1
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Tian Z, Han C, Xu L, Teng Z, Song W. MGCNSS: miRNA-disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy. Brief Bioinform 2024; 25:bbae168. [PMID: 38622356 PMCID: PMC11018511 DOI: 10.1093/bib/bbae168] [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: 12/12/2023] [Revised: 03/14/2024] [Accepted: 03/31/2024] [Indexed: 04/17/2024] Open
Abstract
Identifying disease-associated microRNAs (miRNAs) could help understand the deep mechanism of diseases, which promotes the development of new medicine. Recently, network-based approaches have been widely proposed for inferring the potential associations between miRNAs and diseases. However, these approaches ignore the importance of different relations in meta-paths when learning the embeddings of miRNAs and diseases. Besides, they pay little attention to screening out reliable negative samples which is crucial for improving the prediction accuracy. In this study, we propose a novel approach named MGCNSS with the multi-layer graph convolution and high-quality negative sample selection strategy. Specifically, MGCNSS first constructs a comprehensive heterogeneous network by integrating miRNA and disease similarity networks coupled with their known association relationships. Then, we employ the multi-layer graph convolution to automatically capture the meta-path relations with different lengths in the heterogeneous network and learn the discriminative representations of miRNAs and diseases. After that, MGCNSS establishes a highly reliable negative sample set from the unlabeled sample set with the negative distance-based sample selection strategy. Finally, we train MGCNSS under an unsupervised learning manner and predict the potential associations between miRNAs and diseases. The experimental results fully demonstrate that MGCNSS outperforms all baseline methods on both balanced and imbalanced datasets. More importantly, we conduct case studies on colon neoplasms and esophageal neoplasms, further confirming the ability of MGCNSS to detect potential candidate miRNAs. The source code is publicly available on GitHub https://github.com/15136943622/MGCNSS/tree/master.
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Affiliation(s)
- Zhen Tian
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China
| | - Chenguang Han
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
| | - Lewen Xu
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
| | - Zhixia Teng
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Wei Song
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
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2
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Coleman D, Kuwada S. miRNA as a Biomarker for the Early Detection of Colorectal Cancer. Genes (Basel) 2024; 15:338. [PMID: 38540397 PMCID: PMC10969835 DOI: 10.3390/genes15030338] [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: 02/02/2024] [Revised: 02/26/2024] [Accepted: 03/03/2024] [Indexed: 06/14/2024] Open
Abstract
MicroRNAs (miRNAs) are short, non-coding RNA segments that can be detected in a variety of clinical samples, including serum, stool, and urine. While miRNAs were initially known for their effect on post-translational gene expression, the last decade of research has shown them to be promising biomarkers for the detection of many types of cancer. This paper explores the use of miRNA detection as a tool for colorectal cancer (CRC) screening. We discuss the current state of miRNA detection, compare it to the existing CRC screening tools, and highlight the advantages and drawbacks of this approach from a clinical and logistical perspective. Our research finds that miRNA-based tests for CRC show great potential, but that widespread clinical adoption will be conditional on future research overcoming key hurdles.
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Affiliation(s)
- David Coleman
- John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, Honolulu, HI 96813, USA
| | - Scott Kuwada
- John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, Honolulu, HI 96813, USA
- University of Hawaii Cancer Center, 01 Ilalo Street, Honolulu, HI 96813, USA
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3
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Das R, Mehta DK, Gupta N. Understanding the Potential of mRNA as Biomarker to Revolutionize Diagnosis of Colorectal Cancer. Drug Res (Stuttg) 2024; 74:102-112. [PMID: 38350633 DOI: 10.1055/a-2244-6572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
MicroRNA as potential biomarker for early diagnosis, differentiating various stages, interpreting the success of postoperative curative surgery and predicting early relapse of Colorectal cancer.In the realm of medical research, the quest to find effective biomarkers for various diseases has always been a top priority. Colorectal cancer (CRC), one of the leading causes of cancer-related deaths worldwide, is no exception. The emergence of microRNA (mRNA) as a potential biomarker for CRC has sparked immense interest among scientists and clinicians alike. mRNA, a molecule responsible for translating genetic information into functional proteins, presents a promising avenue for early detection and personalized treatment of this deadly disease. By analyzing the specific patterns and levels of mRNA expression in CRC cells, researchers have the ability to identify signatures that can aid in accurate diagnosis, predict patient prognosis, and even guide targeted therapies. This breakthrough in molecular biology not only enhances our understanding of CRC but also holds the potential to revolutionize the field of cancer diagnostics and treatment. In this article, we will delve deeper into the potential of mRNA as a biomarker for CRC, exploring its benefits and challenges in the field of cancer research.
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Affiliation(s)
- Rina Das
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, HR, India
| | - Dinesh Kumar Mehta
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, HR, India
| | - Nidhi Gupta
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, HR, India
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4
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Al-Nakhle HH. Unraveling the Multifaceted Role of the miR-17-92 Cluster in Colorectal Cancer: From Mechanisms to Biomarker Potential. Curr Issues Mol Biol 2024; 46:1832-1850. [PMID: 38534736 DOI: 10.3390/cimb46030120] [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: 01/20/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Colorectal cancer (CRC) is a complex disease driven by intricate mechanisms, making it challenging to understand and manage. The miR-17-92 cluster has gained significant attention in CRC research due to its diverse functions and crucial role in various aspects of the disease. This cluster, consisting of multiple individual miRNAs, influences critical processes like tumor initiation, angiogenesis, metastasis, and the epithelial-mesenchymal transition (EMT). Beyond its roles in tumorigenesis and progression, miR-17-92's dysregulation in CRC has substantial implications for diagnosis, prognosis, and treatment, including chemotherapy responsiveness. It also shows promise as a diagnostic and prognostic biomarker, offering insights into treatment responses and disease progression. This review provides a comprehensive overview of recent advancements and the context-dependent role of the miR-17-92 cluster in colorectal cancer, drawing from the latest high-quality published data. It summarizes the established mechanisms governing miR-17-92 expression and the molecular pathways under its influence. Furthermore, it examines instances where it functions as an oncogene or a tumor suppressor, elucidating how cellular contexts dictate its biological effects. Ultimately, miR-17-92 holds promise as a biomarker for prognosis and therapy response, as well as a potential target for cancer prevention and therapeutic interventions. In essence, this review underscores the multifaceted nature of miR-17-92 in CRC research, offering promising avenues for enhancing the management of CRC patients.
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Affiliation(s)
- Hakeemah H Al-Nakhle
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Monawarah 42353, Saudi Arabia
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5
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Santos DAR, Gaiteiro C, Santos M, Santos L, Dinis-Ribeiro M, Lima L. MicroRNA Biomarkers as Promising Tools for Early Colorectal Cancer Screening-A Comprehensive Review. Int J Mol Sci 2023; 24:11023. [PMID: 37446201 DOI: 10.3390/ijms241311023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Colorectal cancer (CRC) ranks as the third most prevalent cancer worldwide. Early detection of this neoplasia has proven to improve prognosis, resulting in a 90% increase in survival. However, available CRC screening methods have limitations, requiring the development of new tools. MicroRNA biomarkers have emerged as a powerful screening tool, as they are highly expressed in CRC patients and easily detectable in several biological samples. While microRNAs are extensively studied in blood samples, recent interest has now arisen in other samples, such as stool samples, where they can be combined with existing screening methods. Among the microRNAs described in the literature, microRNA-21-5p and microRNA-92a-3p and their cluster have demonstrated high potential for early CRC screening. Furthermore, the combination of multiple microRNAs has shown improved performance in CRC detection compared to individual microRNAs. This review aims to assess the available data in the literature on microRNAs as promising biomarkers for early CRC screening, explore their advantages and disadvantages, and discuss the optimal study characteristics for analyzing these biomarkers.
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Affiliation(s)
- Daniela A R Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal
- School of Health, Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal
| | - Marlene Santos
- School of Health, Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
- Centro de Investigação em Saúde e Ambiente (CISA), Escola Superior de Saúde, Instituto Politécnico do Porto, 4200-072 Porto, Portugal
- Molecular Oncology & Viral Pathology, IPO-Porto Research Center (CI-IPO), Portuguese Institute of Oncology, 4200-072 Porto, Portugal
| | - Lúcio Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal
- Department of Surgical Oncology, Portuguese Institute of Oncology (IPO-Porto), 4200-072 Porto, Portugal
| | - Mário Dinis-Ribeiro
- Precancerous Lesions and Early Cancer Management Group, Research Center of IPO Porto (CI-IPOP), Rise@CI-IPOP (Health Research Group), Portuguese Institute of Oncology of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal
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6
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D'Agostino E, Muro A, Sgueglia G, Massaro C, Dell'Aversana C, Altucci L. Exosomal MicroRNAs: Comprehensive Methods from Exosome Isolation to miRNA Extraction and Purity Analysis. Methods Mol Biol 2023; 2595:75-92. [PMID: 36441455 DOI: 10.1007/978-1-0716-2823-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exosomes are extracellular vesicles secreted by cells with a key role in a wide range of biological processes including cancer. These vesicles are involved in intercellular communication and deliver diverse cargo molecules, including miRNAs (exo-miRNAs), to recipient cells affecting their physiology. Exo-miRNAs have a role in promoting tumor, progression, metastatization, and remodeling of tumor microenvironment, therefore making them interesting biomarkers to study.Here we provide a detailed technical protocol for exosome isolation (which can be applied to cell culture as well as physiological fluids), validation of their vesicular identity, miRNA extraction, and quantitative and qualitative analysis to evaluate the sample purity and concentration.
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Affiliation(s)
- Erika D'Agostino
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Annamaria Muro
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy.,Università degli studi di Napoli "Federico II", Naples, Italy
| | - Giulia Sgueglia
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Crescenzo Massaro
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Carmela Dell'Aversana
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy. .,Institute Experimental Endocrinology and Oncology 'Gaetano Salvatore' (IEOS)-National Research Council (CNR), Naples, Italy.
| | - Lucia Altucci
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy. .,BIOGEM, Ariano Irpino, Italy.
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7
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Dobre M, Trandafir B, Milanesi E, Salvi A, Bucuroiu I, Vasilescu C, Niculae AM, Herlea V, Hinescu ME, Constantinescu G. Molecular profile of the NF-κB signalling pathway in human colorectal cancer. J Cell Mol Med 2022; 26:5966-5975. [PMID: 36433652 PMCID: PMC9753446 DOI: 10.1111/jcmm.17545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/06/2022] [Accepted: 07/23/2022] [Indexed: 11/27/2022] Open
Abstract
The development and progression of colorectal cancer (CRC) have been associated with inflammation processes that involve the overactivation of the NF-κB signalling pathway. The characterization of the NF-κB expression profile in CRC is an important topic since the suppression of NF-κB represents a potential therapeutic approach. In this study, we assessed the expression levels of 84 NF-κB-related genes in paired tumoral (T) and peritumoral (PT) tissues from 18 CRC patients and 18 normal colonic mucosae, and the expression levels of three miRNAs targeting the most dysregulated genes revealed by the case-control analysis. Comparing the gene expression profile of T and controls, 60 genes were dysregulated. The comparison of T and PT revealed 17 dysregulated genes in the tumoral tissues, with IL1B, CXCL8, IL1A, and CSF2 being the most upregulated. Notably, through a bioinformatics analysis, the differential gene expression of 11 out of the 17 genes was validated on a larger cohort of 308 CRC patients compared with 41 controls. Moreover, a decrease in the levels of RELA, NOD1, CASP8, BCL2L1, ELK1, and IKBKB was identified in poorly differentiated tumours compared to moderately differentiated tumours. The analysis of the three miRNAs targeting IL1B, CXCL8, IL1A, and CSF2 showed that miR-182-5p was upregulated in T compared with PT, whereas miR-10b-5p was downregulated in T compared with PT and control tissues. Our results may contribute to the design of new experimental therapeutic strategies based on endogenous molecules, such as miRNAs, to target the genetic key players of the NF- κB pathway.
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Affiliation(s)
- Maria Dobre
- Victor Babes National Institute of PathologyBucharestRomania
| | - Bogdan Trandafir
- Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania,Fundeni Clinical InstituteBucharestRomania
| | - Elena Milanesi
- Victor Babes National Institute of PathologyBucharestRomania
| | - Alessandro Salvi
- Division of Biology and Genetics, Department of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
| | - Ioana Alina Bucuroiu
- Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania
| | - Catalin Vasilescu
- Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania,Fundeni Clinical InstituteBucharestRomania
| | - Andrei Marian Niculae
- Victor Babes National Institute of PathologyBucharestRomania,Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania
| | | | - Mihail Eugen Hinescu
- Victor Babes National Institute of PathologyBucharestRomania,Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania
| | - Gabriel Constantinescu
- Faculty of MedicineCarol Davila University of Medicine and PharmacyBucharestRomania,Clinical Emergency Hospital BucharestBucharestRomania
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8
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Volovat SR, Augustin I, Zob D, Boboc D, Amurariti F, Volovat C, Stefanescu C, Stolniceanu CR, Ciocoiu M, Dumitras EA, Danciu M, Apostol DGC, Drug V, Shurbaji SA, Coca LG, Leon F, Iftene A, Herghelegiu PC. Use of Personalized Biomarkers in Metastatic Colorectal Cancer and the Impact of AI. Cancers (Basel) 2022; 14:cancers14194834. [PMID: 36230757 PMCID: PMC9562853 DOI: 10.3390/cancers14194834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 12/09/2022] Open
Abstract
Colorectal cancer is a major cause of cancer-related death worldwide and is correlated with genetic and epigenetic alterations in the colonic epithelium. Genetic changes play a major role in the pathophysiology of colorectal cancer through the development of gene mutations, but recent research has shown an important role for epigenetic alterations. In this review, we try to describe the current knowledge about epigenetic alterations, including DNA methylation and histone modifications, as well as the role of non-coding RNAs as epigenetic regulators and the prognostic and predictive biomarkers in metastatic colorectal disease that can allow increases in the effectiveness of treatments. Additionally, the intestinal microbiota’s composition can be an important biomarker for the response to strategies based on the immunotherapy of CRC. The identification of biomarkers in mCRC can be enhanced by developing artificial intelligence programs. We present the actual models that implement AI technology as a bridge connecting ncRNAs with tumors and conducted some experiments to improve the quality of the model used as well as the speed of the model that provides answers to users. In order to carry out this task, we implemented six algorithms: the naive Bayes classifier, the random forest classifier, the decision tree classifier, gradient boosted trees, logistic regression and SVM.
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Affiliation(s)
- Simona-Ruxandra Volovat
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Iolanda Augustin
- Department of Medical Oncology, AI.Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Daniela Zob
- Department of Medical Oncology, AI.Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Diana Boboc
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Florin Amurariti
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Constantin Volovat
- Department of Medical Oncology, “Euroclinic” Center of Oncology, 2 Vasile Conta Str., 700106 Iasi, Romania
- Correspondence: (C.V.); (C.S.)
| | - Cipriana Stefanescu
- Department of Biophysics and Medical Physics-Nuclear Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
- Correspondence: (C.V.); (C.S.)
| | - Cati Raluca Stolniceanu
- Department of Biophysics and Medical Physics-Nuclear Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Manuela Ciocoiu
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Eduard Alexandru Dumitras
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
- Department of Anesthesiology and Intensive Care, Regional Institute of Oncology, 700115 Iasi, Romania
| | - Mihai Danciu
- Pathology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | - Vasile Drug
- Department of Gastroenterology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
- Gastroenterology Clinic, Institute of Gastroenterology and Hepatology, ‘St. Spiridon’ Clinical Hospital, 700115 Iasi, Romania
| | - Sinziana Al Shurbaji
- Gastroenterology Clinic, Institute of Gastroenterology and Hepatology, ‘St. Spiridon’ Clinical Hospital, 700115 Iasi, Romania
| | - Lucia-Georgiana Coca
- Faculty of Computer Science, Alexandru Ioan Cuza University, 700115 Iasi, Romania
| | - Florin Leon
- Faculty of Automatic Control and Computer Engineering, Gheorghe Asachi Technical University, 700115 Iasi, Romania
| | - Adrian Iftene
- Faculty of Computer Science, Alexandru Ioan Cuza University, 700115 Iasi, Romania
| | - Paul-Corneliu Herghelegiu
- Faculty of Automatic Control and Computer Engineering, Gheorghe Asachi Technical University, 700115 Iasi, Romania
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9
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Li C, Zhou T, Chen J, Li R, Chen H, Luo S, Chen D, Cai C, Li W. The role of Exosomal miRNAs in cancer. J Transl Med 2022; 20:6. [PMID: 34980158 PMCID: PMC8722109 DOI: 10.1186/s12967-021-03215-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/22/2021] [Indexed: 02/08/2023] Open
Abstract
Exosomal miRNAs have attracted much attention due to their critical role in regulating genes and the altered expression of miRNAs in virtually all cancers affecting humans (Sun et al. in Mol Cancer 17(1):14, 2018). Exosomal miRNAs modulate processes that interfere with cancer immunity and microenvironment, and are significantly involved in tumor growth, invasion, metastasis, angiogenesis and drug resistance. Fully investigating the detailed mechanism of miRNAs in the occurrence and development of various cancers could help not only in the treatment of cancers but also in the prevention of malignant diseases. The current review highlighted recently published advances regarding cancer-derived exosomes, e.g., sorting and delivery mechanisms for RNAs. Exosomal miRNAs that modulate cancer cell-to-cell communication, impacting tumor growth, angiogenesis, metastasis and multiple biological features, were discussed. Finally, the potential role of exosomal miRNAs as diagnostic and prognostic molecular markers was summarized, as well as their usefulness in detecting cancer resistance to therapeutic agents.
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Affiliation(s)
- Chuanyun Li
- Fengtai District, YouAn Hospital, Capital Medical University, NO. 8, Xitoutiao, Youanmen wai, Beijing, China
| | - Tong Zhou
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Jing Chen
- Fengtai District, YouAn Hospital, Capital Medical University, NO. 8, Xitoutiao, Youanmen wai, Beijing, China.,Beijing Institute of Hepatology, Beijing, China
| | - Rong Li
- Chengde Medical University, Chengde, China
| | - Huan Chen
- Fengtai District, YouAn Hospital, Capital Medical University, NO. 8, Xitoutiao, Youanmen wai, Beijing, China
| | - Shumin Luo
- Fengtai District, YouAn Hospital, Capital Medical University, NO. 8, Xitoutiao, Youanmen wai, Beijing, China.,Beijing Institute of Hepatology, Beijing, China
| | - Dexi Chen
- Fengtai District, YouAn Hospital, Capital Medical University, NO. 8, Xitoutiao, Youanmen wai, Beijing, China.,Beijing Institute of Hepatology, Beijing, China
| | - Cao Cai
- Fengtai District, YouAn Hospital, Capital Medical University, NO. 8, Xitoutiao, Youanmen wai, Beijing, China.
| | - Weihua Li
- Fengtai District, YouAn Hospital, Capital Medical University, NO. 8, Xitoutiao, Youanmen wai, Beijing, China. .,Beijing Institute of Hepatology, Beijing, China.
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10
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Zhao Z, Zhu A, Bhardwaj M, Schrotz-King P, Brenner H. Fecal microRNAs, Fecal microRNA Panels, or Combinations of Fecal microRNAs with Fecal Hemoglobin for Early Detection of Colorectal Cancer and Its Precursors: A Systematic Review. Cancers (Basel) 2021; 14:cancers14010065. [PMID: 35008229 PMCID: PMC8750731 DOI: 10.3390/cancers14010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Screening for colorectal cancer is effective for the reduction of both CRC incidence and mortality in the population at average risk. The use of innovative and robust biomarkers to enhance the potential of noninvasive CRC screening remains desirable. We aimed to conduct a systematic literature review on the diagnostic performance of fecal miRNA markers for CRC and its precursors. Several studies have reported quite promising results, in particular by combining fecal miRNA measurements with fecal hemoglobin. However, current evidence is limited by substantial heterogeneity in the methodology from study design to biosample analysis. Our review is intended to provide a valuable reference for future biomarker studies in early colorectal cancer detection. Looking at fecal miRNAs, we draw attention to the various biases to be avoided or at least minimized, by applying a harmonized methodology including true screening settings and comparable sample pre-analytics, as well as the validation of biomarkers. Abstract Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer mortality globally. Fecal miRNAs have been suggested to be promising biomarkers for CRC early detection. We aimed to conduct a systematic literature review on the diagnostic performance of fecal miRNA markers for CRC and its precursors. PubMed and Web of Science were searched to retrieve relevant articles published up to 7 December 2021. Information on study design, characteristics of study population, pre-analytics (sample collection, processing, and storage), fecal miRNA extraction and quantification technologies, and diagnostic performance (including sensitivity, specificity, and area under the curve (AUC)) were summarized. Twenty studies reporting on 31 individual miRNAs and 16 miRNA panels (with 2–9 markers) for CRC diagnosis were identified. Substantial heterogeneity existed regarding stool sample collection, processing, storage, and miRNA extraction and normalization. For two individual miRNAs and one miRNA panel, values ≥ 80% were reported for both sensitivity and specificity; however, none of these results were either internally or externally validated. In a study among fecal immunochemical test-positive cases recruited from a true screening setting, better diagnostic performance was identified and internally validated for a combination panel including two miRNAs, fecal hemoglobin level, and patient age and sex, compared with fecal hemoglobin concentration alone. Fecal miRNAs or miRNA panels, possibly in combination with fecal hemoglobin test, may be promising candidates for noninvasive CRC early detection. However, large prospective and well-designed studies in CRC screening cohorts are required to validate promising miRNAs or miRNA panels.
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Affiliation(s)
- Zitong Zhao
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (Z.Z.); (A.Z.)
- Medical Faculty Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Anna Zhu
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (Z.Z.); (A.Z.)
- Medical Faculty Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Megha Bhardwaj
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (M.B.); (P.S.-K.)
| | - Petra Schrotz-King
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (M.B.); (P.S.-K.)
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (Z.Z.); (A.Z.)
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (M.B.); (P.S.-K.)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-42-1301
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11
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Azpiroz MA, Orguilia L, Palacio MI, Malpartida A, Mayol S, Mor G, Gutiérrez G. Potential biomarkers of infertility associated with microbiome imbalances. Am J Reprod Immunol 2021; 86:e13438. [PMID: 33960055 PMCID: PMC8464490 DOI: 10.1111/aji.13438] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 12/13/2022] Open
Abstract
PROBLEM The aim of this study was to investigate the possible relationship between vaginal/rectal microbiome disbalances and miRNA expression with infertility. METHOD OF STUDY Observational, exploratory, preliminary study. A total of 287 multiple IVF failure infertile patients were recruited. Twenty fertile women, not IVF failure, were recruited as the control group. Swab samples were collected from the vagina and rectum. Microbial composition by NGS and miRNA expression by real-time PCR of vaginal and rectal samples was measured. Immunometabolic markers from blood (insulin, vitamin D, LDL-cholesterol, ANA, TPO, Tg, and ASCA antibodies) and saliva (sIgA) were analyzed. RESULT(S) Infertile patients showed a lower bacterial richness and increased Firmicutes/Bacteroidetes ratio at rectal level and an increased Lactobacillus brevis/Lactobacillus iners ratio in vaginal samples regarding the fertile group. In the same rectal swab samples, we found that miR-21-5p, which is associated with tight junction disruption and yeast overgrowth, is upregulated and that miR-155-5p, which is associated with inflammation, is overexpressed in the unexplained infertile group (*p < .05). These deregulated miRNAs were also upregulated in the vaginal samples from the same patients (*p < .05). CONCLUSION miRNAs could be potential biomarkers of the inflammatory impact of microbiome disbalances in unexplained infertile women.
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Affiliation(s)
| | - Lucila Orguilia
- Inmunogenesis, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | | | | | | | - Gil Mor
- Wayne State University, Detroit, MI, USA
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12
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Wang YT, Li L, Ji CM, Zheng CH, Ni JC. ILPMDA: Predicting miRNA-Disease Association Based on Improved Label Propagation. Front Genet 2021; 12:743665. [PMID: 34659364 PMCID: PMC8514753 DOI: 10.3389/fgene.2021.743665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/30/2021] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that have been demonstrated to be related to numerous complex human diseases. Considerable studies have suggested that miRNAs affect many complicated bioprocesses. Hence, the investigation of disease-related miRNAs by utilizing computational methods is warranted. In this study, we presented an improved label propagation for miRNA-disease association prediction (ILPMDA) method to observe disease-related miRNAs. First, we utilized similarity kernel fusion to integrate different types of biological information for generating miRNA and disease similarity networks. Second, we applied the weighted k-nearest known neighbor algorithm to update verified miRNA-disease association data. Third, we utilized improved label propagation in disease and miRNA similarity networks to make association prediction. Furthermore, we obtained final prediction scores by adopting an average ensemble method to integrate the two kinds of prediction results. To evaluate the prediction performance of ILPMDA, two types of cross-validation methods and case studies on three significant human diseases were implemented to determine the accuracy and effectiveness of ILPMDA. All results demonstrated that ILPMDA had the ability to discover potential miRNA-disease associations.
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Affiliation(s)
- Yu-Tian Wang
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China
| | - Lei Li
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China
| | - Cun-Mei Ji
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China
| | - Chun-Hou Zheng
- School of Artificial Intelligence, Anhui University, Hefei, China
| | - Jian-Cheng Ni
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China
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13
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He S, Zhou C, Peng H, Lin M. Recent advances in fecal gene detection for colorectal cancer diagnosis. Biomark Med 2021; 15:1299-1308. [PMID: 34544268 DOI: 10.2217/bmm-2021-0269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
There has been a gradual increase in the incidence of colorectal cancer (CRC) in recent years. Most patients lack obvious early symptoms, but are commonly in mid and advanced stages when the symptoms become evident, with rather high mortalities. Early diagnosis, treatment and recurrence monitoring are crucial to improving the recovery rate of CRC. Studies have shown that tumor-related genes can be detected in the feces of CRC patients. Owing to non-invasiveness, convenient sampling and continuous dynamic monitoring, fecal gene detection may be applicable to CRC screening, diagnosis, prognostic assessment and recurrence monitoring. Herein, we review the research advances in fecal gene detection for CRC diagnosis.
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Affiliation(s)
- Siyu He
- Clinical Laboratory, Taizhou People's Hospital (Postgraduate training base of Dalian Medical University), Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Clinical Laboratory, Taizhou People's Hospital (Postgraduate training base of Dalian Medical University), Taizhou, 225300, Jiangsu, China
| | - Hailin Peng
- Clinical Laboratory, Taizhou People's Hospital (Postgraduate training base of Dalian Medical University), Taizhou, 225300, Jiangsu, China
| | - Mei Lin
- Clinical Laboratory, Taizhou People's Hospital (Postgraduate training base of Dalian Medical University), Taizhou, 225300, Jiangsu, China
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14
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Pidíková P, Herichová I. miRNA Clusters with Up-Regulated Expression in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13122979. [PMID: 34198662 PMCID: PMC8232258 DOI: 10.3390/cancers13122979] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/05/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary As miRNAs show the capacity to be used as CRC biomarkers, we analysed experimentally validated data about frequently up-regulated miRNA clusters in CRC tissue. We identified 15 clusters that showed increased expression in CRC: miR-106a/363, miR-106b/93/25, miR-17/92a-1, miR-181a-1/181b-1, miR-181a-2/181b-2, miR-181c/181d, miR-183/96/182, miR-191/425, miR-200c/141, miR-203a/203b, miR-222/221, mir-23a/27a/24-2, mir-29b-1/29a, mir-301b/130b and mir-452/224. Cluster positions in the genome are intronic or intergenic. Most clusters are regulated by several transcription factors, and by long non-coding RNAs. In some cases, co-expression of miRNA with other cluster members or host gene has been proven. miRNA expression patterns in cancer tissue, blood and faeces were compared. The members of the selected clusters target 181 genes. Their functions and corresponding pathways were revealed with the use of Panther analysis. Clusters miR-17/92a-1, miR-106a/363, miR-106b/93/25 and miR-183/96/182 showed the strongest association with metastasis occurrence and poor patient survival, implicating them as the most promising targets of translational research. Abstract Colorectal cancer (CRC) is one of the most common malignancies in Europe and North America. Early diagnosis is a key feature of efficient CRC treatment. As miRNAs can be used as CRC biomarkers, the aim of the present study was to analyse experimentally validated data on frequently up-regulated miRNA clusters in CRC tissue and investigate their members with respect to clinicopathological characteristics of patients. Based on available data, 15 up-regulated clusters, miR-106a/363, miR-106b/93/25, miR-17/92a-1, miR-181a-1/181b-1, miR-181a-2/181b-2, miR-181c/181d, miR-183/96/182, miR-191/425, miR-200c/141, miR-203a/203b, miR-222/221, mir-23a/27a/24-2, mir-29b-1/29a, mir-301b/130b and mir-452/224, were selected. The positions of such clusters in the genome can be intronic or intergenic. Most clusters are regulated by several transcription factors, and miRNAs are also sponged by specific long non-coding RNAs. In some cases, co-expression of miRNA with other cluster members or host gene has been proven. miRNA expression patterns in cancer tissue, blood and faeces were compared. Based on experimental evidence, 181 target genes of selected clusters were identified. Panther analysis was used to reveal the functions of the target genes and their corresponding pathways. Clusters miR-17/92a-1, miR-106a/363, miR-106b/93/25 and miR-183/96/182 showed the strongest association with metastasis occurrence and poor patient survival, implicating them as the most promising targets of translational research.
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15
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O'Brien SJ, Netz U, Hallion J, Bishop C, Stephen V, Burton J, Paas M, Feagins K, Pan J, Rai SN, Galandiuk S. Circulating plasma microRNAs in colorectal neoplasia: A pilot study in assessing response to therapy. Transl Oncol 2020; 14:100962. [PMID: 33285367 PMCID: PMC7720092 DOI: 10.1016/j.tranon.2020.100962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/17/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
This pilot study examines a microRNA panel as a biomarker for response to surgical resection in colorectal cancer or colorectal advanced adenoma. A panel of 11 microRNAs was developed through screening and previous studies. Six miRNA are significantly increased following colorectal cancer resection. Three miRNA are significantly increased following colorectal advanced adenoma resection. The results of this study suggest that serum microRNA expression could be followed as a marker for response to therapy.
Introduction Current serological surveillance markers to monitor colorectal cancer (CRC) or colorectal advanced adenomas (CAA) are hampered by poor sensitivity and specificity. The aim of this study is to identify and validate a panel of plasma microRNAs which change in expression after resection of such lesions. Methods A prospectively maintained colorectal surgery database was queried for patients in whom both pre- and post-procedural serum samples had been obtained. An initial screening analysis of CRC and CAA patients (5 each) was conducted using screening cards for 380 miRNAs. Four identified miRNAs were combined with a previously described panel of 7 miRNAs that were diagnostically predictive of CRC and CAA. Differential miRNA expression was assessed using quantitative real-time polymerase chain reaction(qRT-PCR). Results Fifty patients were included (n = 27 CRC, n = 23 CAA). There was no difference in age, gender, or race profile of CRC patients compared to CAA patients. Six miRNA were significantly increased after CRC resection (miR-324, let7b, miR-454, miR-374a, miR-122, miR-19b, all p<0.05), while three miRNAs were significantly increased following CAA resection (miR-454, miR-374a, miR-122, all p<0.05). Three miRNA were increased in common for both (miR-454, miR-374a, miR-122). Discussion The expression of miRNAs associated with neoplasia (either CRC or CAA) was significantly increased following surgical resection or endoscopic removal of CRC or CAA. Future studies should focus on the evaluation of these miRNAs in CRC and CAA prognosis.
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Affiliation(s)
- Stephen J O'Brien
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Uri Netz
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA; Department of Surgery, Soroka University Medical Center, Beer Sheva, Israel
| | - Jacob Hallion
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Campbell Bishop
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Vincent Stephen
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - James Burton
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Mason Paas
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Kayla Feagins
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Jianmin Pan
- Department of Bioinformatics and Biostatistics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Shesh N Rai
- Department of Bioinformatics and Biostatistics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Susan Galandiuk
- Price Institute of Surgical Research, The Hiram C. Polk Jr. MD Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA.
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16
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Ji BY, You ZH, Chen ZH, Wong L, Yi HC. NEMPD: a network embedding-based method for predicting miRNA-disease associations by preserving behavior and attribute information. BMC Bioinformatics 2020; 21:401. [PMID: 32912137 PMCID: PMC7646193 DOI: 10.1186/s12859-020-03716-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/19/2020] [Indexed: 12/25/2022] Open
Abstract
Background As an important non-coding RNA, microRNA (miRNA) plays a significant role in a series of life processes and is closely associated with a variety of Human diseases. Hence, identification of potential miRNA-disease associations can make great contributions to the research and treatment of Human diseases. However, to our knowledge, many existing computational methods only utilize the single type of known association information between miRNAs and diseases to predict their potential associations, without focusing on their interactions or associations with other types of molecules. Results In this paper, we propose a network embedding-based method for predicting miRNA-disease associations by preserving behavior and attribute information. Firstly, a heterogeneous network is constructed by integrating known associations among miRNA, protein and disease, and the network representation method Learning Graph Representations with Global Structural Information (GraRep) is implemented to learn the behavior information of miRNAs and diseases in the network. Then, the behavior information of miRNAs and diseases is combined with the attribute information of them to represent miRNA-disease association pairs. Finally, the prediction model is established based on the Random Forest algorithm. Under the five-fold cross validation, the proposed NEMPD model obtained average 85.41% prediction accuracy with 80.96% sensitivity at the AUC of 91.58%. Furthermore, the performance of NEMPD is also validated by the case studies. Among the top 50 predicted disease-related miRNAs, 48 (breast neoplasms), 47 (colon neoplasms), 47 (lung neoplasms) were confirmed by two other databases. Conclusions The proposed NEMPD model has a good performance in predicting the potential associations between miRNAs and diseases, and has great potency in the field of miRNA-disease association prediction in the future.
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Affiliation(s)
- Bo-Ya Ji
- Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhu-Hong You
- Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhan-Heng Chen
- Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leon Wong
- Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Cheng Yi
- Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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17
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Sarshar M, Scribano D, Ambrosi C, Palamara AT, Masotti A. Fecal microRNAs as Innovative Biomarkers of Intestinal Diseases and Effective Players in Host-Microbiome Interactions. Cancers (Basel) 2020; 12:cancers12082174. [PMID: 32764361 PMCID: PMC7463924 DOI: 10.3390/cancers12082174] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/30/2020] [Accepted: 08/02/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, short non-coding microRNAs (miRNAs), including circulating and fecal miRNAs have emerged as important modulators of various cellular processes by regulating the expression of target genes. Recent studies revealed the role of miRNAs as powerful biomarkers in disease diagnosis and for the development of innovative therapeutic applications in several human conditions, including intestinal diseases. In this review, we explored the literature and summarized the role of identified dysregulated fecal miRNAs in intestinal diseases, with particular focus on colorectal cancer (CRC) and celiac disease (CD). The aim of this review is to highlight one fascinating aspect of fecal miRNA function related to gut microbiota shaping and bacterial metabolism influencing. The role of miRNAs as “messenger” molecules for inter kingdom communications will be analyzed to highlight their role in the complex host-bacteria interactions. Moreover, whether fecal miRNAs could open up new perspectives to develop novel suitable biomarkers for disease detection and innovative therapeutic approaches to restore microbiota balance will be discussed.
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Affiliation(s)
- Meysam Sarshar
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, 00185 Rome, Italy;
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy;
- Microbiology Research Center (MRC), Pasteur Institute of Iran, 1316943551 Tehran, Iran
- Correspondence: (M.S.); (C.A.)
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy;
- Dani Di Giò Foundation-Onlus, 00193 Rome, Italy
| | - Cecilia Ambrosi
- IRCCS San Raffaele Pisana, Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, 00166 Rome, Italy
- Correspondence: (M.S.); (C.A.)
| | - Anna Teresa Palamara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, 00185 Rome, Italy;
- IRCCS San Raffaele Pisana, Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, 00166 Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy;
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18
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Xiao Z, Chen S, Feng S, Li Y, Zou J, Ling H, Zeng Y, Zeng X. Function and mechanisms of microRNA-20a in colorectal cancer. Exp Ther Med 2020; 19:1605-1616. [PMID: 32104211 PMCID: PMC7027132 DOI: 10.3892/etm.2020.8432] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common malignancy and the second leading cause of cancer-associated mortality worldwide. CRC currently has no specific biomarkers to promote its diagnosis and treatment and the underlying mechanisms regulating its pathogenesis have not yet been determined. MicroRNAs (miRs) are small, non-coding RNAs that exhibit regulatory functions and have been demonstrated to serve a crucial role in the post-transcriptional regulatory processes of gene expression that is associated with cell physiology and disease progression. Recently, abnormal miR-20a expression has been identified in a number of cancers types and this has become a novel focus within cancer research. High levels of miR-20a expression have been identified in CRC tissues, serum and plasma. In a recent study, miR-20a was indicated to be present in feces and to exhibit a high sensitivity to CRC. Therefore, miR-20a may be used as a marker for CRC and an indicator that can prevent the invasive examination of patients with this disease. Changes in the expression of miR-20a during chemotherapy can be used as a biomarker for monitoring resistance to treatment. In conclusion, miR-20a exhibits the potential for clinical application as a novel diagnostic biomarker and therapeutic target for use in patients with CRC. The present study focused on the role and mechanisms of miR-20a in CRC.
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Affiliation(s)
- Zheng Xiao
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, P.R. China.,Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Shi Chen
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, P.R. China.,Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Shujun Feng
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, P.R. China.,Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Yukun Li
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, P.R. China.,Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Juan Zou
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, P.R. China.,Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Hui Ling
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, P.R. China.,Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Ying Zeng
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, P.R. China.,School of Nursing, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Xi Zeng
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, P.R. China.,Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, P.R. China
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Piperigkou Z, Karamanos NK. Dynamic Interplay between miRNAs and the Extracellular Matrix Influences the Tumor Microenvironment. Trends Biochem Sci 2019; 44:1076-1088. [DOI: 10.1016/j.tibs.2019.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022]
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20
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Moody L, Dvoretskiy S, An R, Mantha S, Pan YX. The Efficacy of miR-20a as a Diagnostic and Prognostic Biomarker for Colorectal Cancer: A Systematic Review and Meta-Analysis. Cancers (Basel) 2019; 11:cancers11081111. [PMID: 31382594 PMCID: PMC6721456 DOI: 10.3390/cancers11081111] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
Background: MicroRNAs have altered expression levels in various diseases and may play an important role in the diagnosis and prognosis of colorectal cancer (CRC). Methods: We systemically reviewed and quantitatively synthesized the scientific evidence pertaining to microRNA-20a (miR-20a) as a CRC biomarker. A keyword and reference search in PubMed yielded 32 studies, in which miR-20a was measured in feces, serum, or tumor tissue. Data were extracted from a total of 5014 cancer cases and 2863 controls. Results: Twenty out of 21 relevant studies found that miR-20a was upregulated in CRC patients compared to controls. Meta-analysis revealed a pooled miR-20a fold change of 2.45 (95% CI: 2.24-2.66) in CRC patients versus controls. To estimate sensitivity and specificity of miR-20a as a diagnostic biomarker of CRC, a pooled area under the receiver operating characteristic curve (AUROC) was calculated (0.70, 95% CI: 0.63-0.78). The prognostic capacity of miR-20a was assessed using hazard ratios (HRs) for the overall survival (OS). The meta-analysis estimated the pooled HR for OS to be 2.02 (95% CI: 0.90-3.14) in CRC patients with high miR-20a expression. Conclusions: miR-20a may be a valid biomarker for CRC detection but may not be a strong predictor of poor prognosis in CRC.
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Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Svyatoslav Dvoretskiy
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruopeng An
- Department of Kinesiology and Community Health, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Suparna Mantha
- Carle Physician Group, Carle Cancer Center, Carle Foundation Hospital, Urbana, IL 61802, USA
| | - Yuan-Xiang Pan
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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21
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Circulating biomarkers for early detection and clinical management of colorectal cancer. Mol Aspects Med 2019; 69:107-122. [PMID: 31189073 DOI: 10.1016/j.mam.2019.06.002] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/07/2019] [Accepted: 06/08/2019] [Indexed: 02/06/2023]
Abstract
New non-invasive approaches that can complement and improve on current strategies for colorectal cancer (CRC) screening and management are urgently needed. A growing number of publications have documented that components of tumors, which are shed into the circulation, can be detected in the form of liquid biopsies and can be used to detect CRC at early stages, to predict response to certain therapies and to detect CRC recurrence in a minimally invasive way. The analysis of circulating tumor DNA (ctDNA), tumor-derived cells (CTC, circulating tumor cells) or circulating microRNA (miRNA) in blood and other body fluids, have a great potential to improve different aspects of CRC management. The challenge now is to find which types of components, biofluids and detection methods would be the most suitable to be applied in the different steps of CRC detection and treatment. This chapter will provide an up to date review on ctDNA, CTCs and circulating miRNAs as new biomarkers for CRC, either for clinical management or early detection, highlighting their advantages and limitations.
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22
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Host⁻MicroRNA⁻Microbiota Interactions in Colorectal Cancer. Genes (Basel) 2019; 10:genes10040270. [PMID: 30987065 PMCID: PMC6523287 DOI: 10.3390/genes10040270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 03/27/2019] [Indexed: 12/12/2022] Open
Abstract
Changes in gut microbiota composition have consistently been observed in patients with colorectal cancer (CRC). Yet, it is not entirely clear how the gut microbiota interacts with tumor cells. We know that tumor cells undergo a drastic change in energy metabolism, mediated by microRNAs (miRNAs), and that tumor-derived miRNAs affect the stromal and immune cell fractions of the tumor microenvironment. Recent studies suggest that host intestinal miRNAs can also affect the growth and composition of the gut microbiota. Our previous CRC studies showed a high-level of interconnectedness between host miRNAs and their microbiota. Considering all the evidence to date, we postulate that the altered nutrient composition and miRNA expression in the CRC microenvironment selectively exerts pressure on the surrounding microbiota, leading to alterations in its composition. In this review article, we present our current understanding of the role of miRNAs in mediating host–microbiota interactions in CRC.
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Moreno EC, Pascual A, Prieto-Cuadra D, Laza VF, Molina-Cerrillo J, Ramos-Muñoz ME, Rodríguez-Serrano EM, Soto JL, Carrato A, García-Bermejo ML, Guillén-Ponce C. Novel Molecular Characterization of Colorectal Primary Tumors Based on miRNAs. Cancers (Basel) 2019; 11:cancers11030346. [PMID: 30862091 PMCID: PMC6468580 DOI: 10.3390/cancers11030346] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/13/2022] Open
Abstract
microRNAs (miRNA) expression in colorectal (CR) primary tumours can facilitate a more precise molecular characterization. We identified and validated a miRNA profile associated with clinical and histopathological features that might be useful for patient stratification. In situ hybridization array using paraffin-embedded biopsies of CR primary tumours were used to screen 1436 miRNAs. 17 miRNAs were selected for validation by quantitative reverse transcription polymerase chain reaction (qRT-PCR) (n = 192) and were further correlated with clinical and histopathological data. We demonstrated that miRNAs associated to Colorectal Cancer (CRC) diagnosis age (over 50s and 60s) included miR-1-3p, miR-23b-3p, miR-27b-3p, miR-143-3p, miR-145-5p and miR-193b-5p. miR-23b-3p and miR-24-3p discriminated between Lynch Syndrome and sporadic CRC. miR-10a-5p, miR-20a-5p, miR-642b and Let-7a-5p were associated to stroma abundance. miR-642b and Let-7a-5p were associated with to peritumoral inflammation abundance. miR-1-3p, miR-143-3p and miR-145-5p correlated with mucinous component. miR-326 correlated with tumour location (right or left sided). miR-1-3p associated with tumour grade. miR-20a-5p, miR-193b-5p, miR-320a, miR-326 and miR-642b-3p associated to tumour stage and progression. Remarkably, we also demonstrated that miR-1-3p and miR-326 expression significantly associated with patient overall survival (OS). Hierarchical clustering and bioinformatics analysis indicated that selected miRNAs could re-classify the patients and work cooperatively, modulating common target genes involved in colorectal cancer key signalling pathways. In conclusion, molecular characterization of CR primary tumours based on miRNAs could lead to more accurate patient reclassification and may be useful for efficient patient management.
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Affiliation(s)
- Elisa Conde Moreno
- Biomarkers and Therapeutic Targets Group and Core Facility, Ramon y Cajal Research Institute, (IRYCIS), 28034 Madrid, RedinRen, Spain.
| | - Alejandro Pascual
- Pathology Department, Ramon y Cajal Research Institute, University Hospital, 28034 Madrid, Spain.
| | - Daniel Prieto-Cuadra
- SynlabPathology, Pathology Department, Virgen de la Victoria, University Hospital, 29010 Málaga, Spain.
| | - Val F Laza
- Microbiology Department and Bioinformatics Core Facility, IRYCIS, 28034 Madrid, Spain.
| | - Javier Molina-Cerrillo
- Medical Oncology Department, Ramon y Cajal Research Institute, University Hospital, IRYCIS, 28034 Madrid, Spain.
| | - Miren Edurne Ramos-Muñoz
- Biomarkers and Therapeutic Targets Group and Core Facility, Ramon y Cajal Research Institute, (IRYCIS), 28034 Madrid, RedinRen, Spain.
| | | | - José Luis Soto
- Hereditary Cancer Program Valencian Region, Molecular Genetics Laboratory, Elche University Hospital, Elche, 03202 Alicante, Spain.
| | - Alfredo Carrato
- Medical Oncology Department, Ramon y Cajal Research Institute, University Hospital, IRYCIS, Alcala University, 28034 Ciberonc, Spain.
| | - María Laura García-Bermejo
- Biomarkers and Therapeutic Targets Group and Core Facility, Ramon y Cajal Research Institute, (IRYCIS), 28034 Madrid, RedinRen, Spain.
| | - Carmen Guillén-Ponce
- Medical Oncology Department, Ramon y Cajal Research Institute, University Hospital, IRYCIS, 28034 Madrid, Spain.
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Francavilla A, Tarallo S, Pardini B, Naccarati A. Fecal microRNAs as non-invasive biomarkers for the detection of colorectal cancer: a systematic review. MINERVA BIOTECNOL 2019. [DOI: 10.23736/s1120-4826.18.02495-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Sun Z, Shi K, Yang S, Liu J, Zhou Q, Wang G, Song J, Li Z, Zhang Z, Yuan W. Effect of exosomal miRNA on cancer biology and clinical applications. Mol Cancer 2018; 17:147. [PMID: 30309355 PMCID: PMC6182840 DOI: 10.1186/s12943-018-0897-7] [Citation(s) in RCA: 480] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/25/2018] [Indexed: 02/07/2023] Open
Abstract
Exosomes, extracellular vesicles with diameters ranging from 30 to 150 nm, are widely present in various body fluids. Recently, microRNAs (miRNAs) have been identified in exosomes, the biogenesis, release, and uptake of which may involve the endosomal sorting complex required for transport (ESCRT complex) and relevant proteins. After release, exosomes are taken up by neighboring or distant cells, and the miRNAs contained within modulate such processes as interfering with tumor immunity and the microenvironment, possibly facilitating tumor growth, invasion, metastasis, angiogenesis and drug resistance. Therefore, exosomal miRNAs have a significant function in regulating cancer progression. Here, we briefly review recent findings regarding tumor-derived exosomes, including RNA sorting and delivering mechanism. We then describe the intercommunication occurring between different cells via exosomal miRNAs in tumor microenvironmnt, with impacts on tumor proliferation, vascularization, metastasis and other biological characteristics. Finally, we highlight the potential role of these molecules as biomarkers in cancer diagnosis and prognosis and tumor resistance to therapeutics.
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Affiliation(s)
- Zhenqiang Sun
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Ke Shi
- Department of Plastic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shuaixi Yang
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jinbo Liu
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Quanbo Zhou
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Guixian Wang
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Junmin Song
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhen Li
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhiyong Zhang
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Weitang Yuan
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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High degradation and no bioavailability of artichoke miRNAs assessed using an in vitro digestion/Caco-2 cell model. Nutr Res 2018; 60:68-76. [PMID: 30527261 DOI: 10.1016/j.nutres.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 01/21/2023]
Abstract
Although the cross-kingdom transfer of vegetable miRNAs (miRNAs) in mammalian species, including humans, is still controversial, recent studies have rejected this theory. Based on these recent studies, we hypothesized that artichoke-derived miRNAs (cca-miRNAs) are not adsorbed into human intestinal cells after cooking and in vitro digestion. In order to test this hypothesis, we evaluated miRNA (cca-miRNAs) in the edible part of globe artichokes (head portion), after cooking and digestion by an in vitro digestion system. The cca-miRNA levels were analyzed by real-time PCR (RT-qPCR), and those that withstood cooking and digestion conditions were further analyzed for their bioavailability using an in vitro system (Caco-2/TC7 cell clone). We detected 20 cca-miRNAs after cooking, 5 of which were statistically down-regulated in comparison with uncooked samples. Only 4 cca-miRNAs were found after in vitro digestion. By using scanning electron microscopy (SEM), we also evaluated the extracellular vesicles (EVs) in homogenized artichoke as possible miRNA transporters. However, approximately 81% were degraded after cooking, while the remaining EVs had changed shape from round to elliptical. Finally, we detected no cell-free cca-miRNAs, miRNAs bound to protein complex, and no cca-miRNAs encapsulated in EVs inside Caco-2 cells or in basolateral medium after bioavailability experiments. In conclusion, the data from the present study agrees with recent findings that the human small intestine does not uptake dietary miRNAs from raw or cooked artichoke heads.
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To KKW, Tong CWS, Wu M, Cho WCS. MicroRNAs in the prognosis and therapy of colorectal cancer: From bench to bedside. World J Gastroenterol 2018; 24:2949-2973. [PMID: 30038463 PMCID: PMC6054943 DOI: 10.3748/wjg.v24.i27.2949] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/28/2018] [Accepted: 06/30/2018] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small, single-stranded, noncoding RNAs that can post-transcriptionally regulate the expression of various oncogenes and tumor suppressor genes. Dysregulated expression of many miRNAs have been shown to mediate the signaling pathways critical in the multistep carcinogenesis of colorectal cancer (CRC). MiRNAs are stable and protected from RNase-mediated degradation, thereby enabling its detection in biological fluids and archival tissues for biomarker studies. This review focuses on the role and application of miRNAs in the prognosis and therapy of CRC. While stage II CRC is potentially curable by surgical resection, a significant percentage of stage II CRC patients do develop recurrence. MiRNA biomarkers may be used to stratify such high-risk population for adjuvant chemotherapy to provide better prognoses. Growing evidence also suggests that miRNAs are involved in the metastatic process of CRC. Certain of these miRNAs may thus be used as prognostic biomarkers to identify patients more likely to have micro-metastasis, who could be monitored more closely after surgery and/or given more aggressive adjuvant chemotherapy. Intrinsic and acquired resistance to chemotherapy severely hinders successful chemotherapy in CRC treatment. Predictive miRNA biomarkers for response to chemotherapy may identify patients who will benefit the most from a particular regimen and also spare the patients from unnecessary side effects. Selection of patients to receive the new targeted therapy is becoming possible with the use of predictive miRNA biomarkers. Lastly, forced expression of tumor suppressor miRNA or silencing of oncogenic miRNA in tumors by gene therapy can also be adopted to treat CRC alone or in combination with other chemotherapeutic drugs.
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Affiliation(s)
- Kenneth KW To
- School of Pharmacy, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - Christy WS Tong
- School of Pharmacy, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - Mingxia Wu
- School of Pharmacy, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong, China
| | - William CS Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
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Motieghader H, Kouhsar M, Najafi A, Sadeghi B, Masoudi-Nejad A. mRNA-miRNA bipartite network reconstruction to predict prognostic module biomarkers in colorectal cancer stage differentiation. MOLECULAR BIOSYSTEMS 2018; 13:2168-2180. [PMID: 28861579 DOI: 10.1039/c7mb00400a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biomarker detection is one of the most important and challenging problems in cancer studies. Recently, non-coding RNA based biomarkers such as miRNA expression levels have been used for early diagnosis of many cancer types. In this study, a systems biology approach was used to detect novel miRNA based biomarkers for CRC diagnosis in early stages. The mRNA expression data from three CRC stages (Low-grade Intraepithelial Neoplasia (LIN), High-grade Intraepithelial Neoplasia (HIN) and Adenocarcinoma) were used to reconstruct co-expression networks. The networks were clustered to extract co-expression modules and detected low preserved modules among CRC stages. Then, the experimentally validated mRNA-miRNA interaction data were applied to reconstruct three mRNA-miRNA bipartite networks. Twenty miRNAs with the highest degree (hub miRNAs) were selected in each bipartite network to reconstruct three bipartite subnetworks for further analysis. The analysis of these hub miRNAs in the bipartite subnetworks revealed 30 distinct important miRNAs as prognostic markers in CRC stages. There are two novel CRC related miRNAs (hsa-miR-190a-3p and hsa-miR-1277-5p) in these 30 hub miRNAs that have not been previously reported in CRC. Furthermore, a drug-gene interaction network was reconstructed to detect potential candidate drugs for CRC treatment. Our analysis shows that the hub miRNAs in the mRNA-miRNA bipartite network are very essential in CRC progression and should be investigated precisely in future studies. In addition, there are many important target genes in the results that may be critical in CRC progression and can be analyzed as therapeutic targets in future research.
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Affiliation(s)
- Habib Motieghader
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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29
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Hou N, Guo Z, Zhao G, Jia G, Luo B, Shen X, Bai Y. Inhibition of microRNA-21-3p suppresses proliferation as well as invasion and induces apoptosis by targeting RNA-binding protein with multiple splicing through Smad4/extra cellular signal-regulated protein kinase signalling pathway in human colorectal cancer HCT116 cells. Clin Exp Pharmacol Physiol 2018. [PMID: 29542167 DOI: 10.1111/1440-1681.12931] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
MicroRNA-21-3p (miR-21-3p), the passenger strand of pre-mir-21, has been found to be high-expressing in various cancers and to be associated with tumour malignancy, which is proposed as a novel focus in malignant tumours. Colorectal cancer (CRC), currently known as one of the most prevalent malignancy, is a leading cause of cancer death. This study aimed to investigate the key role of miR-21-3p in CRC by inhibiting its expression using transfection with miR-21-3p inhibitors into human CRC HCT116 cells. Results showed that the expression of miR-21-3p was higher than other CRC cells used in the study including Lovo, HT29, Colo320 and SW480 cells, inhibition of which suppressed the proliferation and induced cell cycle arrest in HCT116 cells. Besides, transfection with miR-21-3p inhibitors also attenuated cell migration and invasion, and induced apoptosis as well. Moreover, luciferase assay confirmed RBPMS as a direct target of miR-21-3p in HCT116 cells. Further, miR-21-3p inhibitors increased the nuclear accumulation of Smad4 and reduced phosphorylation of ERK. Interestingly, we found that silence of RBPMS using RNA interference (siRNA) not only elevated the cell viability but also increased the phosphorylation of ERK and reversed the nuclear accumulation of Smad4 induced by miR-21-3p inhibitors in HCT116 cells. Data suggest that inhibition of miR-21-3p suppresses cell proliferation, invasion as well as migration and induces apoptosis by directly targeting RBPMS through Smad4/ERK signalling pathway in HCT116 cells. Our study demonstrates miR-21-3p as a potent target for suppressing tumour progression of CRC which may have implications in CRC therapy in the future.
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Affiliation(s)
- Nengyi Hou
- Departments of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Zhiyi Guo
- Departments of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Gaoping Zhao
- Departments of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Guiqing Jia
- Departments of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Bin Luo
- Departments of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Xiaogang Shen
- Departments of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Yifeng Bai
- Departments of Oncology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
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30
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Cavallini A, Rotelli MT, Lippolis C, Piscitelli D, Digennaro R, Covelli C, Carella N, Accetturo M, Altomare DF. Human microRNA expression in sporadic and FAP-associated desmoid tumors and correlation with beta-catenin mutations. Oncotarget 2018; 8:41866-41875. [PMID: 28418912 PMCID: PMC5522034 DOI: 10.18632/oncotarget.16383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/22/2017] [Indexed: 11/25/2022] Open
Abstract
Desmoid tumors (DT) are rare, benign, fibroblastic neoplasm with challenging histological diagnosis. DTs can occur sporadically or associated with the familial adenomatous polyposis coli (FAP). Most sporadic DTs are associated with β-catenin gene (CTNNB1) mutations, while mutated APC gene causes FAP disease. microRNAs (miRNAs) are involved in many human carcinogenesis. The miRNA profile was analyzed by microarray in formalin-fixed, paraffin-embedded (FFPE) specimens of 12 patients (8 sporadic, 4 FAP-associated) and 4 healthy controls. One hundred and one mRNAs resulted dysregulated, of which 98 in sporadic DTs and 8 in FAP-associated DTs, 5 were shared by both tumors. Twenty-six miRNAs were then validated by RT-qPCR in 23 sporadic and 7 FAP-associated DT samples matched with healthy controls. The qPCR method was also used to evaluate the CTNNB1 mutational status in sporadic DTs. The correlation between sporadic DTs and miRNA expression showed that miR-21-3p increased in mutated versus wild-type DTs, while miR-197-3p was decreased. The mRNA expression of Tetraspanin3 and Serpin family A member 3, as miR-21-3p targets, and L1 Cell Adhesion Molecule, as miR-197-3p target, was also evaluate. CTNNB1 mutations associated to miRNA dysregulation could affect the genesis and the progression of this disease and help histological diagnosis of sporadic DTs.
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Affiliation(s)
- Aldo Cavallini
- Laboratory of Cellular and Molecular Biology, National Institute for Digestive Diseases, IRCCS "Saverio de Bellis", Castellana Grotte (BA), Italy
| | - Maria Teresa Rotelli
- General Surgery and Liver Transplantation Unit, Department of Emergency and Organ Transplantation (DETO), University of Bari "Aldo Moro", Bari, Italy
| | - Catia Lippolis
- Laboratory of Cellular and Molecular Biology, National Institute for Digestive Diseases, IRCCS "Saverio de Bellis", Castellana Grotte (BA), Italy
| | - Domenico Piscitelli
- Section of Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari " Aldo Moro", Bari, Italy
| | - Rosa Digennaro
- General Surgery and Liver Transplantation Unit, Department of Emergency and Organ Transplantation (DETO), University of Bari "Aldo Moro", Bari, Italy
| | - Claudia Covelli
- Section of Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari " Aldo Moro", Bari, Italy
| | - Nicola Carella
- Laboratory of Cellular and Molecular Biology, National Institute for Digestive Diseases, IRCCS "Saverio de Bellis", Castellana Grotte (BA), Italy
| | - Matteo Accetturo
- Nephrology Unit, Department of Emergency and Organ Transplantation (DETO), University of Bari "Aldo Moro", Bari, Italy
| | - Donato Francesco Altomare
- General Surgery and Liver Transplantation Unit, Department of Emergency and Organ Transplantation (DETO), University of Bari "Aldo Moro", Bari, Italy
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Chen W, Lin G, Yao Y, Chen J, Shui H, Yang Q, Wang X, Weng X, Sun L, Chen F, Yang S, Yang Y, Zhou Y. MicroRNA hsa-let-7e-5p as a potential prognosis marker for rectal carcinoma with liver metastases. Oncol Lett 2018; 15:6913-6924. [PMID: 29731866 DOI: 10.3892/ol.2018.8181] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/19/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that target mRNAs for translational repression or cleavage. The present study was conducted to identify differentially expressed miRNAs in primary tumor tissues of rectal carcinoma (RC) that may be associated with heterochrony hepatic metastasis (HHM). Samples were collected exclusively from patients with RC but not colon cancer (CC); Next-generation high-throughput sequencing technology and bioinformatics tools were used to profile and analyze small RNAs and their corresponding targets in primary tumor tissues with HHM (n=2) or without metastases (non-metastatic, NM; n=2). A total of 24 known miRNAs were identified to be differentially expressed (P<0.01; absolute value of log2-fold change ≥1). Hsa-let-7e-5p exhibited the most significant elevation in tissues with HHM (log2-fold change=2.62). By combining online informatics resources and previous mRNA sequencing data, it was identified that 54 validated target genes of let-7e were downregulated in primary tumor tissues with HHM. A number of these target genes have been demonstrated to be directly involved in tumor metastasis (including MYC proto-oncogene, bHLH transcription factor, high-mobility group AT-Hook 2, peptidase inhibitor 3, KIT proto-oncogene receptor tyrosine kinase, Jun proto-oncogene, AP-1 transcription factor subunit and ribonuclease T2), or have physiological associations to immunity (including C-C motif chemokine receptor 4 and cluster of differentiation 40 ligand) and cellular metabolism (including peroxisome proliferator-activated receptor γ, coactivator 1 α). Next, 14 target genes were selected for reverse transcription-quantitative polymerase chain reaction analysis in non-sequenced samples, and the downregulation of 10 target genes in RC samples with HHM was confirmed. In addition, it was demonstrated that hsa-let-7e-5p stimulated colorectal cancer cell migration in vitro. The miRNA hsa-let-7e-5p may serve as a potential biomarker for rectal carcinoma-associated HHM, facilitating the identification of patients with RC who are at risk of developing HHM.
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Affiliation(s)
- Wenfeng Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P.R. China
| | - Guosheng Lin
- Department of Gastric Surgery, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Yizhou Yao
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P.R. China
| | - Jishen Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P.R. China
| | - Hanli Shui
- Department of Gastric Surgery, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Qinghai Yang
- Department of Molecular Pathology, Fuzhou Maixin Biotech., Co., Ltd., Fuzhou, Fujian 350001, P.R. China
| | - Xiaoya Wang
- Department of Molecular Pathology, Fuzhou Maixin Biotech., Co., Ltd., Fuzhou, Fujian 350001, P.R. China
| | - Xiaoyuan Weng
- Department of Gastric Surgery, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Ling Sun
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P.R. China
| | - Fei Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P.R. China
| | - Sheng Yang
- Department of Gastric Surgery, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Yufeng Yang
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P.R. China
| | - Yongjian Zhou
- Department of Gastric Surgery, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
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Cirera S, Willumsen LM, Johansen TT, Nielsen LN. Evaluation of microRNA stability in feces from healthy dogs. Vet Clin Pathol 2018; 47:115-121. [PMID: 29393972 DOI: 10.1111/vcp.12566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Gastrointestinal cancer accounts for approximately 8% of all canine malignancies. Early detection of cancer may have a tremendous impact on both treatment options and prognosis. MicroRNAs (miRNAs), a class of noncoding RNAs that can be found stably expressed in body fluids and feces, have been suggested as valuable human cancer biomarkers. OBJECTIVES The purpose of the study was to investigate the feasibility of detecting miRNAs in canine feces and to determine the miRNA stability in fecal samples stored at different temperatures for different duration. METHODS The levels of 4 Canine familiaris (cfa) miRNAs (cfa-miR-16, cfa-miR-20a, cfa-miR-21, and cfa-miR-92a) were investigated by quantitative real-time PCR(qPCR) in fecal samples from 10 healthy dogs. Fecal samples were collected at 3 different time points and samples from the first time point were stored at different temperatures and for a different duration. RESULTS A statistically significant difference was found in miRNA levels from samples stored at room temperature compared with samples stored at -20°C for cfa-miR-16 and cfa-miR-21. No significant difference was found in the level of the investigated miRNAs over time. CONCLUSIONS Overall, miRNAs are present in dog feces at measurable levels. Some miRNAs seem to be subject to a higher degree of degradation in samples stored at room temperature for 24 hours compared with samples frozen after collection at -20°C. The investigated miRNAs were stably expressed over time. This study provides the basis for further research on miRNA expression profiles as biomarkers for gastrointestinal cancer in dogs.
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Affiliation(s)
- Susanna Cirera
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line M Willumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thea T Johansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lise N Nielsen
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
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33
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Shao Y, Shen Y, Chen T, Xu F, Chen X, Zheng S. The functions and clinical applications of tumor-derived exosomes. Oncotarget 2018; 7:60736-60751. [PMID: 27517627 PMCID: PMC5312416 DOI: 10.18632/oncotarget.11177] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/1969] [Accepted: 07/13/2016] [Indexed: 02/06/2023] Open
Abstract
Exosomes are extracellular vesicles with diameters ranging from 30 to 150 nm. They can be secreted by all cell types and transfer information in the form of their contents, which include proteins, lipids and nucleic acids, to other cells throughout the body. They have roles in normal physiological processes as well as in disease development. Here, we review recent findings regarding tumor-derived exosomes, including methods for their extraction and preservation. We also describe the actions of exosomes in tumorigenesis. The exosomal antigen-presenting effect during antitumor immune responses and its suppressive function in immune tolerance are discussed. Finally, we describe the potential application of exosomes to cancer therapy and liquid biopsy.
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Affiliation(s)
- Yingkuan Shao
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanwei Shen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ting Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fei Xu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuewen Chen
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Jiao W, Leng X, Zhou Q, Wu Y, Sun L, Tan Y, Ni H, Dong X, Shen T, Liu Y, Li J. Different miR-21-3p isoforms and their different features in colorectal cancer. Int J Cancer 2017; 141:2103-2111. [PMID: 28734015 DOI: 10.1002/ijc.30902] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 05/26/2017] [Accepted: 07/11/2017] [Indexed: 12/22/2022]
Abstract
MiR-21, the only microRNA (miRNA) found to be overexpressed in any type of solid tumor, its guide stand, miR-21-5p, has been studied a lot in colorectal cancer (CRC); however, few researchers focused on its passenger strand, miR-21-3p. In our study, based on The Cancer Genome Atlas (TCGA) data, we found that there were more varieties and quantities of miR-21-3p isoforms in microsatellite instability (MSI)-type CRC. We further examined the role of miR-21-3p by in vitro and in vivo studies. MiR-21-3p may be an oncogene in CRC by promoting cellular mobility through epithelial-mesenchymal transition. However, different isoforms, especially miR-21-3p 0 | 2, may be a favorable prognostic marker for CRC survival, probably due to increased complementary effect of miR-21-5p and/or target genes. Further study investigating the underlying mechanism of miRNA isoforms is needed.
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Affiliation(s)
- Weijuan Jiao
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Xueqin Leng
- Department of Bioinformatics, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Qun Zhou
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yayun Wu
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Lina Sun
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yan Tan
- Department of Pathology, the First People's Hospital of Changzhou, Changzhou, People's Republic of China
| | - Hengli Ni
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Xiaoqiang Dong
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Tong Shen
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yao Liu
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Jianming Li
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
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Yau TO, Wu CW, Tang CM, Chen Y, Fang J, Dong Y, Liang Q, Ng SSM, Chan FKL, Sung JJY, Yu J. MicroRNA-20a in human faeces as a non-invasive biomarker for colorectal cancer. Oncotarget 2016; 7:1559-68. [PMID: 26621842 PMCID: PMC4811480 DOI: 10.18632/oncotarget.6403] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/15/2015] [Indexed: 12/18/2022] Open
Abstract
Objective Detection of microRNA (miRNA) aberrations in human faeces is a new approach for colorectal cancer (CRC) screening. The aim of this study was to characterise miR-20a in faeces as a non-invasive biomarker for diagnosis of CRC. Results miR-20a expression was significantly higher in the 40 CRC tumours compared to their respective adjacent normal tissues (P = 0.0065). Levels of miR-20a were also significantly higher in faecal samples from CRC patients (P < 0.0001). The area under receiver operating characteristic (AUROC) curve for miR-20a was 0.73, with a sensitivity of 55% and specificity of 82% for CRC patients compared with controls. No significant difference in the level of miR-20a was found between patients with proximal, distal, and rectal cancer. The use of antibiotics did not influence faecal miR-20a levels. Patients and Methods miR-20a was selected from an expression microarray containing 667 miRNAs. Further verification of miR-20a was performed in 40 pairs of primary CRC tissues, as well as 595 faecal samples (198 CRCs, 199 adenomas, and 198 healthy controls) using TaqMan probe based quantitative Real-Time PCR (qRT-PCR). Conclusions Faecal-based miR-20a can be utilised as a potential non-invasive biomarker for CRC screening.
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Affiliation(s)
- Tung On Yau
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Chung Wah Wu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Ceen-Ming Tang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.,Oxford University Clinical Academic Graduate School, John Radcliffe Hospital, Oxford, UK
| | - Yingxuan Chen
- Renji Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Jingyuan Fang
- Renji Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Yujuan Dong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.,Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Qiaoyi Liang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Simon Siu Man Ng
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Francis Ka Leung Chan
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Joseph Jao Yiu Sung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
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Wang X, Chen L, Jin H, Wang S, Zhang Y, Tang X, Tang G. Screening miRNAs for early diagnosis of colorectal cancer by small RNA deep sequencing and evaluation in a Chinese patient population. Onco Targets Ther 2016; 9:1159-66. [PMID: 27022275 PMCID: PMC4789834 DOI: 10.2147/ott.s100427] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PURPOSE This study aims to screen microRNAs (miRNAs), for an early diagnosis of colorectal cancer, by deep sequencing and evaluation of total miRNAs using clinical samples from a Chinese patient population. METHODS Total small RNAs from normal colonic mucosa, colonic adenomas, and colorectal cancer tissues were prepared for miRNA analysis by deep sequencing. The sequencing data were then analyzed by bioinformatics for candidate diagnostic miRNAs, which were further validated for their up- or downregulation status. RESULTS Comparison of cancer tissues with normal mucosa identified 99 upregulated and 90 downregulated miRNAs. Comparison of adenomas and normal mucosa found 114 upregulated and 107 downregulated miRNAs. Comparison of cancer and adenoma tissues found 70 upregulated and 27 downregulated miRNAs. Selected up- and downregulated miRNAs were validated for their expressions in 12 cases of patients with cancer and polyps. Specifically, for the upregulated miRNAs, miR-18a-5p and miR-21-3p were significantly upregulated in adenomas and cancer tissues, compared with the normal mucosa; miR-135b-5p, miR-17-5p, miR-182-5p, miR-200a-5p, and miR-200c-3p were significantly upregulated in cancer tissues compared to the normal mucosa, but their differential expression was not significant in adenoma tissues when compared with the normal mucosa. miR-183-5p and miR-96-5p were significantly upregulated in adenoma tissues when compared with normal mucosa, but these differences were not significant in cancer tissues when compared to normal mucosa. For the downregulated miRNAs, miR-133a-3p was significantly downregulated in both adenoma and cancer tissues when compared to normal mucosa; miR-204-5p, miR-125b-5p, miR-139-5p, miR-100-5p, and miR-30a-5p were significantly downregulated in cancer tissues compared to the normal mucosa, but their differential expression was not significant in adenoma tissue compared to normal mucosa. CONCLUSION The findings of this study show that a number of miRNAs might be important in the diagnosis and prognosis of colorectal cancer in Chinese patients using the method of small RNA deep sequencing. Upregulation of miR-18a-5p and miR-21-3p or downregulation of miR-133a-3p in adenoma and cancer tissues may serve as an index for early screening of colorectal cancer. Other miRNAs, such as miR-135b-5p, miR-17-5p, miR-182-5p, miR-200a-5p, miR-200c-3p, miR-183-5p, and miR-96-5p, which were either up- or downregulated, in cancer tissues, but not in adenoma tissues, have limited significance in early diagnosis. Further study is needed to determine a screening index with diagnostic value.
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Affiliation(s)
- Xiaofeng Wang
- National Center of Colorectal Surgery, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
- Graduate School of Nanjing University of Traditional Chinese Medicine, Nanjing, People’s Republic of China
| | - Li Chen
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Heiying Jin
- National Center of Colorectal Surgery, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
- Department of General Surgery, Peking University International Hospital, Beijing, People’s Republic of China
| | - Shuiming Wang
- National Center of Colorectal Surgery, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Yajie Zhang
- National Center of Colorectal Surgery, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Xiaoqing Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
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Cekaite L, Eide PW, Lind GE, Skotheim RI, Lothe RA. MicroRNAs as growth regulators, their function and biomarker status in colorectal cancer. Oncotarget 2016; 7:6476-505. [PMID: 26623728 PMCID: PMC4872728 DOI: 10.18632/oncotarget.6390] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/16/2015] [Indexed: 02/07/2023] Open
Abstract
Gene expression is in part regulated by microRNAs (miRNAs). This review summarizes the current knowledge of miRNAs in colorectal cancer (CRC); their role as growth regulators, the mechanisms that regulate the miRNAs themselves and the potential of miRNAs as biomarkers. Although thousands of tissue samples and bodily fluids from CRC patients have been investigated for biomarker potential of miRNAs (>160 papers presented in a comprehensive tables), none single miRNA nor miRNA expression signatures are in clinical use for this disease. More than 500 miRNA-target pairs have been identified in CRC and we discuss how these regulatory nodes interconnect and affect signaling pathways in CRC progression.
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Affiliation(s)
- Lina Cekaite
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Peter W. Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Guro E. Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Rolf I. Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A. Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
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Igaz I, Igaz P. Diagnostic Relevance of microRNAs in Other Body Fluids Including Urine, Feces, and Saliva. EXPERIENTIA SUPPLEMENTUM (2012) 2015; 106:245-252. [PMID: 26608207 DOI: 10.1007/978-3-0348-0955-9_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Beside blood-borne circulating miRNAs, miRNAs have been identified in other body fluid and excrements including stool, bile, saliva, and urine. Given the direct link of these body fluids to certain organs, their analysis for potential diagnostic miRNA markers is plausible. Several independent findings underline the potential utility of stool-derived miRNAs in the diagnosis of colorectal and pancreatic cancer. Given the difficulties in the diagnosis of cholangiocellular cancer, biliary miRNAs might be envisaged as useful markers. Several miRNAs have been identified in the saliva that could be associated with diseases, including tumors of the oral cavity. The urinary pool of miRNAs could be exploited for the diagnosis of urinary tract diseases and some appear to enable early diagnosis. In this chapter, we present findings supporting the potential diagnostic utility of fecal, biliary, salivary, and urinary miRNAs focusing mostly on tumors.
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Affiliation(s)
- Ivan Igaz
- Department of Gastroenterology, Szt Imre Teaching Hospital Budapest, Tétényi str. 12-16, 1115, Budapest, Hungary.
| | - Peter Igaz
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
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