu
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Jinzhao Long
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Guangcai Duan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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26
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Haque S, Bhushan Raman R, Salam M. Role of Biomarkers in Hepatocellular Carcinoma and Their Disease Progression. LIVER CANCER - GENESIS, PROGRESSION AND METASTASIS 2023. [DOI: 10.5772/intechopen.105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the third leading and common lethal cancers worldwide. Early detection of tumorigenesis of hepatocellular carcinoma is through ultrasonography, computerized tomography (CT) scans, and magnetic resonance imaging (MRI) scans; however, these methods are not up to the mark, so a search for an efficient biomarker for early diagnosis and treatment of hepatocarcinogenesis is important. Proteomic and genomic approaches aid to develop new promising biomarkers for the diagnosis of HCC at the early stages. These biomarkers not only help in prognosis but also provide better therapeutic intervention against HCC. Among the different biomarker candidates, liquid biopsy [including circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA)] has recently emerged as a noninvasive detection technique for the characterization of circulating cells, providing a strong basis and early diagnosis for the individualized treatment of patients. This review provides the current understanding of HCC biomarkers that predict the risk of HCC recurrence.
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27
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Chen Y, Han X, Huang X, Zhou H, Yu H, Wang L, Liu Z, Liu B, Huang J, Xiong Y, Huang J, Shao Y, Zhu D, Liang Z, Yang Z, Su W. Circular RNA-mediated ceRNA network was identified in human lung adenocarcinoma by high-throughput sequencing. Thorac Cancer 2023. [PMID: 37137710 DOI: 10.1111/1759-7714.14884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 05/05/2023] Open
Abstract
OBJECTIVES Aberrantly expressed circular RNAs (circRNAs) have been detected in many types of tumors. Hence, they are currently investigated as candidate biomarkers for diagnostic and potential targets for therapy in cancers. The objective of this study was to assess the expression profile of circRNA in lung adenocarcinoma (LUAD). METHODS This study included 14 pairs of postoperative lung adenocarcinoma specimens, including cancer tissues and matched adjacent tissues. Second-generation sequencing was applied to the specimens to determine the circRNA expression in them among the 5242 distinct circRNAs detected. RESULTS We identified a total of 18 significantly dysregulated circRNAs in the LUAD tissues: upregulation in four and downregulation in 14. ROC (The receiver operating characteristic curve) further suggested that hsa_circ_0120106, has_circ_0007342, has_circ_0005937, and circRNA_0000826 could potentially be used as biomarkers in the diagnosis of LUAD. Furthermore, study of the circRNA-microRNA (miRNA)-messenger RNA (mRNA) revealed interactions between the 18 dysregulated circRNA and several cancer-related miRNAs. Finally, a further Kyoto Encyclopedia of Genes and Genomes analysis showed that the cell cycle phase transition, p53 signaling pathway, AMP-activated protein kinase (AMPK) relative signaling pathway, and so on were key putative pathways in the process of LUAD. CONCLUSIONS These findings demonstrated the correlation between abnormality in circRNA expression and LUAD, which lays the foundation of making CircRNAs candidate biomarkers in the diagnosis of LUAD.
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Affiliation(s)
- Yongyang Chen
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiaoling Han
- Second Faculty of Clinical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiaobi Huang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Honglian Zhou
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Hui Yu
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Lihui Wang
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Center for Translational Medicine & School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - Zijian Liu
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Baiyang Liu
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jian Huang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yinghuan Xiong
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jian Huang
- Department of Thoracic Surgery, Maoming People's Hospital, Maoming, China
| | - Yang Shao
- Technical Department, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Dongqin Zhu
- Technical Department, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Zhu Liang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhixiong Yang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Wenmei Su
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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28
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Sun Y, Qu X, Qiu P, Mao C. A nanoparticle-based molecular beacon for directly detecting attomolar small RNA from plasma without purification. Talanta 2023; 260:124602. [PMID: 37148690 DOI: 10.1016/j.talanta.2023.124602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/08/2023]
Abstract
Molecular beacons (MBs) are DNA-based probes that detect DNA or RNA fragments and hold promise for monitoring diseases and studying protein-nucleic acid interactions. MBs usually use fluorescent molecules as fluorophores for reporting the target detection event. However, the fluorescence of the traditional fluorescent molecules can bleach and even be interfered with the background autofluorescence, reducing the detection performance. Hence, we propose to develop a nanoparticle-based MB (NPMB) that uses upconversion nanoparticles (UCNPs) as a fluorophore, which can be excited by near-infrared light to avoid background autofluorescence and thus enables us to detect small RNA from complicated clinical samples such as plasma. Specifically, we employ a DNA hairpin structure, with one segment complementary to the target RNA, to position a quencher (gold nanoparticles, Au NPs) and the UCNP fluorophore in close proximity, leading to the quenching of the fluorescence of UCNPs in the absence of a target nucleic acid. Only when the hairpin structure is complementary with the detection target, will the hairpin structure be destroyed to separate Au NPs and UCNPs, resulting in the instant recovery of the fluorescence signal of UCNPs and the consequent ultrasensitive detection of the target concentrations. The NPMB has an ultra-low background signal because UCNPs can be excited with NIR light with a wavelength longer than the emitted visible light. We demonstrate that the NPMB can successfully detect a small (22-nt) RNA (using a microRNA cancer biomarker, miR-21, as an example) and a small single-stranded DNA (complementing the cDNA of miR-21) in aqueous solutions from 1 aM to 1 pM, with the linear detection range being 10 aM to 1 pM for the former and 1 aM to 100 fM for the latter. We further show that the NPMB can be used to detect unpurified small RNA (miR-21) in clinical samples such as plasma with the same detection region. Our work suggests that the NPMB is a promising label-free and purification-free method for detecting small nucleic acid biomarkers in clinical samples with a detection limit as low as the aM level.
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Affiliation(s)
- Yueyi Sun
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Xuewei Qu
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Penghe Qiu
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Chuanbin Mao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, PR China.
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29
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Zhang H, Liu L, Liu J, Dang P, Hu S, Yuan W, Sun Z, Liu Y, Wang C. Roles of tumor-associated macrophages in anti-PD-1/PD-L1 immunotherapy for solid cancers. Mol Cancer 2023; 22:58. [PMID: 36941614 PMCID: PMC10029244 DOI: 10.1186/s12943-023-01725-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/16/2023] [Indexed: 03/23/2023] Open
Abstract
In recent years, tumor immunotherapy has made significant progress. However, tumor immunotherapy, particularly immune checkpoint inhibitors (e.g., PD-1/PD-L1 inhibitors), benefits only a tiny proportion of patients in solid cancers. The tumor microenvironment (TME) acts a significant role in tumor immunotherapy. Studies reported that tumor-associated macrophages (TAMs), as one of the main components of TME, seriously affected the therapeutic effect of PD-1/PD-L1 inhibitors. In this review, we analyzed TAMs from epigenetic and single-cell perspectives and introduced the role and mechanisms of TAMs in anti-programmed death protein 1(anti-PD-1) therapy. In addition, we summarized combination regimens that enhance the efficacy of tumor PD-1/PD-L1 inhibitors and elaborated on the role of the TAMs in different solid cancers. Eventually, the clinical value of TAMs by influencing the therapeutic effect of tumor PD-1/PD-L1 inhibitors was discussed. These above are beneficial to elucidate poor therapeutic effect of PD-1/PD-L1 inhibitors in solid tumors from the point of view of TAMs and explore the strategies to improve its objective remission rate of solid cancers.
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Affiliation(s)
- Hao Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Lin Liu
- Henan Institute of Interconnected Intelligent Health Management, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Department of Ultrasound, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Pengyuan Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Shengyun Hu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China.
- Henan Institute of Interconnected Intelligent Health Management, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Yang Liu
- Department of Radiotherapy, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450001, China.
| | - Chengzeng Wang
- Henan Institute of Interconnected Intelligent Health Management, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Department of Ultrasound, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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30
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HAN ZY, HUANG SJ, WANG R, GUAN HQ. Screening of differential circRNAs in the placenta of patients with preeclampsia and their regulatory mechanism. MINERVA BIOTECHNOLOGY AND BIOMOLECULAR RESEARCH 2023. [DOI: 10.23736/s2724-542x.22.02913-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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31
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Lu H, Zhang Z, Yuan X, Song H, Li P. The role of circular RNA hsa_circ_0001789 as a diagnostic biomarker in gastric carcinoma. Scand J Gastroenterol 2023; 58:248-253. [PMID: 36111683 DOI: 10.1080/00365521.2022.2122865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Circular RNA (circRNA) is a kind of endogenous non-coding RNAs and has shown diagnostic values in various cancers. This study aimed to explore whether hsa_circ_0001789 could be a novel biomarker for gastric cancer (GC). METHODS Quantitative reverse transcriptase PCR was used to detect the expression of hsa_circ_0001789 in 108 paired GC and paracancerous tissues as well as in 24 paired plasma specimens. Possible associations between hsa_circ_0001789 expression and clinicopathologic factors of GC patients were examined using one-way ANOVA. A receiver operating characteristic (ROC) curve was established to investigate the diagnostic value of hsa_circ_0001789 in GC. RESULTS GC tissues and plasma samples showed down-regulated hsa_circ_0001789 levels than their counterparts, which were closely correlated with the malignant characteristics of GC. The area under the ROC curve (AUC) of hsa_circ_0001789 in GC tissues was 0.82, while the cut-off value was 9.5, indicating a favorable diagnostic value. Compared with the traditional tumor biomarkers, hsa_circ_0001789 had preferred AUCs that reached 0.786 for predicting the stage of invasion, 0.603 for predicting the stage of lymphatic metastasis, 0.722 for predicting the stage of distant metastasis, and 0.786 for predicting TNM stage. CONCLUSIONS Hsa_circ_0001789 may be a novel biomarker for the diagnosis of gastric carcinoma.
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Affiliation(s)
- Hongpeng Lu
- Department of Gastroenterology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Zhixin Zhang
- Department of Gastroenterology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Xin Yuan
- Department of Gastroenterology, Ningbo First Hospital, Ningbo, Zhejiang Province, China.,College of Medicine, Ningbo University, Ningbo, Zhejiang Province, China
| | - Haojun Song
- Department of Gastroenterology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Peifei Li
- Department of Gastroenterology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
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Long Q, Lv B, Jiang S, Lin J. The Landscape of Circular RNAs in Cardiovascular Diseases. Int J Mol Sci 2023; 24:ijms24054571. [PMID: 36902000 PMCID: PMC10003248 DOI: 10.3390/ijms24054571] [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: 01/24/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Cardiovascular disease (CVD) remains the leading cause of mortality globally. Circular RNAs (circRNAs) have attracted extensive attention for their roles in the physiological and pathological processes of various cardiovascular diseases (CVDs). In this review, we briefly describe the current understanding of circRNA biogenesis and functions and summarize recent significant findings regarding the roles of circRNAs in CVDs. These results provide a new theoretical basis for diagnosing and treating CVDs.
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Affiliation(s)
- Qi Long
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bingjie Lv
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shijiu Jiang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jibin Lin
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Correspondence:
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Zhao D, Chen H, Zhong J, Zhou X, Zhang J, Zhang Y. circRNA-ZCCHC14 affects the chondrogenic differentiation ability of peripheral blood-derived mesenchymal stem cells by regulating GREM1 through miR-181a. Sci Rep 2023; 13:2889. [PMID: 36804426 PMCID: PMC9938902 DOI: 10.1038/s41598-023-29561-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/07/2023] [Indexed: 02/20/2023] Open
Abstract
circRNAs play an important role in the progression of osteoarthritis (OA). Therefore, we aimed to reveal the mechanism of action of circRNA-ZCCHC14 in OA. OA animal and cell models were constructed, and clinical samples were collected. The expression of circRNA-ZCCHC14 and miR-181a was detected by RT‒qPCR. The chondrogenic differentiation ability of peripheral blood-derived mesenchymal stem cells (PBMSCs) was detected by Alcian blue staining. The expression of chondrogenic differentiation-related proteins was detected by Western blotting. Double fluorescein experiments verified the targeting relationship of miR-181a with circRNA-ZCCHC14 and GREM1. Upregulation of circRNA-ZCCHC14 was observed in blood, in BMP-2- and TGF-β3-treated PBMSCs from OA patients and in animal models. Knockdown of circRNA-ZCCHC14 promoted the chondrogenic differentiation ability of PBMSCs. circRNA-ZCCHC14 was found to bind to miR-181a and negatively regulate miR-181a expression. Inhibition of miR-181a reversed the promoting effect of circRNA-ZCCHC14 knockdown on the chondrogenic differentiation ability of PBMSCs. GREM1 was identified as a target of miR-181a. Overexpression and knockdown of GREM1 regulated the expression of BMP2, which in turn affected the chondrogenic differentiation ability of PBMSCs, indicating that GREM1 and BMP2 have antagonistic effects and that they jointly regulate the chondrogenic differentiation of PBMSCs. circRNA-ZCCHC14 may promote the chondrogenic differentiation ability of PBMSCs by regulating miR-181a and inhibiting the expression of GREM1.
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Affiliation(s)
- Daohong Zhao
- Department of Orthopaedics, The Second Affiliated Hospital of Kunming Medical University, Kunming, China.
| | - Hong Chen
- Department of Sports Medicine, The First People’s Hospital of Kunming City, Kunming, China
| | - Jia Zhong
- Department of Orthopaedics, The People’s Hospital of XiShuangBanNa State, Jinghong, China
| | - Xizong Zhou
- Department of Orthopaedics, The People’s Hospital of YanJing County, Zhaotong, China
| | - Jun Zhang
- grid.415444.40000 0004 1800 0367Department of Orthopaedics, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuhao Zhang
- grid.415444.40000 0004 1800 0367Department of Orthopaedics, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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Digby B, Finn SP, Ó Broin P. nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs. BMC Bioinformatics 2023; 24:27. [PMID: 36694127 PMCID: PMC9875403 DOI: 10.1186/s12859-022-05125-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are a class of covalenty closed non-coding RNAs that have garnered increased attention from the research community due to their stability, tissue-specific expression and role as transcriptional modulators via sequestration of miRNAs. Currently, multiple quantification tools capable of detecting circRNAs exist, yet none delineate circRNA-miRNA interactions, and only one employs differential expression analysis. Efforts have been made to bridge this gap by way of circRNA workflows, however these workflows are limited by both the types of analyses available and computational skills required to run them. RESULTS We present nf-core/circrna, a multi-functional, automated high-throughput pipeline implemented in nextflow that allows users to characterise the role of circRNAs in RNA Sequencing datasets via three analysis modules: (1) circRNA quantification, robust filtering and annotation (2) miRNA target prediction of the mature spliced sequence and (3) differential expression analysis. nf-core/circrna has been developed within the nf-core framework, ensuring robust portability across computing environments via containerisation, parallel deployment on cluster/cloud-based infrastructures, comprehensive documentation and maintenance support. CONCLUSION nf-core/circrna reduces the barrier to entry for researchers by providing an easy-to-use, platform-independent and scalable workflow for circRNA analyses. Source code, documentation and installation instructions are freely available at https://nf-co.re/circrna and https://github.com/nf-core/circrna .
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Affiliation(s)
- Barry Digby
- grid.6142.10000 0004 0488 0789School of Mathematical and Statistical Sciences, National University of Ireland, Galway, Ireland
| | - Stephen P. Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Dublin, Ireland
| | - Pilib Ó Broin
- grid.6142.10000 0004 0488 0789School of Mathematical and Statistical Sciences, National University of Ireland, Galway, Ireland
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Yu Q, Dai J, Shu M. Circular RNA-0072309 has antitumor influences in Hep3B cell line by targeting microRNA-665. Biofactors 2023; 49:79-89. [PMID: 32048412 DOI: 10.1002/biof.1618] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Liver cancer is a malignant tumor that occurs in the liver and has a high mortality rate. We strived to detect the role and mechanism of circRNA-0072309 in liver cancer. Hep3B cell line was transfected with pc-circ and si-circ for viability, colony formation, apoptosis, migration, and invasion tests, which were individually performed by CCK-8, colony formation detection, flow cytometry assay, migration and invasion assays. What is more, the luciferase reporter assay was conducted to determine the target relationship between the circRNA-0072309 and microRNA (miR)-665. The expression of circRNA-0072309 was examined by qRT-PCR. The expression of proteins was examined via western blot. CircRNA-0072309 was lowly expressed in liver cancer tissues and positively associated with 5-year survival rate. The viability, colony formation, invasive and migratory ability were inhibited by abundant circRNA-0072309, which promoted cell apoptosis on the contrary. CircRNA-0072309 knockdown induced opposite effects, but could not affect apoptosis. Overexpressed miR-665 in tumor tissues was targeted and negatively controlled by circRNA-0072309. The PI3K/AKT and Wnt/β-catenin pathways were inhibited by abundant circRNA-0072309. miR-665 overexpression disturbed those effects derived from pc-circ. The circRNA-0072309 had antitumor influences in Hep3B cell line through targeting miR-665 relying on the deactivation of PI3K/AKT and Wnt/β-catenin pathways.
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Affiliation(s)
- Qiuyun Yu
- Department of Clinical Laboratory, Hwa Mei Hospital, University of Chinese Academy of Science (Ningbo No.2 Hospital), Ningbo, Zhejiang, China
| | - Jinhua Dai
- Department of Clinical Laboratory, Hwa Mei Hospital, University of Chinese Academy of Science (Ningbo No.2 Hospital), Ningbo, Zhejiang, China
| | - Ming Shu
- Department of Hepatobiliary Surgery, Hwa Mei Hospital, University of Chinese Academy of Science (Ningbo No.2 Hospital), Ningbo, Zhejiang, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, Zhejiang, China
- Ningbo Clinical Research Center for Digestive System Tumors, Ningbo, Zhejiang, China
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Jiang B, Xie D, Wang S, Li X, Wu G. Advances in early detection methods for solid tumors. Front Genet 2023; 14:1091223. [PMID: 36911396 PMCID: PMC9998680 DOI: 10.3389/fgene.2023.1091223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
During the last decade, non-invasive methods such as liquid biopsy have slowly replaced traditional imaging and invasive pathological methods used to diagnose and monitor cancer. Improvements in the available detection methods have enabled the early screening and diagnosis of solid tumors. In addition, advances in early detection methods have made the continuous monitoring of tumor progression using repeat sampling possible. Previously, the focus of liquid biopsy techniques included the following: 1) the isolation of circulating tumor cells, circulating tumor DNA, and extracellular tumor vesicles from solid tumor cells in the patient's blood; in addition to 2) analyzing genomic and proteomic data contained within the isolates. Recently, there has been a rapid devolvement in the techniques used to isolate and analyze molecular markers. This rapid evolvement in detection techniques improves their accuracy, especially when few samples are available. In addition, there is a tremendous expansion in the acquisition of samples and targets for testing; solid tumors can be detected from blood and other body fluids. Test objects have also expanded from samples taken directly from cancer to include indirect objects affected in cancer development. Liquid biopsy technology has limitations. Even so, this detection technique is the key to a new phase of oncogenetics. This review aims to provide an overview of the current advances in liquid biopsy marker selection, isolation, and detection methods for solid tumors. The advantages and disadvantages of liquid biopsy technology will also be explored.
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Affiliation(s)
- Bowen Jiang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Deqian Xie
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shijin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiunan Li
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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Zhang Q, Chen B, Yang P, Wu J, Pang X, Pang C. Bioinformatics-based study reveals that AP2M1 is regulated by the circRNA-miRNA-mRNA interaction network and affects Alzheimer's disease. Front Genet 2022; 13:1049786. [PMID: 36468008 PMCID: PMC9716081 DOI: 10.3389/fgene.2022.1049786] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/31/2022] [Indexed: 09/30/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurological disease that worsens with time. The hallmark illnesses include extracellular senile plaques caused by β-amyloid protein deposition, neurofibrillary tangles caused by tau protein hyperphosphorylation, and neuronal loss accompanying glial cell hyperplasia. Noncoding RNAs are substantially implicated in related pathophysiology, according to mounting data. However, the function of these ncRNAs is mainly unclear. Circular RNAs (circRNAs) include many miRNA-binding sites (miRNA response elements, MREs), which operate as miRNA sponges or competing endogenous RNAs (ceRNAs). The purpose of this study was to look at the role of circular RNAs (circRNAs) and microRNAs (miRNAs) in Alzheimer's disease (AD) as possible biomarkers. The Gene Expression Omnibus (GEO) database was used to obtain an expression profile of Alzheimer's disease patients (GSE5281, GSE122603, GSE97760, GSE150693, GSE1297, and GSE161435). Through preliminary data deletion, 163 genes with significant differences, 156 miRNAs with significant differences, and 153 circRNAs with significant differences were identified. Then, 10 key genes, led by MAPT and AP2M1, were identified by the mediation center algorithm, 34 miRNAs with obvious prognosis were identified by the cox regression model, and 16 key circRNAs were selected by the database. To develop competitive endogenous RNA (ceRNA) networks, hub circRNAs and mRNAs were used. Finally, GO analysis and clinical data verification of key genes were carried out. We discovered that a down-regulated circRNA (has_circ_002048) caused the increased expression of numerous miRNAs, which further inhibited the expression of a critical mRNA (AP2M1), leading to Alzheimer's disease pathology. The findings of this work contribute to a better understanding of the circRNA-miRNA-mRNA regulating processes in Alzheimer's disease. Furthermore, the ncRNAs found here might become novel biomarkers and potential targets for the development of Alzheimer's drugs.
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Affiliation(s)
- Qi Zhang
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Bishuang Chen
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Ping Yang
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Jipan Wu
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Xinping Pang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Chaoyang Pang
- School of Computer Science, Sichuan Normal University, Chengdu, China
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Ding P, Liu P, Wu H, Yang P, Tian Y, Zhao Q. Functional properties of circular RNAs and research progress in gastric cancer. Front Oncol 2022; 12:954637. [DOI: 10.3389/fonc.2022.954637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of closed circular non-coding RNAs widely exist in eukaryotes, with high stability and species conservation. A large number of studies have shown that circRNAs are abnormally expressed in various tumor tissues, and are abundant in plasma with long half-life and high specificity, which may be served as potential tumor biomarkers for early diagnosis, treatment and prognosis of malignant tumors. However, the role of circRNAs is still poorly understood in gastric cancer. This article reviews the research progress of circRNAs in gastric cancer in recent years so as to explore the relationship between circRNAs and the occurrence and the development of gastric cancer, and provide new ideas for the diagnosis and treatment of gastric cancer.
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Wang Y, Li Q, Wang S, Wang BJ, Jin Y, Hu H, Fu QS, Wang JW, Wu Q, Qian L, Cao TT, Xia YB, Huang XX, Xu L. The role of noncoding RNAs in cancer lipid metabolism. Front Oncol 2022; 12:1026257. [PMID: 36452489 PMCID: PMC9704363 DOI: 10.3389/fonc.2022.1026257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/20/2022] [Indexed: 12/03/2023] Open
Abstract
Research on noncoding ribonucleic acids (ncRNAs) is mostly and broadly focused on microRNAs (miRNAs), cyclic RNAs (circRNAs), and long ncRNAs (lncRNAs), which have been confirmed to play important roles in tumor cell proliferation, invasion, and migration. Specifically, recent studies have shown that ncRNAs contribute to tumorigenesis and tumor development by mediating changes in enzymes related to lipid metabolism. The purpose of this review is to discuss the characterized ncRNAs involved in the lipid metabolism of tumors to highlight ncRNA-mediated lipid metabolism-related enzyme expression in malignant tumors and its importance to tumor development. In this review, we describe the types of ncRNA and the mechanism of tumor lipid metabolism and analyze the important role of ncRNA in tumor lipid metabolism and its future prospects from the perspectives of ncRNA biological function and lipid metabolic enzyme classification. However, several critical issues still need to be resolved. Because ncRNAs can affect tumor processes by regulating lipid metabolism enzymes, in the future, we can study the unique role of ncRNAs from four aspects: disease prevention, detection, diagnosis, and treatment. Therefore, in the future, the development of ncRNA-targeted therapy will become a hot direction and shoulder a major task in the medical field.
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Affiliation(s)
- Ye Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Qian Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Song Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Bi-jun Wang
- Department of Clinical Medicine, Clinical College of Anhui Medical University, Hefei, Anhui, China
| | - Yan Jin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Hao Hu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Qing-sheng Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Jia-wei Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Qing Wu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Long Qian
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Ting-ting Cao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Ya-bin Xia
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Xiao-xu Huang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Li Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
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Xie J, Jiang H, Zhao Y, Jin XR, Li B, Zhu Z, Zhang L, Liu J. Prognostic and diagnostic value of circRNA expression in prostate cancer: A systematic review and meta-analysis. Front Oncol 2022; 12:945143. [PMID: 36419885 PMCID: PMC9676972 DOI: 10.3389/fonc.2022.945143] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/10/2022] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are receiving increasing attention as novel biomarkers. Our goal was to investigate the diagnostic, clinicopathological, and prognostic utility of circRNAs in prostate cancer (PCa). METHODS Relevant literature was searched in PubMed, Web of Science, and EMBASE. Sensitivity, specificity, diagnostic odds ratio (DOR), negative likelihood ratio (NLR), positive likelihood ratio (PLR), and the area under the curve (AUC) were calculated to evaluate the diagnostic accuracy of circRNA expression. circRNAs' clinical, pathological, and prognostic value was examined using pooled odds ratios (ORs) and hazard ratios (HRs). RESULTS This meta-analysis included 23 studies, with 5 for diagnosis, 16 for clinicopathological parameters, and 10 for prognosis. For diagnostic value, the pooled sensitivity, pooled specificity, PLR, NLR, DOR, and AUC were 0.82, 0.62, 2.17, 0.29, 7.37, and 0.81, respectively. Upregulation of carcinogenic circRNAs was associated with poor clinical parameters (Gleason score: OR = 0.222, 95% CI: 0.145-0.340; T classification: OR = 0.274, 95% CI: 0.175-0.430; lymph node metastasis: OR = 0.353, 95% CI: 0.175-0.716; tumor size: OR = 0.226, 95% CI: 0.099-0.518) and could predict poor survival outcomes (HR = 2.408, 95% CI: 1.559-3.720, p < 0.001). Conversely, downregulation of tumor-suppressor circRNAs was also associated with poor clinical parameters (Gleason score: OR = 1.689, 95% CI: 1.144-2.493; T classification: OR = 2.586, 95% CI: 1.779-3.762) and worse prognosis (HR = 1.739, 95% CI: 1.147-2.576, p = 0.006). CONCLUSION Our results showed that circRNAs might be useful biomarkers for the diagnosis and prognosis of PCa. SYSTEMATIC REVIEW REGISTRATION https://www.crd.york.ac.uk/prospero/, identifier CRD42021284785.
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Affiliation(s)
| | | | | | | | | | | | | | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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Lan W, Dong Y, Chen Q, Liu J, Wang J, Chen YPP, Pan S. IGNSCDA: Predicting CircRNA-Disease Associations Based on Improved Graph Convolutional Network and Negative Sampling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3530-3538. [PMID: 34506289 DOI: 10.1109/tcbb.2021.3111607] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accumulating evidences have shown that circRNA plays an important role in human diseases. It can be used as potential biomarker for diagnose and treatment of disease. Although some computational methods have been proposed to predict circRNA-disease associations, the performance still need to be improved. In this paper, we propose a new computational model based on Improved Graph convolutional network and Negative Sampling to predict CircRNA-Disease Associations. In our method, it constructs the heterogeneous network based on known circRNA-disease associations. Then, an improved graph convolutional network is designed to obtain the feature vectors of circRNA and disease. Further, the multi-layer perceptron is employed to predict circRNA-disease associations based on the feature vectors of circRNA and disease. In addition, the negative sampling method is employed to reduce the effect of the noise samples, which selects negative samples based on circRNA's expression profile similarity and Gaussian Interaction Profile kernel similarity. The 5-fold cross validation is utilized to evaluate the performance of the method. The results show that IGNSCDA outperforms than other state-of-the-art methods in the prediction performance. Moreover, the case study shows that IGNSCDA is an effective tool for predicting potential circRNA-disease associations.
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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.
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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,
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Gong Z, Rong X, Li X, Wang H, Liu D, He L, Pan J, Shen Q, Peng Y. Male mice exposed to chronic intermittent ethanol exposure exhibit significant upregulation or downregulation of circular RNAs. THE AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE 2022; 48:562-572. [PMID: 35838410 DOI: 10.1080/00952990.2022.2073449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
B a ckground: Circular RNAs (circRNAs) have been crucially implicated in various diseases, however, their involvement in chronic intermittent ethanol (CIE) exposure remains unclear.O bjective: The present study was conducted to evaluate the circular RNA expression alteration in brain samples and to identify the molecular mechanisms underlying chronic intermittent ethanol exposure.M ethods: Male C57BL/6J mice (10 for each group) were given 4 weeks of chronic intermittent ethanol exposure. Whole brain samples were collected for high-throughput sequencing and circRNA bioinformatic analysis. Real-time quantitative PCR (RI-qPCR) and agarose electrophoresis were used to validate the differentially expressed circRNAs. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis were performed. A p level < 0.05 was considered statistically significant.R esults: Compared with the control group and baseline values, the CIE group showed a significant increase in ethanol intake. High-throughput sequencing revealed 399 significantly different circRNAs in CIE mice, including 150 up-regulated circRNAs and 249 down-regulated circRNAs. GO analysis showed that the most significantly enriched term for biological process, cellular component, and molecular function were GO:0050885, GO:0016020 and GO:0005515, respectively. The most enriched pathways in KEGG analysis were GABAergic synapse (mmu04727), followed by retrograde endocannabinoid (eCB) signaling (mmu04723) and morphine addiction (mmu05032). Among the circRNAs, RT-qPCR confirmed 14 upregulated and 13 downregulated circRNAs in the brain tissues with 9 upregulated and 10 downregulated circRNAs being observed in blood samples.C onclusions: Our study suggests that chronic ethanol exposure upregulates or downregulates circRNAs in the brain, which, in turn, could alter neurotransmitter release and signal transduction.
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Affiliation(s)
- Zhe Gong
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China.,Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoming Rong
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Xiangpen Li
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Hongxuan Wang
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Dandan Liu
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Lei He
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Jingrui Pan
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Qingyu Shen
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Ying Peng
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China.,Memorial Hospital, Sun Yat-sen UniversityGuangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-sen, Guangzhou, China
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Hanineva A, Park KS, Wang JJ, DeAngelis MM, Farkas MH, Zhang SX. Emerging roles of circular RNAs in retinal diseases. Neural Regen Res 2022; 17:1875-1880. [PMID: 35142661 PMCID: PMC8848606 DOI: 10.4103/1673-5374.335691] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Retinal disorders are a group of ocular diseases whose onset is associated with a number of aberrant molecular and cellular processes or physical damages that affect retinal structure and function resulting in neural and vascular degeneration in the retina. Current research has primarily focused on delaying retinal disease with minimal success in preventing or reversing neuronal degeneration. In this review, we explore a relatively new field of research involving circular RNAs, whose potential roles as biomarkers and mediators of retinal disease pathogenesis have only just emerged. While knowledge of circular RNAs function is limited given its novelty, current evidence has highlighted their roles as modulators of microRNAs, regulators of gene transcription, and biomarkers of disease development and progression. Here, we summarize how circular RNAs may be implicated in the pathogenesis of common retinal diseases including diabetic retinopathy, glaucoma, proliferative vitreoretinopathy, and age-related macular degeneration. Further, we explore the potential of circular RNAs as novel biomarkers and therapeutic targets for the diagnosis and treatment of retinal diseases.
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Affiliation(s)
- Aneliya Hanineva
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Karen Sophia Park
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Joshua J Wang
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Margaret M DeAngelis
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York; Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, USA
| | - Michael H Farkas
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York; Research Service, Veterans Administration Western New York Healthcare System; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Sarah X Zhang
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
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Sohn EJ. Differentially expression and function of circular RNAs in ovarian cancer stem cells. J Ovarian Res 2022; 15:97. [PMID: 35978436 PMCID: PMC9382745 DOI: 10.1186/s13048-022-01014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background Circular RNAs (circRNAs) are noncoding RNAs that regulate miRNA expression; however, their functions in cancer stem cells (CSCs) are not well known. Methods To determine the function of differentially expression of circRNAs associated with ovarian CSCs, circRNA profiling was conducted using a circRNA-based microarray on sphere-forming cells derived from A2780 and SKOV3 epithelial ovarian cancer cells termed A2780-SP and SKOV3-SP compared to monolayer cells such as A2780 and SKOV3 cells, respectively. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to predict the biological functions of the circRNAs expressed in CSCs. Results The circRNA-based microarray data showed that 159 circRNAs were significantly upregulated (fold change > 1.5) and 55 circRNAs were downregulated in ovarian CSCs compared to monolayer cells. GO and KEGG enrichment analysis of differentially expressed circRNAs in ovarian CSCs showed that they were mainly involved in cell cycle, histone modification, cellular protein metabolic process, cell cycle, apoptotic signaling pathway, and ubiquitin-mediated proteolysis in ovarian cancer. In addition, the hsa-circRNA000963-miRNA-mRNA regulatory network was constructed based on potential target of miRNAs. These analyses involved that the biological function of the hsa-circRNA00096/miRNA/mRNA network was involved in signaling pathways regulating pluripotency of stem cells, PI3K-Akt signaling pathway, cell cycle, p53 signaling pathway, Wnt signaling pathway, calcium modulating pathway, and production of miRNAs involved in gene silencing by miRNA. Conclusions Our data demonstrate the expression profiles of circRNAs in ovarian CSCs and suggest that circRNAs may be potential diagnostic and predictive biomarkers of ovarian cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-022-01014-z.
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Affiliation(s)
- Eun Jung Sohn
- Pusan National University, Yangsan, 50612, Republic of Korea.
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Role of circular RNAs in disease progression and diagnosis of cancers: An overview of recent advanced insights. Int J Biol Macromol 2022; 220:973-984. [PMID: 35977596 DOI: 10.1016/j.ijbiomac.2022.08.085] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/19/2022] [Accepted: 08/11/2022] [Indexed: 02/07/2023]
Abstract
Tumor microenvironment (TME) is a crucial regulator of tumor progression and cells in the TME release a number of molecules that are responsible for anaplasticity, invasion, metastasis of tumor, establishing stem cell niches, up-regulation and down-regulation of various pathways in cancer cells, interfering with immune surveillance and immune escape. Moreover, they can serve as diagnostic markers, and determine effective therapies. Among them, CircRNAs have gained special attention due to their involvement in mutated pathways in cancers. By functioning as a molecular sponge for miRNAs, binding with proteins, and directing selective splicing. CircRNAs modify the immunological environment of cancers to promote their growth. Besides of critical role in tumor growth, circRNAs are emerging as potential candidates as biomarkers for diagnosis cancer therapy. Also, circRNAs vaccination even offers a novel approach to tumor immunotherapy. Over the recent years, studies are advocating that circRNAs have tissue specific tumor specific expression patterns, which indicates their potential clinical utility. Especially, circRNAs have emerged as potential predictive and prognostic biomarkers. Although, there has been significant progress in deciphering the role of circRNA in cancers, literature lacks comprehensive overview on this topic. Keeping in view of these significant discoveries, this review systematically discusses circRNA and their role in the tumor in different dimensions.
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Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Circ-LocNet: A Computational Framework for Circular RNA Sub-Cellular Localization Prediction. Int J Mol Sci 2022; 23:ijms23158221. [PMID: 35897818 PMCID: PMC9329987 DOI: 10.3390/ijms23158221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Circular ribonucleic acids (circRNAs) are novel non-coding RNAs that emanate from alternative splicing of precursor mRNA in reversed order across exons. Despite the abundant presence of circRNAs in human genes and their involvement in diverse physiological processes, the functionality of most circRNAs remains a mystery. Like other non-coding RNAs, sub-cellular localization knowledge of circRNAs has the aptitude to demystify the influence of circRNAs on protein synthesis, degradation, destination, their association with different diseases, and potential for drug development. To date, wet experimental approaches are being used to detect sub-cellular locations of circular RNAs. These approaches help to elucidate the role of circRNAs as protein scaffolds, RNA-binding protein (RBP) sponges, micro-RNA (miRNA) sponges, parental gene expression modifiers, alternative splicing regulators, and transcription regulators. To complement wet-lab experiments, considering the progress made by machine learning approaches for the determination of sub-cellular localization of other non-coding RNAs, the paper in hand develops a computational framework, Circ-LocNet, to precisely detect circRNA sub-cellular localization. Circ-LocNet performs comprehensive extrinsic evaluation of 7 residue frequency-based, residue order and frequency-based, and physio-chemical property-based sequence descriptors using the five most widely used machine learning classifiers. Further, it explores the performance impact of K-order sequence descriptor fusion where it ensembles similar as well dissimilar genres of statistical representation learning approaches to reap the combined benefits. Considering the diversity of statistical representation learning schemes, it assesses the performance of second-order, third-order, and going all the way up to seventh-order sequence descriptor fusion. A comprehensive empirical evaluation of Circ-LocNet over a newly developed benchmark dataset using different settings reveals that standalone residue frequency-based sequence descriptors and tree-based classifiers are more suitable to predict sub-cellular localization of circular RNAs. Further, K-order heterogeneous sequence descriptors fusion in combination with tree-based classifiers most accurately predict sub-cellular localization of circular RNAs. We anticipate this study will act as a rich baseline and push the development of robust computational methodologies for the accurate sub-cellular localization determination of novel circRNAs.
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Affiliation(s)
- Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
- Correspondence:
| | - Muhammad Ali Ibrahim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Imran Malik
- School of Computer Science & Electrical Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan;
| | - Andreas Dengel
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- DeepReader GmbH, Trippstadter Str. 122, 67663 Kaiserslautern, Germany
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Wei Y, Wang J, Wang Q, Cong B, Li S. The estimation of bloodstain age utilizing circRNAs and mRNAs biomarkers. Forensic Sci Int 2022; 338:111408. [PMID: 35901585 DOI: 10.1016/j.forsciint.2022.111408] [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: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/19/2022]
Abstract
Determining the time since deposition (TsD) of bloodstains can provide forensic investigators with additional clues, as it can corroborate eyewitness accounts, limit the number of suspects, and help confirm alibis. Bloodstains are the most common bodily fluid stains at crime scenes. In this study, we examined the relative expression levels (REs) of circRNAs and mRNAs data in bloodstains over ten time points by Real-time quantitative polymerase chain reaction (qPCR), to determine the utility of the relative expression levels of RNA markers for TsD estimation. Forensic samples more than just appear in indoor settings, we also evaluated the use of RNA degradation rate to indicate the age of bloodstains in different environments including indoor and outdoor conditions. The expression levels of six blood-specific mRNA markers (GYPA, CD93, ALAS2, SPTB, HBB, HBA), three highly expressed circRNAs in human peripheral blood (hsa_circ_0001445, hsa_circ_0000972, hsa_circ_0000095) and three reference genes (18 S, ACTB and U6) were analyzed across numerous ageing time points. Analysis of the degradation rates of individual RNAs under indoor and outdoor conditions showed that they exhibited a unique degradation profile during the four-month storage interval, with both circRNAs and mRNAs linearly showing continuous degradation, while U6 is more stable than other reference gene markers. In the current study, we firstly used circRNAs as additional novel biomarkers for bloodstain age estimation, and at the same time proved that different environments had a significant impact on the REs of certain blood biomarkers, and sex differences did not affect the age estimation of bloodstains. The REs of the selected RNA molecules in this study showed a non-linear relationship with bloodstain age and the mathematical formula for estimating the bloodstain age based on the relative expression levels of hsa_circ_0001445, ALAS2 and HBB can be used to estimate the TsD of bloodstains from the REs of bloodstains of unknown age, which represent a potentially effective approach to looking for time-dependent changes and TsD estimation.
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Affiliation(s)
- Yangyan Wei
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Junyan Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
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Zhang Y, Jiao Z, Chen M, Shen B, Shuai Z. Roles of Non-Coding RNAs in Primary Biliary Cholangitis. Front Mol Biosci 2022; 9:915993. [PMID: 35874606 PMCID: PMC9305664 DOI: 10.3389/fmolb.2022.915993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Primary biliary cholangitis (PBC) is an autoimmune-mediated chronic cholestatic liver disease, fatigue, and skin itching are the most common clinical symptoms. Its main pathological feature is the progressive damage and destruction of bile duct epithelial cells. Non-coding RNA (NcRNA, mainly including microRNA, long non-coding RNA and circular RNA) plays a role in the pathological and biological processes of various diseases, especially autoimmune diseases. Many validated ncRNAs are expected to be biomarkers for the diagnosis or treatment of PBC. This review will elucidate the pathogenesis of PBC and help to identify potential ncRNA biomarkers for PBC.
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Affiliation(s)
- Yaqin Zhang
- Department of Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ziying Jiao
- Department of Physiology, School of Basic Medicine of Anhui Medical University, Hefei, China
| | - Mingwei Chen
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bing Shen
- Department of Physiology, School of Basic Medicine of Anhui Medical University, Hefei, China
| | - Zongwen Shuai
- Department of Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Zongwen Shuai,
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Role of Circular RNA in Brain Tumor Development. Cells 2022; 11:cells11142130. [PMID: 35883576 PMCID: PMC9315629 DOI: 10.3390/cells11142130] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
Central nervous system tumors are a leading cause of cancer-related death in children and adults, with medulloblastoma (MB) and glioblastoma (GBM) being the most prevalent malignant brain tumors, respectively. Despite tremendous breakthroughs in neurosurgery, radiation, and chemotherapeutic techniques, cell heterogeneity and various genetic mutations impacting cell cycle control, cell proliferation, apoptosis, and cell invasion result in unwanted resistance to treatment approaches, with a 5-year survival rate of 70–80% for medulloblastoma, and the median survival time for patients with glioblastoma is only 15 months. Developing new medicines and utilizing combination medications may be viewed as excellent techniques for battling MB and GBM. Circular RNAs (circRNAs) can affect cancer-developing processes such as cell proliferation, cell apoptosis, invasion, and chemoresistance in this regard. As a result, several compounds have been introduced as prospective therapeutic targets in the fight against MB and GBM. The current study aims to elucidate the fundamental molecular and cellular mechanisms underlying the pathogenesis of GBM in conjunction with circRNAs. Several mechanisms were examined in detail, including PI3K/Akt/mTOR signaling, Wnt/-catenin signaling, angiogenic processes, and metastatic pathways, in order to provide a comprehensive knowledge of the involvement of circRNAs in the pathophysiology of MB and GBM.
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