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Hatiboglu MA, Karacam B, Khan I, Akdur K, Elbasan EB, Mahfooz S, Seyithanoglu MH, Cetin G, Papaker MG, Oztanir MN. Liquid biopsy for CNS lymphoma: CSF exosomes and CSF exosomal miR-15a, miR-21, miR-155, miR-210, and miR-19b are promising biomarkers for diagnosis. Mol Biol Rep 2024; 51:1035. [PMID: 39361107 DOI: 10.1007/s11033-024-09967-8] [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: 07/29/2024] [Accepted: 09/23/2024] [Indexed: 10/05/2024]
Abstract
BACKGROUND Central nervous system lymphoma (CNSL) is a devastating disease with a poor prognosis. Early diagnosis, monitoring of the treatment response, and outcome prediction carry the utmost importance in the management of patients with CNSL. Surgical biopsy is the gold standard for tissue diagnosis, however, this procedure has potential complications. Therefore, there is a need for a method that provides information about diagnosis and patient monitoring to avoid surgical risks. The study aimed to investigate potential diagnostic biomarkers for patients with CNSL. METHODS AND RESULTS Patients with secondary CNSL were included in this study. Serum and cerebrospinal fluid (CSF) samples were collected before treatment and after completion of the treatment. Cell-free DNA (cfDNA), exosomes, free and exosomal microRNA (miR)-15a, miR-21, miR-155, miR-210, and miR-19b in both serum and CSF were examined, and they were compared with the controls. Also, their levels before and after treatment were compared. Nine patients with the diagnosis of secondary CNSL were reviewed. cfDNA, miR-15a, and miR-155 in serum, and exosome in CSF were found to be significantly higher in CNSL patients compared to the controls. Exosomal miR-15a, miR-21, miR-155, miR-210, and miR-19b in CSF were found to be significantly higher in CNSL patients compared to controls, whereas their levels in serum were not significantly high. CONCLUSIONS Our findings suggested that exosomes and exosomal miR-15a, miR-21, miR-155, miR-210 and miR-19b in CSF would be promising biomarkers for the diagnosis of patients with CNSL. Further studies are needed to confirm our findings.
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Affiliation(s)
- Mustafa Aziz Hatiboglu
- Department of Neurosurgery, Bezmialem Vakif University Medical School, Vatan Street, Fatih, Istanbul, Turkey.
- Department of Molecular Biology, Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Yalikoy, Beykoz, Istanbul, Turkey.
| | - Busra Karacam
- Department of Molecular Biology, Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Yalikoy, Beykoz, Istanbul, Turkey
| | - Imran Khan
- Department of Molecular Biology, Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Yalikoy, Beykoz, Istanbul, Turkey
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kerime Akdur
- Department of Neurosurgery, Bezmialem Vakif University Medical School, Vatan Street, Fatih, Istanbul, Turkey
| | - Elif Burce Elbasan
- Department of Molecular Biology, Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Yalikoy, Beykoz, Istanbul, Turkey
| | - Sadaf Mahfooz
- Department of Molecular Biology, Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Yalikoy, Beykoz, Istanbul, Turkey
| | - Mehmet Hakan Seyithanoglu
- Department of Neurosurgery, Bezmialem Vakif University Medical School, Vatan Street, Fatih, Istanbul, Turkey
| | - Guven Cetin
- Department of Hematology, Bezmialem Vakif University Medical School, Vatan Street, Fatih, Istanbul, Turkey
| | - Meliha Gundag Papaker
- Department of Neurosurgery, Bezmialem Vakif University Medical School, Vatan Street, Fatih, Istanbul, Turkey
| | - Mustafa Namik Oztanir
- Department of Neurosurgery, Bezmialem Vakif University Medical School, Vatan Street, Fatih, Istanbul, Turkey
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Saleem HM, Ramaiah P, Gupta J, Jalil AT, Kadhim NA, Alsaikhan F, Ramírez-Coronel AA, Tayyib NA, Guo Q. Nanotechnology-empowered lung cancer therapy: From EMT role in cancer metastasis to application of nanoengineered structures for modulating growth and metastasis. ENVIRONMENTAL RESEARCH 2023:115942. [PMID: 37080268 DOI: 10.1016/j.envres.2023.115942] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/09/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Lung cancer is one of the leading causes of death in both males and females, and it is the first causes of cancer-related deaths. Chemotherapy, surgery and radiotherapy are conventional treatment of lung cancer and recently, immunotherapy has been also appeared as another therapeutic strategy for lung tumor. However, since previous treatments have not been successful in cancer therapy and improving prognosis and survival rate of lung tumor patients, new studies have focused on gene therapy and targeting underlying molecular pathways involved in lung cancer progression. Nanoparticles have been emerged in treatment of lung cancer that can mediate targeted delivery of drugs and genes. Nanoparticles protect drugs and genes against unexpected interactions in blood circulation and improve their circulation time. Nanoparticles can induce phototherapy in lung cancer ablation and mediating cell death. Nanoparticles can induce photothermal and photodynamic therapy in lung cancer. The nanostructures can impair metastasis of lung cancer and suppress EMT in improving drug sensitivity. Metastasis is one of the drawbacks observed in lung cancer that promotes migration of tumor cells and allows them to establish new colony in secondary site. EMT can occur in lung cancer and promotes tumor invasion. EMT is not certain to lung cancer and it can be observed in other human cancers, but since lung cancer has highest incidence rate, understanding EMT function in lung cancer is beneficial in improving prognosis of patients. EMT induction in lung cancer promotes tumor invasion and it can also lead to drug resistance and radio-resistance. Moreover, non-coding RNAs and pharmacological compounds can regulate EMT in lung cancer and EMT-TFs such as Twist and Slug are important modulators of lung cancer invasion that are discussed in current review.
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Affiliation(s)
- Hiba Muwafaq Saleem
- Department of Medical Laboratory Techniques, Al-Maarif University College, AL-Anbar, Iraq.
| | | | - Jitendra Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, Pin Code 281406, UP, India
| | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla, 51001, Iraq.
| | | | - Fahad Alsaikhan
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Andrés Alexis Ramírez-Coronel
- Azogues Campus Nursing Career, Health and Behavior Research Group (HBR), Psychometry and Ethology Laboratory, Catholic University of Cuenca, Ecuador; Epidemiology and Biostatistics Research Group, CES University, Colombia; Educational Statistics Research Group (GIEE), National University of Education, Ecuador
| | - Nahla A Tayyib
- Faculty of Nursing, Umm Al- Qura University, Makkah, Saudi Arabia
| | - Qingdong Guo
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China.
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Toyokawa G, Bersani F, Bironzo P, Picca F, Tabbò F, Haratake N, Takenaka T, Seto T, Yoshizumi T, Novello S, Scagliotti GV, Taulli R. Tumor plasticity and therapeutic resistance in oncogene-addicted non-small cell lung cancer: from preclinical observations to clinical implications. Crit Rev Oncol Hematol 2023; 184:103966. [PMID: 36925092 DOI: 10.1016/j.critrevonc.2023.103966] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The identification of actionable targets in oncogene-addicted non-small cell lung cancer (NSCLC) has fueled biomarker-directed strategies, especially in advanced stage disease. Despite the undeniable success of molecular targeted therapies, duration of clinical response is relatively short-lived. While extraordinary efforts have defined the complexity of tumor architecture and clonal evolution at the genetic level, not equal interest has been given to the dynamic mechanisms of phenotypic adaptation engaged by cancer during treatment. At the clinical level, molecular targeted therapy of EGFR-mutant and ALK-rearranged tumors often results in epithelial-to-mesenchymal transition (EMT) and histological transformation of the original adenocarcinoma without the acquisition of additional genetic lesions, thus limiting subsequent therapeutic options and patient outcome. Here we provide an overview of the current understanding of the genetic and non-genetic molecular circuits governing this phenomenon, presenting current strategies and potentially innovative therapeutic approaches to interfere with lung cancer cell plasticity.
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Affiliation(s)
- Gouji Toyokawa
- Department of Oncology, University of Torino, Regione Gonzole 10, 10043 Orbassano, Italy; Center for Experimental Research and Medical Studies (CeRMS), AOU Città della Salute e della Scienza di Torino, Torino, Italy; Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Francesca Bersani
- Department of Oncology, University of Torino, Regione Gonzole 10, 10043 Orbassano, Italy; Center for Experimental Research and Medical Studies (CeRMS), AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Paolo Bironzo
- Department of Oncology, University of Torino, AOU S. Luigi Gonzaga, Regione Gonzole 10, 10043 Orbassano, Italy
| | - Francesca Picca
- Department of Oncology, University of Torino, Regione Gonzole 10, 10043 Orbassano, Italy; Center for Experimental Research and Medical Studies (CeRMS), AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Fabrizio Tabbò
- Department of Oncology, University of Torino, AOU S. Luigi Gonzaga, Regione Gonzole 10, 10043 Orbassano, Italy
| | - Naoki Haratake
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoyoshi Takenaka
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Seto
- Department of Thoracic Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Silvia Novello
- Department of Oncology, University of Torino, AOU S. Luigi Gonzaga, Regione Gonzole 10, 10043 Orbassano, Italy
| | - Giorgio V Scagliotti
- Department of Oncology, University of Torino, AOU S. Luigi Gonzaga, Regione Gonzole 10, 10043 Orbassano, Italy.
| | - Riccardo Taulli
- Department of Oncology, University of Torino, Regione Gonzole 10, 10043 Orbassano, Italy; Center for Experimental Research and Medical Studies (CeRMS), AOU Città della Salute e della Scienza di Torino, Torino, Italy.
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Ha J, Park S. NCMD: Node2vec-Based Neural Collaborative Filtering for Predicting MiRNA-Disease Association. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1257-1268. [PMID: 35849666 DOI: 10.1109/tcbb.2022.3191972] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Numerous studies have reported that micro RNAs (miRNAs) play pivotal roles in disease pathogenesis based on the deregulation of the expressions of target messenger RNAs. Therefore, the identification of disease-related miRNAs is of great significance in understanding human complex diseases, which can also provide insight into the design of novel prognostic markers and disease therapies. Considering the time and cost involved in wet experiments, most recent works have focused on the effective and feasible modeling of computational frameworks to uncover miRNA-disease associations. In this study, we propose a novel framework called node2vec-based neural collaborative filtering for predicting miRNA-disease association (NCMD) based on deep neural networks. Initially, NCMD exploits Node2vec to learn low-dimensional vector representations of miRNAs and diseases. Next, it utilizes a deep learning framework that combines the linear ability of generalized matrix factorization and nonlinear ability of a multilayer perceptron. Experimental results clearly demonstrate the comparable performance of NCMD relative to the state-of-the-art methods according to statistical measures. In addition, case studies on breast cancer, lung cancer and pancreatic cancer validate the effectiveness of NCMD. Extensive experiments demonstrate the benefits of modeling a neural collaborative-filtering-based approach for discovering novel miRNA-disease associations.
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5
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Ha J. SMAP: Similarity-based matrix factorization framework for inferring miRNA-disease association. Knowl Based Syst 2023. [DOI: 10.1016/j.knosys.2023.110295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Shang C, Chen Q, Zu F, Ren W. Integrated analysis identified prognostic microRNAs in breast cancer. BMC Cancer 2022; 22:1170. [DOI: 10.1186/s12885-022-10242-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
MicroRNAs (miRNAs) play pivotal roles in the development and progression of breast cancer (BC). In this study, we attempted to identify miRNAs associated with BC prognosis and progression via integrated analysis.
Methods
We first screened 83 differentially expressed miRNAs (DEMs) in 1249 BC samples and 151 normal samples. We then validated their roles in expression and prognosis of BC, identified two survival-related DEMs, and established a risk model. The prediction efficiency was assessed in both the training and validation groups. Tissue and cell experiments were conducted to verify the regulatory effects of miR-127 in BC.
Results
The ROC curve indicated good prediction ability with 1-, 3-, and 5-year survival rates of 0.73, 0.72, and 0.72, respectively. Moreover, hsa-miR-127 was found to be an independent prognostic factor of BC. Functional analyses revealed that it is involved in various cancer pathways such as the PI3K-Akt and p53 pathways. miR-127 expression was down-regulated in both BC tissues and cell lines. The knockdown of miR-127 substantially increased, whereas overexpression decreased BC cell proliferation, invasion, and migration. This effect of miR-127 was consistent with its tumorigenic ability and tumor volume in nude mice.
Conclusions
These findings indicate that low expression of miR-127 contributes to BC migration, invasion, and tumorigenesis and that it can be a therapeutic target and prognostic biomarker for BC.
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Liu Z, Zhao W, Yang R. MiR-1246 is responsible for lung cancer cells-derived exosomes-mediated promoting effects on lung cancer stemness via targeting TRIM17. ENVIRONMENTAL TOXICOLOGY 2022; 37:2651-2659. [PMID: 35894553 DOI: 10.1002/tox.23625] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/01/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
The stemness of lung cancer cells contributes to drug resistance, tumor occurrence, progression, and recurrence; however, the underlying mechanisms are still fragmentary. In the present study, it was found that exosomes from cisplatin-resistant cells and spheres derived from lung cancer cells enhanced the stemness of the parental lung cancer cells. Then we screened the upregulated miRNAs in spheres derived from lung cancer cells and cisplatin-resistant lung cancer cells/exosomes compared to that in the parental lung cancer cells. It was found that miR-1246 was remarkably enriched in cisplatin-resistant lung cancer cells/exosomes and spheres. Additionally, inhibition of miR-1246 attenuated the stemness of lung cancer cells induced by exosomes from cisplatin-resistant cells and spheres. Furthermore, TRIM17 was identified to the direct target of miR-1246 in lung cancer cells. Our findings suggest that exosomal miR-1246 could be as a potential target for lung cancer treatment.
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Affiliation(s)
- Zhengcheng Liu
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, China
| | - Wei Zhao
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon, Hong Kong
| | - Rusong Yang
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, China
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Li L, Gao Z, Zheng CH, Qi R, Wang YT, Ni JC. Predicting miRNA-Disease Association Based on Improved Graph Regression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3604-3613. [PMID: 34757912 DOI: 10.1109/tcbb.2021.3127017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recently, as a growing number of associations between microRNAs (miRNAs) and diseases are discovered, researchers gradually realize that miRNAs are closely related to several complicated biological processes and human diseases. Hence, it is especially important to construct availably models to infer associations between miRNAs and diseases. In this study, we presented Improved Graph Regression for miRNA-Disease Association Prediction (IGRMDA) to observe potential relationship between miRNAs and diseases. In order to reduce the inherent noise existing in the acquired biological datasets, we utilized matrix decomposition algorithm to process miRNA functional similarity and disease semantic similarity and then combining them with existing similarity information to obtain final miRNA similarity data and disease similarity data. Then, we applied miRNA-disease association data, miRNA similarity data and disease similarity data to form corresponding latent spaces. Furthermore, we performed improved graph regression algorithm in latent spaces, which included miRNA-disease association space, miRNA similarity space and disease similarity space. Non-negative matrix factorization and partial least squares were used in the graph regression process to obtain important related attributes. The cross validation experiments and case studies were also implemented to prove the effectiveness of IGRMDA, which showed that IGRMDA could predict potential associations between miRNAs and diseases.
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9
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Liu Z, Zhang W, Zhang B, Chen S, Ling C. MiR-504-3p Has Tumor-Suppressing Activity and Decreases IFITM1 Expression in Non-Small Cell Lung Cancer Cells. Genet Test Mol Biomarkers 2022; 26:351-359. [PMID: 36027039 DOI: 10.1089/gtmb.2021.0158] [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: 11/13/2022] Open
Abstract
Objective: To analyze the impact of expression of miR-504-3p on the proliferation, migration, cell cycle transit and rate of apoptosis of NSCLC cells and explore the underlying mechanisms. Methods: The Cancer Genome Atlas (TCGA) database was used to compare the expression levels of miR-504 between NSCLC tissues and normal lung tissues. NSCLC cells were transfected with lentiviral vectors that either overexpressed or knocked down miR-504-3p to evaluate its effects on NSCLC biological behavior. Quantitative Real Time Polymerase Chain Reaction was used to measure the levels of miR-504-3p and Interferon-Induced Transmembrane Protein 1 (IFITM1). A luciferase reporter array was used to reveal whether miR-504-3p directly targets IFITM1. Results: The expression of miR-504 was significantly down-regulated in lung cancer tissues compared to normal lung tissues. Overexpression of miR-504-3p in NSCLC cell lines inhibited cell proliferation, migration and promoted cell apoptosis. Meanwhile, changes in the expression level of miR-504-3p had no significant effect on NSCLC cell cycle progression. Moreover, over-expressed miR-504-3p following its transfection significantly decreased the expression of IFITM1 in NSCLC cell lines and suppressed the activity of the luciferase reporter containing wild type but not mutant IFITM1 3' -UTR. Conclusion: miR-504-3p inhibits cell proliferation and migration and promotes cell apoptosis in NSCLC cells. MiR-504-3p decreases IFITM1 expression in NSCLC cells, which may be a potential mechanism of its tumor-suppressive functions in NSCLC.
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Affiliation(s)
- Zining Liu
- Department of Respiratory Diseases, Suzhou Municipal Hospital, Suzhou, China.,Department of Gastroenterology, Xiangcheng People's Hospital, Suzhou, China.,Department of Respiratory Diseases and The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Weili Zhang
- Department of Gastroenterology, Xiangcheng People's Hospital, Suzhou, China
| | - Biao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Shaomu Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chunhua Ling
- Department of Respiratory Diseases and The First Affiliated Hospital of Soochow University, Suzhou, China
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10
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Expression Level, Correlation, and Diagnostic Value of Serum miR-127 in Patients with Acute Respiratory Distress Syndrome. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:2257764. [PMID: 34603466 PMCID: PMC8483901 DOI: 10.1155/2021/2257764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/06/2021] [Indexed: 11/17/2022]
Abstract
Objective To analyze the expression of miR-127 in the serum of patients with acute respiratory distress syndrome (ARDS) and to explore its correlation with the severity of ARDS patients and its value as a molecular marker for diagnosis of ARDS. Methods 70 patients with ARDS admitted to our hospital from September 2017 to September 2019 were selected as the observation group, and 60 healthy persons with physical examination were collected as the control group. RT-PCR was used to detect the serum miR-127 levels of all subjects, and the serum miR-127 levels of the observation group and control group were compared. The oxygenation index (PaO2/FiO2) of ARDS patients was recorded and divided into three subgroups: mild group, moderate group, and severe group. Serum miR-127 levels of patients in the mild group, moderate group, and severe group were compared. Pearson correlation was used to analyze the relationship between serum miR-127 levels and the severity of ARDS patients. The receiver operating characteristic curve (ROC) was drawn, and the area under the ROC curve (AUC) was used to evaluate the diagnostic value of miR-127 in patients with ARDS. Results The serum level of miR-127 (10.15 ± 1.03) in the observation group was significantly higher than that in the control group (3.09 ± 0.62). And in the three subgroups of mild, moderate, and severe, the serum miR-127 level in the moderate group (10.43 ± 0.71) and the severe group miR-127 level (11.05 ± 1.26) were significantly higher than those in the mild group level (9.38 ± 1.24). Pearson correlation analysis showed that the serum miR-127 level was negatively correlated with PaO2/FiO2 (r = −0.715, P < 0.05), that is, the serum miR-127 level was positively correlated with the severity of ARDS patients. The area under the curve (AUC) of the diagnostic value of serum miR-127 for ARDS was 0.732 (95% CI 0.607–0.858). When the optimal cutoff value was 0.380, the sensitivity was 59.1% and the specificity was 78.6%, which suggested that miR-127 can be used as a marker for ARDS diagnosis. Conclusion There is an increase in miR-127 levels in the serum of ARDS patients. The serum miR-127 level is positively correlated with the severity of ARDS. The higher the level of miR-127, the worse the condition of ARDS, which is positively correlated with the severity of the condition. It suggests that the serum miR-127 level is an important indicator for evaluating the severity of ARDS patients. It can be used as a molecular marker for clinical diagnosis of ARDS.
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Hussen BM, Shoorei H, Mohaqiq M, Dinger ME, Hidayat HJ, Taheri M, Ghafouri-Fard S. The Impact of Non-coding RNAs in the Epithelial to Mesenchymal Transition. Front Mol Biosci 2021; 8:665199. [PMID: 33842553 PMCID: PMC8033041 DOI: 10.3389/fmolb.2021.665199] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) is a course of action that enables a polarized epithelial cell to undertake numerous biochemical alterations that allow it to adopt features of mesenchymal cells such as high migratory ability, invasive properties, resistance to apoptosis, and importantly higher-order formation of extracellular matrix elements. EMT has important roles in implantation and gastrulation of the embryo, inflammatory reactions and fibrosis, and transformation of cancer cells, their invasiveness and metastatic ability. Regarding the importance of EMT in the invasive progression of cancer, this process has been well studies in in this context. Non-coding RNAs (ncRNAs) have been shown to exert critical function in the regulation of cellular processes that are involved in the EMT. These processes include regulation of some transcription factors namely SNAI1 and SNAI2, ZEB1 and ZEB2, Twist, and E12/E47, modulation of chromatin configuration, alternative splicing, and protein stability and subcellular location of proteins. In the present paper, we describe the influence of ncRNAs including microRNAs and long non-coding RNAs in the EMT process and their application as biomarkers for this process and cancer progression and their potential as therapeutic targets.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Pharmacognosy Department, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Mahdi Mohaqiq
- Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University, Winston-Salem, NC, United States
| | - Marcel E. Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University-Erbil, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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12
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Noncoding RNAs Associated with Therapeutic Resistance in Pancreatic Cancer. Biomedicines 2021; 9:biomedicines9030263. [PMID: 33799952 PMCID: PMC7998345 DOI: 10.3390/biomedicines9030263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Therapeutic resistance is an inevitable impediment towards effective cancer therapies. Evidence accumulated has shown that the signaling pathways and related factors are fundamentally responsible for therapeutic resistance via regulating diverse cellular events, such as epithelial-to-mesenchymal transition (EMT), stemness, cell survival/apoptosis, autophagy, etcetera. Noncoding RNAs (ncRNAs) have been identified as essential cellular components in gene regulation. The expression of ncRNAs is altered in cancer, and dysregulated ncRNAs participate in gene regulatory networks in pathological contexts. An in-depth understanding of molecular mechanisms underlying the modulation of therapeutic resistance is required to refine therapeutic benefits. This review presents an overview of the recent evidence concerning the role of human ncRNAs in therapeutic resistance, together with the feasibility of ncRNAs as therapeutic targets in pancreatic cancer.
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Sun Y, Sun W, Hua H, Zhang J, Yu Q, Wang J, Liu X, Dong A. Overexpression of miR-127 Predicts Poor Prognosis and Contributes to the Progression of Papillary Thyroid Cancer by Targeting REPIN1. Horm Metab Res 2021; 53:197-203. [PMID: 33339069 DOI: 10.1055/a-1322-3160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Papillary thyroid cancer (PTC) is a major kind of thyroid cancer with increasing recurrence and metastasis. MiR-127 has been demonstrated to play roles in many cancers with dysregulation. However, the function of miR-127 is still unknown. This study aimed to explore a novel biomarker for the progression and prognosis of PTC. A set of 118 patients with PTC were collected from the Affiliated Hospital of Qingdao University. qRT-PCR was used to detect the expression of miR-127 in PTC tissues and cells. The association between miR-127 expression and the clinicopathological features of patients were evaluated by the χ2 test, and the prognostic value of miR-127 was evaluated by Kaplan-Meier analysis and Cox regression analysis. The effect of miR-127 on cell proliferation, migration, and invasion of PTC was analyzed by CCK-8 and transwell assay. miR-127 was found to be upregulated in PTC tissues and cells correlated with the TNM stage and poor prognosis of PTC patients. MiR-127 and the TNM stage were considered as two independent prognostic indicators for PTC. Moreover, overexpression of miR-127 significantly enhanced cell proliferation, migration, and invasion of PTC by targeting REPIN1. miR-127 may be involved in the progression of PTC, which provides a new therapeutic strategy for PTC.
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Affiliation(s)
- Yinghe Sun
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P. R. China
| | - Wenhai Sun
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P. R. China
| | - Hui Hua
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P. R. China
| | - Jianhua Zhang
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P. R. China
| | - Qianqian Yu
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P. R. China
| | - Jueru Wang
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P. R. China
| | - Xiaomin Liu
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P. R. China
| | - Anbing Dong
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P. R. China
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14
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Pan G, Liu Y, Shang L, Zhou F, Yang S. EMT-associated microRNAs and their roles in cancer stemness and drug resistance. Cancer Commun (Lond) 2021; 41:199-217. [PMID: 33506604 PMCID: PMC7968884 DOI: 10.1002/cac2.12138] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Epithelial‐to‐mesenchymal transition (EMT) is implicated in a wide array of malignant behaviors of cancers, including proliferation, invasion, and metastasis. Most notably, previou studies have indicated that both cancer stem‐like properties and drug resistance were associated with EMT. Furthermore, microRNAs (miRNAs) play a pivotal role in the regulation of EMT phenotype, as a result, some miRNAs impact cancer stemness and drug resistance. Therefore, understanding the relationship between EMT‐associated miRNAs and cancer stemness/drug resistance is beneficial to both basic research and clinical treatment. In this review, we preliminarily looked into the various roles that the EMT‐associated miRNAs play in the stem‐like nature of malignant cells. Then, we reviewed the interaction between EMT‐associated miRNAs and the drug‐resistant complex signaling pathways of multiple cancers including lung cancer, gastric cancer, gynecologic cancer, breast cancer, liver cancer, colorectal cancer, pancreatic cancer, esophageal cancer, and nasopharyngeal cancer. We finally discussed the relationship between EMT, cancer stemness, and drug resistance, as well as looked forward to the potential applications of miRNA therapy for malignant tumors.
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Affiliation(s)
- Guangtao Pan
- Department of Traditional Chinese Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, P. R. China
| | - Yuhan Liu
- Department of Traditional Chinese Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, P. R. China
| | - Luorui Shang
- Department of Traditional Chinese Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, P. R. China
| | - Fangyuan Zhou
- Department of Traditional Chinese Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, P. R. China
| | - Shenglan Yang
- Department of Traditional Chinese Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, P. R. China
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15
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MicroRNAs: Emerging oncogenic and tumor-suppressive regulators, biomarkers and therapeutic targets in lung cancer. Cancer Lett 2021; 502:71-83. [PMID: 33453304 DOI: 10.1016/j.canlet.2020.12.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 11/24/2020] [Accepted: 12/26/2020] [Indexed: 02/05/2023]
Abstract
Lung cancer is one of the most common solid tumors worldwide and the leading cause of cancer-related deaths, causing a devastating impact on human health. The clinical prognosis of lung cancer is usually restricted by delayed diagnosis and resistance to anticancer therapies. MicroRNAs, a range of small endogenous noncoding RNAs 22 nucleotides in length, have emerged as one of the most important players in cancer initiation and progression in recent decades. Current evidence reveals pivotal roles of microRNAs in regulating cell proliferation, migration, invasion and metastasis in lung cancer. An increasing number of preclinical and clinical studies have also explored the potential of microRNAs as promising biomarkers and new therapeutic targets for lung cancer. The current review summarizes the most recent progress on the functional mechanisms of microRNAs involved in lung cancer development and progression and further discusses the clinical application of miRNAs as putative therapeutic targets for molecular diagnosis and prognostic prediction in lung cancer.
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16
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Lu MD, Liu D, Li YX. LINC01436 Promotes the Progression of Gastric Cancer via Regulating miR-513a-5p/APE1 Axis. Onco Targets Ther 2020; 13:10607-10619. [PMID: 33116638 PMCID: PMC7585552 DOI: 10.2147/ott.s257747] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/19/2020] [Indexed: 12/21/2022] Open
Abstract
Background Gastric cancer (GC) is one of the deadliest cancer worldwide. Multiple long non-coding RNAs (lncRNAs) are recently identified as crucial oncogenic factors or tumor suppressors in GC. In this study, we aimed to probe into the effect of LINC01436 on GC progression. Methods LINC01436 and miR-513a-5p expressions in GC tissue samples were measured using quantitative real-time polymerase chain reaction (qRT-PCR). Western blot was used to detect the expression of apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) expression. Human GC cell lines AGS and BGC-823 were employed to investigate the function and mechanism of LINC01436 in GC. Cell counting kit-8 (CCK-8) assay was used to assess the effect of LINC01436 on proliferation. Flow cytometry was utilized to explore the effect of LINC01436 on apoptosis, and Transwell assay was conducted to detect the effect of LINC01436 on the migration and invasion. Colony formation assay was performed to evaluate the effect of LINC01436 on radioresistance of GC cells. Furthermore, luciferase reporter assay and RNA immunoprecipitation assay were conducted to confirm the binding relationship between miR-513a-5p and LINC01436. Additionally, Western blot was used to study the regulatory function of LINC01436 and miR-513a-5p on APE1. Results LINC01436 expression of GC clinical samples was remarkably increased and LINC01436 was correlated with unfavorable pathological indexes. LINC01436 high expression was associated with shorter overall survival time. Its overexpression observably promoted the proliferation, metastasis and radioresistance of GC cells, and its knockdown suppressed the malignant phenotypes of GC cells. LINC01436 overexpression markedly reduced the miR-513a-5p expression via sponging it and enhanced the APE1 expression. MiR-513a-5p overexpression or APE1 knockdown reversed the effects of LINC01436 on GC cells. Conclusion LINC01436 is a molecular sponge of tumor suppressor miR-513a-5p, which indirectly enhances the APE1 expression and functions as the oncogenic lncRNA in GC.
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Affiliation(s)
- Ming-Dian Lu
- Department of Gastrointestinal Surgery and General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, People's Republic of China
| | - Dong Liu
- Department of Gastrointestinal Surgery and General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, People's Republic of China
| | - Yong-Xiang Li
- Department of Gastrointestinal Surgery and General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, People's Republic of China
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17
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Feng L, Wang K, Tang P, Chen S, Liu T, Lei J, Yuan R, Hu Z, Li W, Yu X. Deubiquitinase USP18 promotes the progression of pancreatic cancer via enhancing the Notch1-c-Myc axis. Aging (Albany NY) 2020; 12:19273-19292. [PMID: 33051403 PMCID: PMC7732327 DOI: 10.18632/aging.103760] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/06/2020] [Indexed: 01/24/2023]
Abstract
The dysregulation of deubiquitinating enzymes (DUBs), which regulate the stability of most cellular proteins, has been implicated in many human diseases, including cancers. Thus, DUBs can be considered potential therapeutic targets for many cancers. However, the role of deubiquitinase ubiquitin-specific protease 18 (USP18) in pancreatic cancer remains unknown. Here, we found that the deubiquitinase ubiquitin-specific protease 18 (USP18) is significantly upregulated in pancreatic cancer and is correlated with a shorter median overall and relapse-free survival. A functional assay demonstrated that overexpression of USP18 resulted in increased proliferation of pancreatic cancer cells. Conversely, these phenomena were reversed after USP18 was silenced in pancreatic cancer cells. Further investigation revealed that USP18 promoted cell progression by increasing c-Myc expression, which has been reported to control pancreatic cancer progression, and our data demonstrated that c-Myc is key for USP18-mediated pancreatic cancer cell progression in vitro and in vivo. Moreover, we found that USP18 promoted pancreatic cancer progression via upregulation of Notch-1-dependent c-Myc. Mechanistically, USP18 interacts with and removes K48-linked ubiquitin chains from Notch1, thereby stabilizing Notch1 and promoting the Notch1-c-Myc pathway. Our work identifies and validates USP18 as a pancreatic cancer oncogene and provides a potential druggable target for this intractable disease.
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Affiliation(s)
- Long Feng
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Kai Wang
- Hepatopancreatobiliary Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Ping Tang
- Hepatopancreatobiliary Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China,Department of General Surgery, Hunan Youxian People's Hospital, Youxian, China
| | - Suyun Chen
- The Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Tiande Liu
- Hepatopancreatobiliary Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Jun Lei
- Hepatopancreatobiliary Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Rongfa Yuan
- Hepatopancreatobiliary Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Zhigang Hu
- Hepatopancreatobiliary Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Wen Li
- Hepatopancreatobiliary Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Xin Yu
- Hepatopancreatobiliary Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
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18
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Žlajpah M, Boštjančič E, Zidar N. (Epi)genetic regulation of osteopontin in colorectal cancerogenesis. Epigenomics 2020; 12:1389-1403. [PMID: 32921164 DOI: 10.2217/epi-2020-0032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: To identify (epi)genetic regulators of osteopontin (OPN, encoded by SPP1 gene) from normal colon mucosa to adenoma, adenoma with early carcinoma and advanced carcinoma. Patients & methods: Biopsy samples of 41 patients with different patohistologic diagnosis were used. Using qPCR, pyrosequencing and statistical analysis, we determined the expression level of osteopontin regulatory miRNAs, its copy number and methylation status. Results & conclusion: We showed that hsa-miR-146a-5p expression is inversely proportional to the expression level of SPP1 and that expression might be also controlled by copy number and methylation. These results suggest that not only expression of SPP1 but also its copy number, methylation status and expression of its regulators might be used as a potential biomarker of colorectal cancer.
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Affiliation(s)
- Margareta Žlajpah
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nina Zidar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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19
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Wang W, Wang S, Pan L. Identification of key differentially expressed mRNAs and microRNAs in non-small cell lung cancer using bioinformatics analysis. Exp Ther Med 2020; 20:3720-3732. [PMID: 32855723 PMCID: PMC7444408 DOI: 10.3892/etm.2020.9105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a leading cause of mortality worldwide. However, the pathogenesis of NSCLC remains to be fully elucidated. Therefore, the present study aimed to explore the differential expression of mRNAs and microRNAs (miRNAs/miRs) in NSCLC and to determine how these RNA molecules interact with one another to affect disease progression. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were identified from the GSE18842, GSE32863 and GSE29250 datasets downloaded from the Gene Expression Omnibus (GEO database). Functional and pathway enrichment analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. STRING, Cytoscape and MCODE were applied to construct a protein-protein interaction (PPI) network and to screen hub genes. The interactions between miRNAs and mRNAs were predicted using miRWalk 3.0 and a miRNA-mRNA regulatory network was constructed. The prognostic value of the identified hub genes was then evaluated via Kaplan-Meier survival analyses using datasets from The Cancer Genome Atlas. A total of 782 DEGs and 46 DEMs were identified from the 3 GEO datasets. The enriched pathways and functions of the DEGs and target genes of the DEMs included osteoclast differentiation, cell adhesion, response to a drug, plasma membrane, extracellular exosome and protein binding. A subnetwork composed of 11 genes was extracted from the PPI network and the genes in this subnetwork were mainly involved in the cell cycle, cell division and DNA replication. A miRNA-gene regulatory network was constructed with 247 miRNA-gene pairs based on 6 DEMs and 210 DEGs. Kaplan-Meier survival analysis indicated that the expression of ubiquitin E2 ligase C, cell division cycle protein 20, DNA topoisomerase IIα, aurora kinase A and B, cyclin B2, maternal embryonic leucine zipper kinase, slit guidance ligand 3, phosphoglucomutase 5, endomucin, cysteine dioxygenase type 1, dihydropyrimidinase-like 2, miR-130b, miR-1181 and miR-127 was significantly associated with overall survival of patients with lung adenocarcinoma. In the present study, a miRNA-mRNA regulatory network in NSCLC was established, which may provide future avenues for scientific exploration and therapeutic targeting of NSCLC.
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Affiliation(s)
- Weiwei Wang
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Shanshan Wang
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Lei Pan
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
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20
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Drees EEE, Pegtel DM. Circulating miRNAs as Biomarkers in Aggressive B Cell Lymphomas. Trends Cancer 2020; 6:910-923. [PMID: 32660885 DOI: 10.1016/j.trecan.2020.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/23/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
B cell lymphomas are heterogeneous malignancies of hematological origin with vastly different biology and clinical outcomes. Histopathology of tissue biopsies and image-based assessment guide clinical decisions. Given that tissue biopsies cannot be frequently repeated and will not inform on systemic responses to the treatment, more accessible biomarkers, such as circulating miRNAs, are considered. Aberrant miRNA expression in lymphoma tissues and ongoing immune reactions may lead to miRNA alterations in circulation. miRNAs bound to extracellular vesicles (EVs) are of interest because of their role in intercellular communication and organ crosstalk. Herein, we highlight the role of miRNAs and EVs in B cell lymphomagenesis and explain how circulating miRNAs may be turned into robust liquid biopsy tests for aggressive B cell lymphoma.
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Affiliation(s)
- Esther E E Drees
- Amsterdam UMC, Vrije Universiteit Amsterdam, Exosomes Research Group, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - D Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Exosomes Research Group, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.
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21
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miR-410 induces both epithelial-mesenchymal transition and radioresistance through activation of the PI3K/mTOR pathway in non-small cell lung cancer. Signal Transduct Target Ther 2020; 5:85. [PMID: 32528035 PMCID: PMC7290026 DOI: 10.1038/s41392-020-0182-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/02/2020] [Accepted: 01/13/2020] [Indexed: 02/05/2023] Open
Abstract
Radiotherapy remains one of the major treatments for non-small cell lung cancer (NSCLC) patients; whereas intrinsic or acquired radioresistance limits its efficacy. Nevertheless, most studies so far have only focused on acquired resistance. The exact mechanisms of intrinsic radioresistance in NSCLC are still unclear. A few studies have suggested that epithelial–mesenchymal transition (EMT) is associated with radioresistance in NSCLC. However, little is known about whether the abnormal expression of specific microRNAs induces both EMT and radioresistance. We previously found that miR-410 has multiple roles as an oncomiRNA in NSCLC. In this study, we revealed that miR-410 overexpression promoted EMT and radioresistance, accompanied by enhanced DNA damage repair both in vitro and in vivo. Conversely, knockdown of miR-410 showed the opposite effects. We further demonstrated that PTEN was a direct target of miR-410 by using bioinformatic tools and dual-luciferase reporter assays, and the miR-410-induced EMT and radioresistance were reversed by PI3K, Akt, and mTOR inhibitors or by restoring the expression of PTEN in NSCLC cells. In addition, we preliminarily found that the expression of miR-410 was positively correlated with EMT and negatively associated with the expression of PTEN in NSCLC specimens. In summary, these results demonstrated that miR-410 is an important regulator on enhancing both NSCLC EMT and radioresistance by targeting the PTEN/PI3K/mTOR axis. The findings suggest that miR-410-induced EMT might significantly contribute to the enhanced radioresistance. Therefore, miR-410 may serve as a potential biomarker or therapeutic target for NSCLC radiotherapy.
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22
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MicroRNA-127 inhibits cell proliferation via targeting Kif3b in pancreatic β cells. Aging (Albany NY) 2020; 11:1342-1355. [PMID: 30822278 PMCID: PMC6428088 DOI: 10.18632/aging.101835] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/17/2019] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) have been implicated in β cells dysfunction. Previous studies indicated that miR-127 was specifically abundant in β cells and one of its target genes, Kif3b, promoted cell proliferation. However, the impact of the miR-127-Kif3b axis on β cells remains unknown. In this study, we revealed that miR-127 level was declined both in islets from the mice with a high-fat diet and in MIN6 cells with elevated glucose treatment. The elevated level of miR-127 attenuated β cell proliferation by repressing Kif3b expression without affecting apoptosis and cell cycle, and it dampened insulin secretion. Moreover, β cell-derived miR-127 could also affect the islet endothelial cell-line, MS1, in vitro via the transfer of extracellular vesicles (EVs). Treating MS1 cells with the EVs secreted by MIN6 cells exhibited a higher ability in cell migration and tube formation. However, this effect was abolished by the miR-127 inhibitor co-cultured with EVs-treated MS1 cells. Thus, we define that miR-127 is a crucial regulator of insulin secretion and cell proliferation in pancreatic β cells as well as a potential functional regulation factor in islet endothelial cells.
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23
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Liu J, Dai X, Guo X, Cheng A, Mac SM, Wang Z. Circ-OXCT1 Suppresses Gastric Cancer EMT and Metastasis by Attenuating TGF-β Pathway Through the Circ-OXCT1/miR-136/SMAD4 Axis. Onco Targets Ther 2020; 13:3987-3998. [PMID: 32523351 PMCID: PMC7236241 DOI: 10.2147/ott.s239789] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 04/28/2020] [Indexed: 12/24/2022] Open
Abstract
Background Circular RNAs (circRNAs) have been proven to play important roles in tumorigenesis. However, the mechanism by which circRNAs act on gastric cancer (GC) through epithelial-to-mesenchymal transition (EMT) is unclear. In this study, we identified circ-OXCT1 and elucidated its function on EMT in GC. Methods Tissue circRNA microarray analysis and qRT-PCR were utilized to determine the expression level of circ-OXCT1 in GC. Luciferase reporter assay and FISH were employed to confirm the interaction between circ-OXCT1 and miR-136. CCK-8, cloning formation, transwell, wound healing, nude mice experiment, circ-OXCT1 overexpression and silencing were conducted to elucidate the function of circ-OXCT1 in vivo and in vitro. Western blot and rescue experiment were carried out to evaluate the changes of EMT-related proteins induced by circ-OXCT1 overexpression or silencing. Results Circ-OXCT1 was downregulated in GC tissues and cell lines. Its expression level was significantly associated with lymph node metastasis, pathologic stage and overall survival rate through clinicopathologic data analysis. Circ-OXCT1 silencing downregulated SMAD4 expression and accordingly regulated expression of E-cadherin, N-cadherin and vimentin through the transforming growth factor-beta (TGF-β)/Smad signaling pathway by a circ-OXCT1/miR-136/SMAD4 axis, resulting in enhancement of EMT and subsequent boost of cell migration, invasion and nude mice lung metastasis. Conclusion Our data showed that circ-OXCT1 suppresses gastric cancer EMT and metastasis through TGF-β/Smad signaling pathway. The clinicopathologic data analysis revealed that circ-OXCT1 overexpression could be a novel treatment for advanced GC especially with distant metastasis by targeting the circ-OXCT1/miR-136/SMAD4 axis.
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Affiliation(s)
- Jianjun Liu
- Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, People's Republic of China
| | - Xinglong Dai
- Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, People's Republic of China
| | - Xiong Guo
- Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, People's Republic of China
| | - Anqi Cheng
- Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, People's Republic of China
| | - Sandrie Mariella Mac
- Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, People's Republic of China
| | - Ziwei Wang
- Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, People's Republic of China
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24
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Zhao G, Zhang Y, Zhao Z, Cai H, Zhao X, Yang T, Chen W, Yao C, Wang Z, Wang Z, Han C, Wang H. MiR-153 reduces stem cell-like phenotype and tumor growth of lung adenocarcinoma by targeting Jagged1. Stem Cell Res Ther 2020; 11:170. [PMID: 32375892 PMCID: PMC7201619 DOI: 10.1186/s13287-020-01679-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/27/2020] [Accepted: 04/15/2020] [Indexed: 12/15/2022] Open
Abstract
Background Cancer stem cells (CSCs) have been proposed to be responsible for tumor recurrence and chemo-resistance. Previous studies suggested that miR-153 played essential roles in lung cancer. However, the molecular mechanism of miR-153 in regulating the stemness of non-small cell lung cancer (NSCLC) remains poorly understood. In this study, we investigated the role of miR-153 in regulation of the stemness of NSCLC. Methods The stemness property of lung stem cancer cells was detected by sphere formation assay, immunofluorescence, and Western blot. Luciferase reporter assay was performed to investigate the direct binding of miR-153 to the 3′-UTR of JAG1 mRNA. Animal study was conducted to evaluate the effect of miR-153 on tumor growth in vivo. The clinical relevance of miR-153 in NSCLC was evaluated by Rt-PCR and Kaplan-Meier analysis. Results MiR-153 expression was decreased in lung cancer tissues. Reduced miR-153 expression was associated with lung metastasis and poor overall survival of lung cancer patients. Jagged1, one of the ligands of Notch1, is targeted by miR-153 and inversely correlates with miR-153 in human lung samples. More importantly, we found that miR-153 inhibited stem cell-like phenotype and tumor growth of lung adenocarcinoma through inactivating the Jagged1/Notch1 axis. Conclusion MiR-153 suppresses the stem cell-like phenotypes and tumor growth of lung adenocarcinoma by targeting Jagged1 and provides a potential therapeutic target in lung cancer therapy.
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Affiliation(s)
- Guoli Zhao
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, Shandong, China.,School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Yueying Zhang
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, Shandong, China. .,School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China.
| | - Zhonghua Zhao
- Department of Rehabilitation and Physiotherapy, The People's Hospital of Huaiyin, Jinan, 250000, China
| | - Haibo Cai
- Department of Thoracic Surgery, The Affiliated First People's Hospital of Jining Medical University, Jining, 272011, Shandong, China
| | - Xiaogang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, 250000, Shandong, China
| | - Tong Yang
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, Shandong, China.,School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Weijun Chen
- Department of Medical Oncology, Yantaishan Hospital, Yantai, 264000, Shandong, China
| | - Chengfang Yao
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, Shandong, China.,School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Zhaopeng Wang
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, Shandong, China
| | - Zhaoxia Wang
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, Shandong, China
| | - Chen Han
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, Shandong, China
| | - Hengxiao Wang
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, Shandong, China
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25
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Baj J, Korona-Głowniak I, Forma A, Maani A, Sitarz E, Rahnama-Hezavah M, Radzikowska E, Portincasa P. Mechanisms of the Epithelial-Mesenchymal Transition and Tumor Microenvironment in Helicobacter pylori-Induced Gastric Cancer. Cells 2020; 9:1055. [PMID: 32340207 PMCID: PMC7225971 DOI: 10.3390/cells9041055] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori (H. pylori) is one of the most common human pathogens, affecting half of the world's population. Approximately 20% of the infected patients develop gastric ulcers or neoplastic changes in the gastric stroma. An infection also leads to the progression of epithelial-mesenchymal transition within gastric tissue, increasing the probability of gastric cancer development. This paper aims to review the role of H. pylori and its virulence factors in epithelial-mesenchymal transition associated with malignant transformation within the gastric stroma. The reviewed factors included: CagA (cytotoxin-associated gene A) along with induction of cancer stem-cell properties and interaction with YAP (Yes-associated protein pathway), tumor necrosis factor α-inducing protein, Lpp20 lipoprotein, Afadin protein, penicillin-binding protein 1A, microRNA-29a-3p, programmed cell death protein 4, lysosomal-associated protein transmembrane 4β, cancer-associated fibroblasts, heparin-binding epidermal growth factor (HB-EGF), matrix metalloproteinase-7 (MMP-7), and cancer stem cells (CSCs). The review summarizes the most recent findings, providing insight into potential molecular targets and new treatment strategies for gastric cancer.
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Affiliation(s)
- Jacek Baj
- Chair and Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland;
| | - Izabela Korona-Głowniak
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1 Street, 20-093 Lublin, Poland;
| | - Alicja Forma
- Chair and Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland;
| | - Amr Maani
- Chair and Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland;
| | - Elżbieta Sitarz
- Chair and 1st Department of Psychiatry, Psychotherapy and Early Intervention, Medical University of Lublin, Gluska Street 1, 20-439 Lublin, Poland;
| | - Mansur Rahnama-Hezavah
- Chair and Department of Oral Surgery, Medical University of Lublin, 20-081 Lublin, Poland;
| | - Elżbieta Radzikowska
- Department of Plastic Surgery, Central Clinical Hospital of the MSWiA in Warsaw, 01-211 Warsaw, Poland;
| | - Piero Portincasa
- Clinica Medica A. Murri, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro Medical School, 70126 Bari, Italy;
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Ha J, Park C, Park C, Park S. IMIPMF: Inferring miRNA-disease interactions using probabilistic matrix factorization. J Biomed Inform 2020; 102:103358. [DOI: 10.1016/j.jbi.2019.103358] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/11/2019] [Accepted: 12/12/2019] [Indexed: 12/09/2022]
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Liu X, Mao Y, Kang Y, He L, Zhu B, Zhang W, Lu Y, Wu Q, Xu D, Shi L. MicroRNA-127 Promotes Anti-microbial Host Defense through Restricting A20-Mediated De-ubiquitination of STAT3. iScience 2020; 23:100763. [PMID: 31958753 PMCID: PMC6992901 DOI: 10.1016/j.isci.2019.100763] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/29/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
The increasing rising of multiple drug-resistant Staphylococcus aureus has become a major public health concern, underscoring a pressing need for developing therapies essentially based on the understanding of host defensive mechanism. In the present study, we showed that microRNA (miR)-127 played a key role in controlling bacterial infection and conferred a profound protection against staphylococcal pneumonia. The protective effect of miR-127 was largely dependent on its regulation of macrophage bactericidal activity and the generation of IL-22, IL-17, and anti-microbial peptides (AMPs), the pathway primarily driven by STAT3. Importantly, we revealed that the ubiquitin-editing enzyme A20, a genuine target of miR-127, specifically interacted with and repressed K63-ubiquitination of STAT3, thereby compromising its phosphorylation upon bacterial infection. Thus, our data not only identify miR-127 as a non-coding molecule with anti-bacterial activity but also delineate an unappreciated mechanism whereby A20 regulates STAT3-driven anti-microbial signaling via modulating its ubiquitination.
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Affiliation(s)
- Xiaoyi Liu
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yun Mao
- Key Laboratory of Inflammation and Immunoregulation, Hangzhou Normal University School of Medicine, Hangzhou, China
| | - Yanhua Kang
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, China; Key Laboratory of Inflammation and Immunoregulation, Hangzhou Normal University School of Medicine, Hangzhou, China
| | - Long He
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bo Zhu
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Zhang
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qinan Wu
- Collaborative Innovation Centers of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Hudson Institute of Medical Research, Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Liyun Shi
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, China; Key Laboratory of Inflammation and Immunoregulation, Hangzhou Normal University School of Medicine, Hangzhou, China.
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28
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microRNA: The Impact on Cancer Stemness and Therapeutic Resistance. Cells 2019; 9:cells9010008. [PMID: 31861404 PMCID: PMC7016867 DOI: 10.3390/cells9010008] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Cancer ranks as the second leading cause of death worldwide, causing a large social and economic burden. However, most anti-cancer treatments face the problems of tumor recurrence and metastasis. Therefore, finding an effective cure for cancer needs to be solved urgently. Recently, the discovery of cancer stem cells (CSCs) provides a new orientation for cancer research and therapy. CSCs share main characteristics with stem cells and are able to generate an entire tumor. Besides, CSCs usually escape from current anti-cancer therapies, which is partly responsible for tumor recurrence and poor prognosis. microRNAs (miRNAs) belong to small noncoding RNA and regulate gene post-transcriptional expression. The dysregulation of miRNAs leads to plenty of diseases, including cancer. The aberrant miRNA expression in CSCs enhances stemness maintenance. In this review, we summarize the role of miRNAs on CSCs in the eight most common cancers, hoping to bridge the research of miRNAs and CSCs with clinical applications. We found that miRNAs can act as tumor promoter or suppressor. The dysregulation of miRNAs enhances cell stemness and contributes to tumor metastasis and therapeutic resistance via the formation of feedback loops and constitutive activation of carcinogenic signaling pathways. More importantly, some miRNAs may be potential targets for diagnosis, prognosis, and cancer treatments.
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Xie GY, Xia M, Miao YR, Luo M, Zhang Q, Guo AY. FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human. Bioinformatics 2019; 36:2605-2607. [DOI: 10.1093/bioinformatics/btz929] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/01/2019] [Accepted: 12/09/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Summary
Transcription factors (TFs) and microRNAs (miRNAs) are two kinds of important regulators for transcriptional and post-transcriptional regulations. Understanding cross-talks between the two regulators and their targets is critical to reveal complex molecular regulatory mechanisms. Here, we developed FFLtool, a web server for detecting potential feed forward loop (FFL) of TF-miRNA-target regulation in human. In FFLtool, we integrated comprehensive regulations of TF-target and miRNA-target, and developed two functional modules: (i) The ‘FFL Analysis’ module can detect potential FFLs and internal regulatory networks in a user-defined gene set. FFLtool also provides three levels of evidence to illustrate the reliability for each FFL and enrichment functions for co-target genes of the same TF and miRNA; (ii) The ‘Browse FFLs’ module displays FFLs comprised of differentially or specifically expressed TFs and miRNAs and their target genes in cancers. FFLtool is a valuable resource for investigating gene expression regulation and mechanism study in biological processes and diseases.
Availability and implementation
FFLtool is available on http://bioinfo.life.hust.edu.cn/FFLtool/.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gui-Yan Xie
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Mengxuan Xia
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ya-Ru Miao
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Mei Luo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qiong Zhang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - An-Yuan Guo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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30
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Umeh-Garcia M, Simion C, Ho PY, Batra N, Berg AL, Carraway KL, Yu A, Sweeney C. A Novel Bioengineered miR-127 Prodrug Suppresses the Growth and Metastatic Potential of Triple-Negative Breast Cancer Cells. Cancer Res 2019; 80:418-429. [PMID: 31694904 DOI: 10.1158/0008-5472.can-19-0656] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/21/2019] [Accepted: 11/01/2019] [Indexed: 12/31/2022]
Abstract
miR-127 is downregulated in breast cancer, where it has been shown to suppress the proliferation, migration, and invasion of breast cancer cells. In triple-negative breast cancer (TNBC), miR-127 downregulation correlates with decreased disease-free and overall patient survival. Tumor suppressor miRNAs may hold therapeutic promise but progress has been limited by several factors, including the lability and high cost of miRNA mimics. Here, we take a novel approach to produce a miR-127 prodrug (miR-127PD), which we demonstrate is processed to mature, functional miR-127-3p in TNBC tumor cells. miR-127PD decreased the viability and motility of TNBC cells, sensitized TNBC cells to chemotherapy, and restricted the TNBC stem cell population. Furthermore, systemic delivery of miR-127PD suppressed tumor growth of MDA-MB-231 and MDA-MB-468 TNBC cells and spontaneous metastasis of MDA-MB-231 cells. In addition, CERK, NANOS1, FOXO6, SOX11, SOX12, FASN, and SUSD2 were identified as novel, functionally important targets of miR-127. In conclusion, our study demonstrates that miR-127 functions as a tumor and metastasis suppressor in TNBC and that delivery of miR-127 may hold promise as a novel therapy. SIGNIFICANCE: Exogenous administration of miR-127, which is functionally activated in target cells, inhibits growth and spontaneous metastasis of triple-negative breast cancer.
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Affiliation(s)
- Maxine Umeh-Garcia
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Catalina Simion
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Pui-Yan Ho
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Anastasia L Berg
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Kermit L Carraway
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Aiming Yu
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Colleen Sweeney
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California.
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Ning J, Li P, Zhang B, Han B, Su X, Wang Q, Wang X, Li B, Kang H, Zhou L, Chu C, Zhang N, Pang Y, Niu Y, Zhang R. miRNAs deregulation in serum of mice is associated with lung cancer related pathway deregulation induced by PM2.5. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:112875. [PMID: 31377334 DOI: 10.1016/j.envpol.2019.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/23/2019] [Accepted: 07/09/2019] [Indexed: 05/28/2023]
Abstract
Ambient fine particulate matter (PM2.5) as an environmental pollution has been associated with the lung cancer. However, the mechanism of epigenetics such as miRNAs deregulation between PM2.5-exposure and lung cancer has not been elucidated clearly. Twenty C57BL/6 mice were divided randomly into 2 groups and exposed to the filtered air (FA) and the concentrated air (CA), respectively. The FA mice were exposed to filtered air in chambers with a high-efficient particulate air filter (HEPA-filter), and the CA mice were exposed to concentration ambient PM2.5. The total duration of exposure was performed 6 h per day from December 1st, 2017 to January 27th, 2018. The mice exposed 900.21 μg/m3 PM2.5 for 6 h per day in CA chamber, which was nearly equaled to 225.05 μg/m3 for 24-h calculatingly. After exposure, the serum miRNAs levels were detected by microarray. Genetic and pathological alterations in lung of mice with/without PM2.5 exposure were detected. 38 differential miRNAs in serum of mice were found after PM2.5 exposure for 8 weeks. Among of them, 13 miRNAs related with lung cancer were consistent in serum and lung of mice. The target genes of 13 deregulated miRNAs including CRK, NR2F2, VIM, RASSF1, CCND2, PRKCA, SIRT1, CDK6, MAP3K7, HIF1A, UBE2V2, ATG10, BAX, E2F1, RASSF5 and CTNNB1, could involve in the pathway of lung cancer developing. Compared with the FA group, the significantly increases of histopathological changes, ROS and DNA damage were observed in lung of mice in CA group. Our study suggested that miRNAs in serum could be identified as candidate biomarkers to predict the lung cancer development during early PM2.5 exposure.
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Affiliation(s)
- Jie Ning
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Peiyuan Li
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Boyuan Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Bin Han
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Xuan Su
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Qian Wang
- Experimental Center, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Xiurong Wang
- Department of Immunology, School of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Binghua Li
- Department of Occupation Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, 050051, PR China
| | - Hui Kang
- Department of Occupation Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, 050051, PR China
| | - Lixiao Zhou
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Chen Chu
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Ning Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yaxian Pang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yujie Niu
- Department of Occupation Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, 050051, PR China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, PR China
| | - Rong Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, PR China.
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Zheng H, Hu S, Cao J, Yao L, Zhang N. Long non-coding RNA TUG1 alleviates LPS-induced injury of PC-12 cells by down-regulating microRNA-127. Exp Mol Pathol 2019; 110:104287. [DOI: 10.1016/j.yexmp.2019.104287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 01/05/2023]
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Yang Y, Li Z, Yuan H, Ji W, Wang K, Lu T, Yu Y, Zeng Q, Li F, Xia W, Lu S. Reciprocal regulatory mechanism between miR-214-3p and FGFR1 in FGFR1-amplified lung cancer. Oncogenesis 2019; 8:50. [PMID: 31492847 PMCID: PMC6731303 DOI: 10.1038/s41389-019-0151-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/11/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNA (miRNA) and fibroblast growth factor receptor 1 (FGFR1) dysregulation are considered to play an important role in tumor proliferation, invasion, and metastasis. However, the regulatory mechanism between miRNAs and FGFR1 in lung cancer remains unclear and extremely critical. miR-214-3p was sharply decreased and showed a significantly negative correlation with FGFR1 in lung cancer patients (n = 30). Luciferase reporter assay confirmed that miR-214-3p could downregulate FGFR1 by directly targeting 3′-untranslated region (UTR). miR-214-3p inhibited the processes of epithelial–mesenchymal transition and Wnt/MAPK/AKT (Wnt/mitogen-activated protein kinase/AKT) signaling pathway by targeting FGFR1. Moreover, miR-214-3p not only established a negative feedback regulation loop with FGFR1 through ERK (extracellular signal-regulated kinase) but also developed a synergism with FGFR1 inhibitor AZD4547. In conclusion, our study demonstrated the regulatory mechanism between miR-214-3p and FGFR1 in lung cancer. miR-214-3p acts as a vital target in FGFR1-amplified lung cancer by forming a miR-214-3p-FGFR1-Wnt/MAPK/AKT signaling pathway network. Co-targeting miR-214-3p and FGFR1 could provide greater benefits to patients with FGFR1-amplified lung cancer.
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Affiliation(s)
- Ying Yang
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, 20030, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Huashan Road 1954, 200030, Shanghai, China
| | - Ziming Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, 20030, Shanghai, China
| | - Hong Yuan
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, 20030, Shanghai, China
| | - Wenxiang Ji
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, 20030, Shanghai, China
| | - Kaixuan Wang
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, 20030, Shanghai, China
| | - Tingting Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, 20030, Shanghai, China
| | - Yongfeng Yu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, 20030, Shanghai, China
| | - Qingyu Zeng
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Huashan Road 1954, 200030, Shanghai, China
| | - Fan Li
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Huashan Road 1954, 200030, Shanghai, China
| | - Weiliang Xia
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Huashan Road 1954, 200030, Shanghai, China.
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, 20030, Shanghai, China.
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Yurikova OY, Aisina DE, Niyazova RE, Atambayeva SA, Labeit S, Ivashchenko AT. The Interaction of miRNA-5p and miRNA-3p with the mRNAs of Orthologous Genes. Mol Biol 2019. [DOI: 10.1134/s0026893319040174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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35
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Pasini L, Ulivi P. Liquid Biopsy for the Detection of Resistance Mechanisms in NSCLC: Comparison of Different Blood Biomarkers. J Clin Med 2019; 8:E998. [PMID: 31323990 PMCID: PMC6678791 DOI: 10.3390/jcm8070998] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 12/17/2022] Open
Abstract
The use of targeted agents and immunotherapy for the treatment of advanced non-small-cell lung cancer (NSCLC) has made it mandatory to characterize tumor tissue for patient selection. Moreover, the development of agents that are active against specific resistance mechanisms arising during treatment make it equally important to characterize the tumor tissue at progression by performing tissue re-biopsy. Given that tumor tissue is not always available for molecular characterization due to the paucity of diagnostic specimens or problems relating to the carrying out of invasive procedures, the use of liquid biopsy represents a valid approach to overcoming these difficulties. The most common material used for liquid biopsy in this setting is plasma-derived cell free DNA (cfDNA), which originates from cells undergoing apoptosis or necrosis. However, other sources of tumor material can be considered, such as extracellular vesicle (EV)-derived nucleic acids, which are actively secreted from living cells and closely correspond to tumor dynamics. In this review, we discuss the role of liquid biopsy in the therapeutic management of NSCLC with particular regard to targeted therapy and immunotherapy, and analyze the pros and cons of the different types of samples used in this context.
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Affiliation(s)
- Luigi Pasini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
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Chi Y, Wang F, Zhang T, Xu H, Zhang Y, Shan Z, Wu S, Fan Q, Sun Y. miR-516a-3p inhibits breast cancer cell growth and EMT by blocking the Pygo2/Wnt signalling pathway. J Cell Mol Med 2019; 23:6295-6307. [PMID: 31273950 PMCID: PMC6714144 DOI: 10.1111/jcmm.14515] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/13/2019] [Accepted: 06/11/2019] [Indexed: 01/06/2023] Open
Abstract
miR‐516a‐3p has been reported to play a suppressive role in several types of human tumours. However, the expression level, biological function and fundamental mechanisms of miR‐516a‐3p in breast cancer remain unclear. In the present study, we found that miR‐516a‐3p expression was down‐regulated and Pygopus2 (Pygo2) expression was up‐regulated in human breast cancer tissues and cells. Through analysing the clinicopathological characteristics, we demonstrated that low miR‐516a‐3p expression or positive Pygo2 expression was a predictor of poor prognosis for patients with breast cancer. The results of a dual luciferase reporter assay and Western blot analysis indicated that Pygo2 was a target gene of miR‐516a‐3p. Moreover, overexpression of miR‐516a‐3p inhibited cell growth, migration and invasion as well as epithelial‐mesenchymal transition (EMT) of breast cancer cells, whereas reduced miR‐516a‐3p expression promoted breast cancer cell growth, migration, invasion and EMT. Furthermore, we showed that miR‐516a‐3p suppressed cell proliferation, metastasis and EMT of breast cancer cells by inhibiting Pygo2 expression. We confirmed that miR‐516a‐3p exerted an anti‐tumour effect by inhibiting the activation of the Wnt/β‐catenin pathway. Finally, xenograft tumour models were used to show that miR‐516a‐3p inhibited breast cancer cell growth and EMT via suppressing the Pygo2/Wnt signalling pathway. Taken together, these results show that miR‐516a‐3p inhibits breast cancer cell growth, metastasis and EMT by blocking the Pygo2/ Wnt/β‐catenin pathway.
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Affiliation(s)
- Yanyan Chi
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tengfei Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Han Xu
- Department of Breast Disease Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yana Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhengzheng Shan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shaoxuan Wu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qingxia Fan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Sun
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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miR-25 Promotes Cell Proliferation, Migration, and Invasion of Non-Small-Cell Lung Cancer by Targeting the LATS2/YAP Signaling Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:9719723. [PMID: 31316723 PMCID: PMC6604298 DOI: 10.1155/2019/9719723] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/20/2019] [Indexed: 12/18/2022]
Abstract
Metastasis is the leading cause of high mortality in lung cancer patients, and metastatic lung cancer is difficult to treat. miRNAs are involved in various biological processes of cancer, including metastasis. Our previous studies revealed that miR-25 promoted non-small-cell lung cancer (NSCLC) cell proliferation and suppressed cell apoptosis by directly targeting TP53 and MOAP1. In this work, we further explored the miR-25 expression in NSCLC patients in the Cancer Genome Atlas (TCGA) database and measured the miR-25 expression levels in the tissues of NSCLC patients and cell lines. miR-25 was overexpressed in both NSCLC tissues and cell lines. NSCLC patients who expressed a higher level of miR-25 exhibited worse overall survival than those with a lower level of miR-25. Overexpression of miR-25 enhanced NSCLC cell migration and invasion, while the inhibition of miR-25 exhibited the opposite effects. We identified the large tumor suppressor homology 2 (LATS2) as a new target gene of miR-25 in lung cancer. The effects of miR-25 on promoting NSCLC cell migration and invasion were at least partially due to activation of the Hippo signaling pathway. Additionally, miR-25 antagomir inhibited xenograft tumor growth and metastasis by the upregulation of LATS2. Taken together, our findings demonstrate that miR-25 contribute to lung cancer cell proliferation and metastasis by targeting the LATS2/YAP signaling pathway, which implicate miR-25 as a promising therapeutic target for lung cancer metastasis. Given that oxidative stress induces the overexpression of miR-25 and plays a critical role in cancer progression, this study establishes miR-25 as an intermediate between oxidative stress and lung cancer metastasis.
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38
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Filippova EA, Loginov VI, Pronina IV, Khodyrev DS, Burdennyy AM, Kazubskaya TP, Braga EA. A Group of Hypermethylated miRNA Genes in Breast Cancer and Their Diagnostic Potential. Mol Biol 2019. [DOI: 10.1134/s0026893319030051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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39
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Li R, Jiang S, Li W, Hong H, Zhao C, Huang X, Zhang Z, Li H, Chen H, Bo X. Exploration of prognosis-related microRNA and transcription factor co-regulatory networks across cancer types. RNA Biol 2019; 16:1010-1021. [PMID: 31046554 PMCID: PMC6602415 DOI: 10.1080/15476286.2019.1607714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The study of cancer prognosis serves as an important part of cancer research. Large-scale cancer studies have identified numerous genes and microRNAs (miRNAs) associated with prognosis. These informative genes and miRNAs represent potential biomarkers to predict survival and to elucidate the molecular mechanism of tumour progression. MiRNAs and transcription factors (TFs) can work cooperatively as essential mediators of gene expression, and their dysregulation affects cancer prognosis. A panoramic view of cancer prognosis at the system level, considering the co-regulation roles of miRNA and TF, remains elusive. Here, we establish 12 prognosis-related miRNA-TF co-regulatory networks. The characteristics of prognostic target genes and their regulators in the network are depicted. Although the target genes and co-regulatory patterns exhibit cancer-specific properties, some miRNAs and TFs are highly conserved across cancers. We illustrate and interpret the roles of these conserved regulators by building a model associated with cancer hallmarks, functional enrichment analysis, network community detection, and exhaustive literature research. The elaborated system-level prognostic miRNA-TF co-regulation landscape, including the highlighted roles of conserved regulators, provides a novel and powerful insights into further biological and medical discoveries.
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Affiliation(s)
- Ruijiang Li
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Shuai Jiang
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Wanying Li
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Hao Hong
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Chenghui Zhao
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Xin Huang
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Zhuo Zhang
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Hao Li
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Hebing Chen
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
| | - Xiaochen Bo
- a Department of Biotechnology , Beijing Institute of Radiation Medicine , Beijing , P.R.China
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40
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Ha J, Park C, Park S. PMAMCA: prediction of microRNA-disease association utilizing a matrix completion approach. BMC SYSTEMS BIOLOGY 2019; 13:33. [PMID: 30894171 PMCID: PMC6425656 DOI: 10.1186/s12918-019-0700-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 01/29/2019] [Indexed: 01/29/2023]
Abstract
Background Numerous experimental results have indicated that microRNAs (miRNAs) play a vital role in biological processes, as well as outbreaks of diseases at the molecular level. Despite their important role in biological processes, knowledge regarding specific functions of miRNAs in the development of human diseases is very limited. While attempting to solve this problem, many computational approaches have been proposed and attracted significant attention. However, most previous approaches suffer from the common problem of being inapplicable to new diseases without any known miRNA-disease associations. Results This paper proposes a novel method for inferring disease-miRNA associations utilizing a machine learning technique called matrix factorization, which is widely used in recommendation systems. In recommendation systems, the goal is to predict rating scores that a user might assign to specific items. By replacing users with miRNAs and items with diseases, we can efficiently predict miRNA-disease associations without seed miRNAs. As a result, our proposed model, called prediction of microRNA-disease association utilizing a matrix completion approach, achieves excellent performance compared to previous approaches with a reliable AUC value of 0.882 by implementing five-fold cross validation. Conclusions To the best of our knowledge, the proposed method applies the matrix completion technique to infer miRNA-disease associations and overcome the seed-miRNA problem negatively affects existing computational models. Electronic supplementary material The online version of this article (10.1186/s12918-019-0700-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jihwan Ha
- Department of Computer Science, Yonsei University, 134 Sinchon-dong, Seodaemun-gu, Seoul, South Korea
| | - Chihyun Park
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, 9211 Euclid Ave., Cleveland, OH, 44106, USA
| | - Sanghyun Park
- Department of Computer Science, Yonsei University, 134 Sinchon-dong, Seodaemun-gu, Seoul, South Korea.
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Hsa-mir-127 impairs survival of patients with glioma and promotes proliferation, migration and invasion of cancerous cells by modulating replication initiator 1. Neuroreport 2019; 29:1166-1173. [PMID: 29979259 DOI: 10.1097/wnr.0000000000001089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work aimed to investigate the inter-regulatory functions of hsa-mir-127 and replication initiator 1 (REPIN1) on the proliferation and metastasis of glioma cells. The in-silico data on the implication of hsa-mir-127 and REPIN1 in glioma were retrieved from The Cancer Genome Atlas (TCGA). The expression levels of hsa-mir-127 and REPIN1 mRNA were determined by qRT-PCR, whereas Western blot was used to detect REPIN1 protein expression in glioma cell lines. The proliferation of glioma cells was determined by means of the MTT assay, whereas the transwell assay was employed for assessing the extent of cell migration and invasion. The interaction among REPIN1 and hsa-mir-127 was checked using the luciferase reporter assay. The expression of hsa-mir-127 was markedly increased in clinical data obtained from TCGA and in glioma cells compared with normal tissues and control cells, respectively. Increased expression of hsa-mir-127 and decreased expression of REPIN1 were both associated with poor overall survival. Moreover, hsa-mir-127 overexpression noticeably promoted proliferation, inhibited apoptosis and increased the invasive and migratory capacities of glioma cells. Inverse effects were found with hsa-mir-127 antisense inhibitor. Interestingly, overexpression of hsa-mir-127 downregulated REPIN1 expression, and luciferase reporter assay showed that the tumorigenesis effect of hsa-mir-127 requires, in part, its direct targeting of REPIN1. In conclusion, the hsa-mir-127/REPIN1 pathway is involved in gliomas and could be a potential therapeutic target.
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Crisafulli L, Muggeo S, Uva P, Wang Y, Iwasaki M, Locatelli S, Anselmo A, Colombo FS, Carlo-Stella C, Cleary ML, Villa A, Gentner B, Ficara F. MicroRNA-127-3p controls murine hematopoietic stem cell maintenance by limiting differentiation. Haematologica 2019; 104:1744-1755. [PMID: 30792210 PMCID: PMC6717575 DOI: 10.3324/haematol.2018.198499] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/14/2019] [Indexed: 12/12/2022] Open
Abstract
The balance between self-renewal and differentiation is crucial to ensure the homeostasis of the hematopoietic system, and is a hallmark of hematopoietic stem cells. However, the underlying molecular pathways, including the role of micro-RNA, are not completely understood. To assess the contribution of micro-RNA, we performed micro-RNA profiling of hematopoietic stem cells and their immediate downstream progeny multi-potent progenitors from wild-type control and Pbx1-conditional knockout mice, whose stem cells display a profound self-renewal defect. Unsupervised hierarchical cluster analysis separated stem cells from multi-potent progenitors, suggesting that micro-RNA might regulate the first transition step in the adult hematopoietic development. Notably, Pbx1-deficient and wild-type cells clustered separately, linking micro-RNAs to self-renewal impairment. Differential expression analysis of micro-RNA in the physiological stem cell-to-multi-potent progenitor transition and in Pbx1-deficient stem cells compared to control stem cells revealed miR-127-3p as the most differentially expressed. Furthermore, miR-127-3p was strongly stem cell-specific, being quickly down-regulated upon differentiation and not re-expressed further downstream in the bone marrow hematopoietic hierarchy. Inhibition of miR-127-3p function in Lineage-negative cells, achieved through a lentiviral-sponge vector, led to severe stem cell depletion, as assessed with serial transplantation assays. miR-127-3p-sponged stem cells displayed accelerated differentiation, which was uncoupled from proliferation, accounting for the observed stem cell reduction. miR-127-3p overexpression in Lineage-negative cells did not alter stem cell pool size, but gave rise to lymphopenia, likely due to lack of miR-127-3p physiological downregulation beyond the stem cell stage. Thus, tight regulation of miR-127-3p is crucial to preserve the self-renewing stem cell pool and homeostasis of the hematopoietic system.
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Affiliation(s)
- Laura Crisafulli
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Milan, Italy.,Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Sharon Muggeo
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Milan, Italy.,Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Paolo Uva
- CRS4, Science and Technology Park Polaris, Pula, Cagliari, Italy
| | - Yulei Wang
- Genentech Inc., South San Francisco, CA, USA
| | - Masayuki Iwasaki
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Silvia Locatelli
- Department of Oncology and Hematology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Achille Anselmo
- Flow Cytometry Core, Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Federico S Colombo
- Flow Cytometry Core, Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Carmelo Carlo-Stella
- Department of Oncology and Hematology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy.,Humanitas Huniversity, Department of Biomedical Sciences, Pieve Emanuele, Milan, Italy
| | - Michael L Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna Villa
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Milan, Italy.,San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Ficara
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Milan, Italy .,Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
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A Novel Regulatory Axis, CHD1L-MicroRNA 486-Matrix Metalloproteinase 2, Controls Spermatogonial Stem Cell Properties. Mol Cell Biol 2019; 39:MCB.00357-18. [PMID: 30455250 DOI: 10.1128/mcb.00357-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Spermatogonial stem cells (SSCs) are unipotent germ cells that are at the foundation of spermatogenesis and male fertility. However, the underlying molecular mechanisms governing SSC stemness and growth properties remain elusive. We have recently identified chromodomain helicase/ATPase DNA binding protein 1-like (Chd1l) as a novel regulator for SSC survival and self-renewal, but how these functions are controlled by Chd1l remains to be resolved. Here, we applied high-throughput small RNA sequencing to uncover the microRNA (miRNA) expression profiles controlled by Chd1l and showed that the expression levels of 124 miRNA transcripts were differentially regulated by Chd1l in SSCs. KEGG pathway analysis shows that the miRNAs that are differentially expressed upon Chd1l repression are significantly enriched in the pathways associated with stem cell pluripotency and proliferation. As a proof of concept, we demonstrate that one of the most highly upregulated miRNAs, miR-486, controls SSC stemness gene expression and growth properties. The matrix metalloproteinase 2 (MMP2) gene has been identified as a novel miR-486 target gene in the context of SSC stemness gene regulation and growth properties. Data from cotransfection experiments showed that Chd1l, miR-486, and MMP2 work in concert in regulating SSC stemness gene expression and growth properties. Finally, our data also revealed that MMP2 regulates SSC stemness gene expression and growth properties through activating β-catenin signaling by cleaving N-cadherin and increasing β-catenin nuclear translocation. Our data demonstrate that Chd1l-miR-486-MMP2 is a novel regulatory axis governing SSC stemness gene expression and growth properties, offering a novel therapeutic opportunity for treating male infertility.
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44
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Wang L, Wang X, Jiang X. miR-127 suppresses gastric cancer cell migration and invasion via targeting Wnt7a. Oncol Lett 2019; 17:3219-3226. [PMID: 30867752 PMCID: PMC6396225 DOI: 10.3892/ol.2019.9955] [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: 01/04/2018] [Accepted: 01/04/2019] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) is a malignant tumor originating from the mucosal epithelium of the stomach. Patients suffering from this disease may have occurrence of residual GC due to delay in diagnosis and treatment. In addition, abnormal expression of microRNAs (miRNAs) is involved in GC progression. Therefore, we examined the underlying mechanism of miR-127 in GC. The expression of miR-127 and Wnt7a was examined in GC using RT-qPCR and western blot analysis. A Transwell assay was used to assess the ability of GC cell migration and invasion. Luciferase reporter assay was used to verify the specific target of miR-127 in GC. The results showed miR-127 expression was lower in GC than normal samples, while Wnt7a expression was detected at a higher level in GC than normal samples. The association between miR-127 and Wnt7a expression was negatively correlated in GC tissues. miR-127 mimic in the two GC cell lines markedly curbed cell migration and invasion, while inhibition of miR-127 showed the opposite effect. In addition, Wnt7a siRNA significantly inhibited GC cell migration and invasion and Wnt7a was verified as a specific target of miR-127 in GC cells. Wnt7a reversed the ability of GC cell migration and invasion regulated by miR-127. In conclusion, miR-127 could curb GC cell migration and invasion by upregulating Wnt7a, indicating its potential application in GC diagnosis and therapy.
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Affiliation(s)
- Linlin Wang
- Ultrasound Department of China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Xufei Wang
- Department of Opthalmology, Jilin Province People's Hospital, Changchun, Jilin 130021, P.R. China
| | - Xuefeng Jiang
- Gastroenterology Department of China-Japan Union Hospital, Jilin University, Changchun, Jilin 130000, P.R. China
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45
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Cheng H, Ge X, Zhuo S, Gao Y, Zhu B, Zhang J, Shang W, Xu D, Ge W, Shi L. β-Elemene Synergizes With Gefitinib to Inhibit Stem-Like Phenotypes and Progression of Lung Cancer via Down-Regulating EZH2. Front Pharmacol 2018; 9:1413. [PMID: 30555330 PMCID: PMC6284059 DOI: 10.3389/fphar.2018.01413] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/16/2018] [Indexed: 12/29/2022] Open
Abstract
The inhibitors for EGF receptor tyrosine kinase (EGFR-TKIs) such as gefitinib have been used as a standard treatment for non-small cell lung cancer (NSCLC), but the increasingly occurrence of drug resistance, the associated adverse effects and the enrichment of cancer stem cells significantly impedes its clinical application. β-elemene is a natural sesquiterpene with potent anti-cancer ability, and also it is renowned for its plant-origin, safety and the additive effect with traditional therapies, which prompt us to explore its potential to co-operate with TKIs to achieve greater therapeutic efficacy. Impressively, our study demonstrates that, elemene, in combination of gefitinib, displayed a significantly higher activity in inhibiting lung cancer cellular proliferation, migration and invasion. More importantly, combinative treatment profoundly impaired the epithelial to mesenchymal transition (EMT), the stem-like properties and the self-renewal capacity of lung cancer cells, and hence impeded the in vivo tumor development. We also reveal that the synergistic anti-tumor effect of elemene and gefitinib was largely mediated their regulation of enhancer of zeste homolog 2 (EZH2), an oncogenic histone methyltransferase and gene transcriptional regulator. Thus, our data indicate that combinative treatment of elemene and gefitinib has greater anti-neoplastic activity and greater efficacies in targeting cancer stem-like properties, mainly through regulating the malignant gene modifier and hence the subsequent effector molecules required for cancer progression. The findings may have potential implications for treating aggressive and resistant lung cancers.
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Affiliation(s)
- Haibo Cheng
- Collaborative Innovation Center of Cancer Prevention and Treatment, The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaoyin Ge
- School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shiqin Zhuo
- School of Pharmaceutics, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yanan Gao
- School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bo Zhu
- School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junfeng Zhang
- School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenbin Shang
- Collaborative Innovation Center of Cancer Prevention and Treatment, The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Lab of Inflammation and Immunoregulation, Hangzhou Normal University School of Medicine, Hangzhou, China
- Hudson Institute of Medical Research, Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Weihong Ge
- School of Pharmaceutics, Zhejiang Chinese Medical University, Hangzhou, China
| | - Liyun Shi
- School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Key Lab of Inflammation and Immunoregulation, Hangzhou Normal University School of Medicine, Hangzhou, China
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46
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Zhu J, Tao L, Jin L. MicroRNA‑506‑3p reverses gefitinib resistance in non‑small cell lung cancer by targeting Yes‑associated protein 1. Mol Med Rep 2018; 19:1331-1339. [PMID: 30535506 DOI: 10.3892/mmr.2018.9710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 09/11/2018] [Indexed: 11/06/2022] Open
Abstract
Epidermal growth factor receptor‑tyrosine kinase inhibitors, such as gefitinib, have been found to be clinically effective in the treatment of patients with non‑small cell lung cancer (NSCLC). However, the therapeutic effect of gefitinib is often limited by the development of gefitinib resistance. MicroRNAs (miRNAs), a group of small non‑coding RNAs, have been demonstrated to be frequently dysregulated in human malignancies. For instance, the downregulation of miR‑506‑3p has been reported in NSCLC patients. The aim of the present study was to determine the role and underlying molecular mechanism of miR‑506‑3p in the regulation of gefitinib sensitivity in NSCLC. A gefitinib‑resistant PC‑9 (PC‑9GR) cell line was established, and reduced miR‑506‑3p expression was observed in PC‑9GR cells as compared with that in parental cells. The results of cell cytotoxicity and cell apoptosis assays indicated that PC‑9GR cells were more sensitive to gefitinib following the transfection with an miR‑506‑3p mimic, while transfection with an miR‑506‑3p antagonist reduced the sensitivity of PC‑9GR cells to gefitinib. It was further revealed that Yes‑associated protein 1 (YAP1) was directly suppressed by miR‑506‑3p in PC‑9GR cells. The elevated sensitivity of PC‑9GR cells to gefitinib following transfection with the miR‑506‑3p mimic was counteracted by the overexpression of YAP1. Furthermore, an inverse correlation between the miR‑506‑3p and YAP1 mRNA levels was detected in lung adenocarcinoma specimens. Collectively, the results of the present study suggested that the downregulation of miR‑506‑3p contributes to gefitinib resistance, and thus, the restoration of miR‑506‑3p may be a potential therapeutic approach for overcoming NSCLC gefitinib resistance.
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Affiliation(s)
- Junfei Zhu
- Department of Respiratory Medicine, Taizhou Central Hospital, Taizhou, Zhejiang 318000, P.R. China
| | - Lianqin Tao
- Department of Respiratory Medicine, Taizhou Central Hospital, Taizhou, Zhejiang 318000, P.R. China
| | - Litong Jin
- Department of Emergency, Taizhou Central Hospital, Taizhou, Zhejiang 318000, P.R. China
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47
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Yang L, Shang Z, Long S, Wang N, Shan G, Zhang R. Roles of genetic and microenvironmental factors in cancer epithelial-to-mesenchymal transition and therapeutic implication. Exp Cell Res 2018; 370:190-197. [PMID: 30075173 DOI: 10.1016/j.yexcr.2018.07.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/27/2018] [Accepted: 07/28/2018] [Indexed: 01/11/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a process in which epithelial cells lose their cell-cell contacts resulting in the formation of mesenchymal cells with migratory properties. Increasing evidence indicate EMT plays a key role in the invasion, metastasis and therapeutic resistance of cancer and maintenance of the phenotype of cancer stem cells (CSCs), which makes the prognosis of patients worse. The progression of cancer from epithelial tissue towards a malignant phenotype is driven by multiple factors that remodel the tissue architecture. This review summarizes and analyzes current studies of genetic and microenvironmental factors in inducing and maintaining cancer EMT and therapeutic implications. This will enable a better understanding of the contribution of EMT-associated factors to cancer progression and highlights that genetic factors and tumor microenvironment responsible for EMT could be used as attractive targets for therapeutic intervention.
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Affiliation(s)
- Liuqi Yang
- Department of Immunology, Basic Medical School, Guizhou Medical University, Guiyang 550004, China.
| | - Zhengling Shang
- Department of Immunology, Basic Medical School, Guizhou Medical University, Guiyang 550004, China
| | - Shiqi Long
- Department of Immunology, Basic Medical School, Guizhou Medical University, Guiyang 550004, China
| | - Nianxue Wang
- Department of Immunology, Basic Medical School, Guizhou Medical University, Guiyang 550004, China
| | - Ge Shan
- Department of Immunology, Basic Medical School, Guizhou Medical University, Guiyang 550004, China
| | - Ruya Zhang
- Department of Immunology, Basic Medical School, Guizhou Medical University, Guiyang 550004, China
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48
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Liu C, Hu W, Li LL, Wang YX, Zhou Q, Zhang F, Song-Yang YY, Zhu W, Sun CC, Li DJ. Roles of miR-200 family members in lung cancer: more than tumor suppressors. Future Oncol 2018; 14:2875-2886. [PMID: 30208739 DOI: 10.2217/fon-2018-0155] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
miRNAs are a class of single-stranded noncoding RNAs, which have no coding potential, but modulate many molecular mechanisms including cancer pathogenesis. miRNAs participate in cell proliferation, differentiation, apoptosis, as well as carcinogenesis or cancer progression, and their involvement in lung cancer has been recently shown. They are suggested to have bidirectional functions on important cancer-related genes so as to enhance or attenuate tumor genesis. Epithelial-mesenchymal transition (EMT) is a fundamental process which contributes to integrity of organogenesis and tissue differentiation as well as tissue repair, organ fibrosis and the progression of carcinoma, and several miRNAs were suggested to form the network regulating EMT in lung cancer, among which, miR-200 family members (miR-200a, miR-200b, miR-200c, miR-429 and miR-141) play crucial roles in the suppression of EMT.
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Affiliation(s)
- Cong Liu
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - Wei Hu
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - Lin-Lin Li
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - Yu-Xuan Wang
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - Qun Zhou
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - Feng Zhang
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - Yi-Yan Song-Yang
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - Wei Zhu
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - Cheng-Chao Sun
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
| | - De-Jia Li
- Department of Occupational & Environmental Health, Wuhan University School of Health Sciences, Wuhan, Hubei 430071, PR China
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Zhao Y, Chen X, Yin J. A Novel Computational Method for the Identification of Potential miRNA-Disease Association Based on Symmetric Non-negative Matrix Factorization and Kronecker Regularized Least Square. Front Genet 2018; 9:324. [PMID: 30186308 PMCID: PMC6111239 DOI: 10.3389/fgene.2018.00324] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence has indicated that microRNAs (miRNAs) are associated with numerous human diseases. Studying the associations between miRNAs and diseases contributes to the exploration of effective diagnostic and treatment approaches for diseases. Unfortunately, the use of biological experiments to reveal the potential associations between miRNAs and diseases is time consuming and costly. Therefore, it is very necessary to use simple and efficient calculation models to predict potential disease-related miRNAs. Considering the limitations of other previous methods, we proposed a novel computational model of Symmetric Nonnegative Matrix Factorization for MiRNA-Disease Association prediction (SNMFMDA) to reveal the relation of miRNA-disease pairs. SNMFMDA could be applied to predict miRNAs associated with new diseases. Compared to the direct use of the integrated similarity in previous computational models, the integrated similarity need to be interpolated by symmetric non-negative matrix factorization (SymNMF) before application in SNMFMDA, and the relevant probability of disease-miRNA was obtained mainly through Kronecker regularized least square (KronRLS) method in our model. What's more, the AUC of global leave-one-out cross validation (LOOCV) reached 0.9007, and the AUC based on local LOOCV was 0.8426. Besides, the mean and the standard deviation of AUCs achieved 0.8830 and 0.0017 respectively in 5-fold cross validation. All of the above results demonstrated the superior prediction performance of SNMFMDA. We also conducted three different case studies on Esophageal Neoplasms, Breast Neoplasms and Lung Neoplasms, and 49, 49, and 48 of the top 50 of their predicted miRNAs respectively were confirmed by databases or related literatures. It could be expected that SNMFMDA would be a model with the ability to predict disease-related miRNAs efficiently and accurately.
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Affiliation(s)
- Yan Zhao
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Jun Yin
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
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50
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Han Q, Kremerskothen J, Lin X, Zhang X, Rong X, Zhang D, Wang E. WWC3 inhibits epithelial-mesenchymal transition of lung cancer by activating Hippo-YAP signaling. Onco Targets Ther 2018; 11:2581-2591. [PMID: 29780251 PMCID: PMC5951220 DOI: 10.2147/ott.s162387] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background Though we recently reported that the WWC3 inhibits the invasiveness and metastasis of lung cancer by activating the Hippo pathway, the impact and underlying mechanisms of this process still remain unclear. Methods To identify the role of WWC3 in epithelial-mesenchymal transition of lung cancer, we performed immunohistochemistry to detect the expression levels of WWC3 and EMT-related biomarker, and analyzed their correlations in a cohort of 127 patients with NSCLC. Wound healing assay and cell invasion assay were applied to explore cell invasive ability change after WWC3 knockdown. qRT-PCR and immunoblotting were performed to assess mRNA and protein levels of EMT-related biomarkers and the main molecules changes of Hippo signaling caused by WWC3. Immunoprecipition was to examine WWC3 and LATS1 interaction. Results WWC3 knockdown drives a pronounced shift from the epithelial to the mesenchymal phenotype in lung cancer cells. In addition, WWC3 ectopic expression in lung cancer cells attenuates mesenchymal markers and increases the epithelial markers expressions; however, WWC3-ΔWW plasmid abrogated these effects. WWC3 silencing by shRNA exerts the opposite effect. Furthermore, WWC3 levels were inversely correlated with the levels of EMT inducers (Snail and Slug) in lung cancer cells and specimens. Immunoblotting revealed that WWC3 wild-type upregulates large tumor suppressor (LATS1) and yes-associated protein (YAP) phosphorylation through its WW domain, hence activating Hippo pathway. Knockdown of YAP and LATS1, as well as the as the Verteporfin (VP) usage, could reverse this effect caused by WWC3 silencing. Conclusion These findings suggest that WWC3 works as a tumor suppressor to inhibit EMT process and confer its candidacy as a potential therapeutic target in lung cancer.
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Affiliation(s)
- Qiang Han
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Joachim Kremerskothen
- Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology, University Hospital Muenster, Muenster, Germany
| | - Xuyong Lin
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Xiupeng Zhang
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Xuezhu Rong
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Di Zhang
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Enhua Wang
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
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