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Tariq M, Richard V, Kerin MJ. MicroRNAs as Molecular Biomarkers for the Characterization of Basal-like Breast Tumor Subtype. Biomedicines 2023; 11:3007. [PMID: 38002007 PMCID: PMC10669494 DOI: 10.3390/biomedicines11113007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Breast cancer is a heterogeneous disease highlighted by the presence of multiple tumor variants and the basal-like breast cancer (BLBC) is considered to be the most aggressive variant with limited therapeutics and a poor prognosis. Though the absence of detectable protein and hormonal receptors as biomarkers hinders early detection, the integration of genomic and transcriptomic profiling led to the identification of additional variants in BLBC. The high-throughput analysis of tissue-specific micro-ribonucleic acids (microRNAs/miRNAs) that are deemed to have a significant role in the development of breast cancer also displayed distinct expression profiles in each subtype of breast cancer and thus emerged to be a robust approach for the precise characterization of the BLBC subtypes. The classification schematic of breast cancer is still a fluid entity that continues to evolve alongside technological advancement, and the transcriptomic profiling of tissue-specific microRNAs is projected to aid in the substratification and diagnosis of the BLBC tumor subtype. In this review, we summarize the current knowledge on breast tumor classification, aim to collect comprehensive evidence based on the microRNA expression profiles, and explore their potential as prospective biomarkers of BLBC.
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Affiliation(s)
| | - Vinitha Richard
- Discipline of Surgery, Lambe Institute for Translational Research, H91 TK33 Galway, Ireland;
| | - Michael J. Kerin
- Discipline of Surgery, Lambe Institute for Translational Research, H91 TK33 Galway, Ireland;
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2
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Asghariazar V, Kadkhodayi M, Sarailoo M, Jolfayi AG, Baradaran B. MicroRNA-143 as a potential tumor suppressor in cancer: An insight into molecular targets and signaling pathways. Pathol Res Pract 2023; 250:154792. [PMID: 37689002 DOI: 10.1016/j.prp.2023.154792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/25/2023] [Accepted: 09/02/2023] [Indexed: 09/11/2023]
Abstract
MicroRNAs (MiRNAs), which are highly conserved and small noncoding RNAs, negatively regulate gene expression and influence signaling pathways involved in essential biological activities, including cell proliferation, differentiation, apoptosis, and cell invasion. MiRNAs have received much attention in the past decade due to their significant roles in cancer development. In particular, microRNA-143 (miR-143) is recognized as a tumor suppressor and is downregulated in most cancers. However, it seems that miR-143 is upregulated in rare cases, such as prostate cancer stem cells, and acts as an oncogene. The present review will outline the current studies illustrating the impact of miR-143 expression levels on cancer progression and discuss its target genes and their relevant signaling pathways to discover a potential therapeutic way for cancer.
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Affiliation(s)
- Vahid Asghariazar
- Cancer Immunology and Immunotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Deputy of Research and Technology, Ardabil University of Medical Sciences, Ardabil, Iran.
| | - Mahtab Kadkhodayi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Animal Biology, Faculty of Natural Sciences, The University of Tabriz, Tabriz, Iran
| | - Mehdi Sarailoo
- Students Research Committee, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Amir Ghaffari Jolfayi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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Li B, Xu X, Zheng L, Jiang X, Lin J, Zhang G. MiR-590-5p promotes cisplatin resistance via targeting hMSH2 in ovarian cancer. Mol Biol Rep 2023; 50:6819-6827. [PMID: 37392283 DOI: 10.1007/s11033-023-08599-8] [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: 01/24/2023] [Accepted: 06/15/2023] [Indexed: 07/03/2023]
Abstract
OBJECTIVE The mechanisms of ovarian cancer generate chemotherapy resistance are still unclear. This study aimed to explore the role of microRNA (miR)-590-5p in regulating hMSH2 expression and cisplatin resistance in ovarian cancer. METHODS MiR-590-5p was identified as a regulator of hMSH2 with miRDB database and Target Scan database. Then cisplatin sensitive cell line (SKOV3) and resistant cell line (SKOV3-DDP) of ovarian cancer were cultured for cell functional assay and molecular biology assay. The expression levels of MiR-590-5p and hMSH2 were compared between the two cell lines. Dual luciferase reporter assay was used to verify the targeted regulatory relationship between miR-590-5p and hMSH2. CCK-8 assay and cell apoptosis assay were utilized to assess the role of MiR-590-5p and hMSH2 in cell viability under cisplatin. RESULTS The expression of hMSH2 was significantly decreased, and miR-590-5p was significantly up-regulated in SKOV3-DDP. Up-regulation of hMSH2 weakened the viability of SKOV3 and SKOV3-DDP cell under cisplatin. Transfection with miR‑590-5p mimics reduced the expression of hMSH2 and enhanced the viability of ovarian cancer cells under cisplatin, whereas inhibition of miR‑590-5p increased the expression of hMSH2, and decreased ovarian cancer cells' viability under cisplatin. Furthermore, luciferase reporter assay showed that hMSH2 was a direct target of miR-590-5p. CONCLUSION The present study demonstrates that miR‑590-5p promotes cisplatin resistance of ovarian cancer via negatively regulating hMSH2 expression. Inhibition of miR‑590-5p decreases ovarian cancer cells' viability under cisplatin. Thus miR‑590-5p and hMSH2 may serve as therapeutic targets for cisplatin resistant ovarian cancer.
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Affiliation(s)
- Bing Li
- Department of Medical Oncology, the Affiliated Hospital of Putian University, Putian, 351100, Fujian province, China
| | - Xuejie Xu
- Department of Medical Oncology, the Affiliated Hospital of Putian University, Putian, 351100, Fujian province, China
| | - Linlin Zheng
- Department of Medical Oncology, the Affiliated Hospital of Putian University, Putian, 351100, Fujian province, China
| | - Xiaojie Jiang
- Department of Hepatobiliary Surgery, the Affiliated Hospital of Putian University, Putian, 351100, Fujian province, China
| | - Jing Lin
- Department of Pathology, the Affiliated Hospital of Putian University, Putian, 351100, Fujian province, China
| | - Guoliang Zhang
- Department of Thyroid Surgery, the Affiliated Hospital of Putian University, Putian, 351100, Fujian province, China.
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4
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Ozyurt R, Ozpolat B. Molecular Mechanisms of Anti-Estrogen Therapy Resistance and Novel Targeted Therapies. Cancers (Basel) 2022; 14:5206. [PMID: 36358625 PMCID: PMC9655708 DOI: 10.3390/cancers14215206] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 07/29/2023] Open
Abstract
Breast cancer (BC) is the most commonly diagnosed cancer in women, constituting one-third of all cancers in women, and it is the second leading cause of cancer-related deaths in the United States. Anti-estrogen therapies, such as selective estrogen receptor modulators, significantly improve survival in estrogen receptor-positive (ER+) BC patients, which represents about 70% of cases. However, about 60% of patients inevitably experience intrinsic or acquired resistance to anti-estrogen therapies, representing a major clinical problem that leads to relapse, metastasis, and patient deaths. The resistance mechanisms involve mutations of the direct targets of anti-estrogen therapies, compensatory survival pathways, as well as alterations in the expression of non-coding RNAs (e.g., microRNA) that regulate the activity of survival and signaling pathways. Although cyclin-dependent kinase 4/6 and phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) inhibitors have significantly improved survival, the efficacy of these therapies alone and in combination with anti-estrogen therapy for advanced ER+ BC, are not curative in advanced and metastatic disease. Therefore, understanding the molecular mechanisms causing treatment resistance is critical for developing highly effective therapies and improving patient survival. This review focuses on the key mechanisms that contribute to anti-estrogen therapy resistance and potential new treatment strategies alone and in combination with anti-estrogen drugs to improve the survival of BC patients.
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Affiliation(s)
- Rumeysa Ozyurt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Houston Methodist Research Institute, Department of Nanomedicine, 6670 Bertner Ave, Houston, TX 77030, USA
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Houston Methodist Research Institute, Department of Nanomedicine, 6670 Bertner Ave, Houston, TX 77030, USA
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5
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Bang D, Gu J, Park J, Jeong D, Koo B, Yi J, Shin J, Jung I, Kim S, Lee S. A Survey on Computational Methods for Investigation on ncRNA-Disease Association through the Mode of Action Perspective. Int J Mol Sci 2022; 23:ijms231911498. [PMID: 36232792 PMCID: PMC9570358 DOI: 10.3390/ijms231911498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/18/2022] [Accepted: 09/26/2022] [Indexed: 02/01/2023] Open
Abstract
Molecular and sequencing technologies have been successfully used in decoding biological mechanisms of various diseases. As revealed by many novel discoveries, the role of non-coding RNAs (ncRNAs) in understanding disease mechanisms is becoming increasingly important. Since ncRNAs primarily act as regulators of transcription, associating ncRNAs with diseases involves multiple inference steps. Leveraging the fast-accumulating high-throughput screening results, a number of computational models predicting ncRNA-disease associations have been developed. These tools suggest novel disease-related biomarkers or therapeutic targetable ncRNAs, contributing to the realization of precision medicine. In this survey, we first introduce the biological roles of different ncRNAs and summarize the databases containing ncRNA-disease associations. Then, we suggest a new trend in recent computational prediction of ncRNA-disease association, which is the mode of action (MoA) network perspective. This perspective includes integrating ncRNAs with mRNA, pathway and phenotype information. In the next section, we describe computational methodologies widely used in this research domain. Existing computational studies are then summarized in terms of their coverage of the MoA network. Lastly, we discuss the potential applications and future roles of the MoA network in terms of integrating biological mechanisms for ncRNA-disease associations.
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Affiliation(s)
- Dongmin Bang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Jeonghyeon Gu
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul 08826, Korea
| | - Joonhyeong Park
- Department of Computer Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Dabin Jeong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Bonil Koo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Jungseob Yi
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul 08826, Korea
| | - Jihye Shin
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Inuk Jung
- Department of Computer Science and Engineering, Kyungpook National University, Daegu 41566, Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul 08826, Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul 08826, Korea
- MOGAM Institute for Biomedical Research, Yongin-si 16924, Korea
| | - Sunho Lee
- AIGENDRUG Co., Ltd., Seoul 08826, Korea
- Correspondence:
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6
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Szczepanek J, Skorupa M, Tretyn A. MicroRNA as a Potential Therapeutic Molecule in Cancer. Cells 2022; 11:1008. [PMID: 35326459 PMCID: PMC8947269 DOI: 10.3390/cells11061008] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 12/11/2022] Open
Abstract
Small noncoding RNAs, as post-translational regulators of many target genes, are not only markers of neoplastic disease initiation and progression, but also markers of response to anticancer therapy. Hundreds of miRNAs have been identified as biomarkers of drug resistance, and many have demonstrated the potential to sensitize cancer cells to therapy. Their properties of modulating the response of cells to therapy have made them a promising target for overcoming drug resistance. Several methods have been developed for the delivery of miRNAs to cancer cells, including introducing synthetic miRNA mimics, DNA plasmids containing miRNAs, and small molecules that epigenetically alter endogenous miRNA expression. The results of studies in animal models and preclinical studies for solid cancers and hematological malignancies have confirmed the effectiveness of treatment protocols using microRNA. Nevertheless, the use of miRNAs in anticancer therapy is not without limitations, including the development of a stable nanoconstruct, delivery method choices, and biodistribution. The aim of this review was to summarize the role of miRNAs in cancer treatment and to present new therapeutic concepts for these molecules. Supporting anticancer therapy with microRNA molecules has been verified in numerous clinical trials, which shows great potential in the treatment of cancer.
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Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Ul. Wilenska 4, 87-100 Torun, Poland;
| | - Monika Skorupa
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Ul. Wilenska 4, 87-100 Torun, Poland;
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Ul. Lwowska 1, 87-100 Torun, Poland;
| | - Andrzej Tretyn
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Ul. Lwowska 1, 87-100 Torun, Poland;
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7
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MicroRNAs and drug resistance in colorectal cancer with special focus on 5-fluorouracil. Mol Biol Rep 2022; 49:5165-5178. [PMID: 35212928 DOI: 10.1007/s11033-022-07227-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/03/2022] [Indexed: 02/08/2023]
Abstract
Colorectal cancer is globally one of the most common cancers in all age groups. The current chemotherapy combinations for colorectal cancer treatment include 5-fluorouracil-based regimens; however, drug resistance remains one of the main reasons for chemotherapy failure and disease recurrence. Many studies have determined colorectal cancer chemoresistance mechanisms such as drug efflux, cell cycle arrest, DNA damage repair, apoptosis, autophagy, vital enzymes, epigenetic, epithelial-mesenchymal transition, stem cells, and immune system suppression. Several microRNAs affect drug resistance by regulating the drug resistance-related target genes in colorectal cancer. These drug resistance-related miRNAs may be used as promising biomarkers for predicting drug response or as potential therapeutic targets for treating patients with colorectal cancer. This work reviews and discuss the role of selected microRNAs in 5-fluorouracil resistance and their molecular mechanisms in colorectal cancer.
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8
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Zhao Y, Wang X, Liu Y, Wang HY, Xiang J. The effects of estrogen on targeted cancer therapy drugs. Pharmacol Res 2022; 177:106131. [DOI: 10.1016/j.phrs.2022.106131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 10/19/2022]
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9
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Sadighbathi S, Mobed A. Genosensors, a nanomaterial-based platform for microRNA-21 detection, non-invasive methods in early detection of cancer. Clin Chim Acta 2022; 530:27-38. [PMID: 35227654 DOI: 10.1016/j.cca.2022.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 01/27/2023]
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10
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de Klerk DJ, de Keijzer MJ, Dias LM, Heemskerk J, de Haan LR, Kleijn TG, Franchi LP, Heger M. Strategies for Improving Photodynamic Therapy Through Pharmacological Modulation of the Immediate Early Stress Response. Methods Mol Biol 2022; 2451:405-480. [PMID: 35505025 DOI: 10.1007/978-1-0716-2099-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Photodynamic therapy (PDT) is a minimally to noninvasive treatment modality that has emerged as a promising alternative to conventional cancer treatments. PDT induces hyperoxidative stress and disrupts cellular homeostasis in photosensitized cancer cells, resulting in cell death and ultimately removal of the tumor. However, various survival pathways can be activated in sublethally afflicted cancer cells following PDT. The acute stress response is one of the known survival pathways in PDT, which is activated by reactive oxygen species and signals via ASK-1 (directly) or via TNFR (indirectly). The acute stress response can activate various other survival pathways that may entail antioxidant, pro-inflammatory, angiogenic, and proteotoxic stress responses that culminate in the cancer cell's ability to cope with redox stress and oxidative damage. This review provides an overview of the immediate early stress response in the context of PDT, mechanisms of activation by PDT, and molecular intervention strategies aimed at inhibiting survival signaling and improving PDT outcome.
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Affiliation(s)
- Daniel J de Klerk
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Mark J de Keijzer
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Lionel M Dias
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Faculdade de Ciências da Saúde (FCS-UBI), Universidade da Beira Interior, Covilhã, Portugal
| | - Jordi Heemskerk
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
| | - Lianne R de Haan
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Tony G Kleijn
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Leonardo P Franchi
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas (ICB) 2, Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
- Faculty of Philosophy, Department of Chemistry, Center of Nanotechnology and Tissue Engineering-Photobiology and Photomedicine Research Group, Sciences, and Letters of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Michal Heger
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China.
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands.
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
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11
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Crosstalk between non-coding RNAs expression profile, drug resistance and immune response in breast cancer. Pharmacol Res 2021; 176:106041. [PMID: 34952200 DOI: 10.1016/j.phrs.2021.106041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/15/2021] [Accepted: 12/19/2021] [Indexed: 12/18/2022]
Abstract
Drug resistance is one of the most critical challenges facing researchers in treating breast cancer. Despite numerous treatments for breast cancer, including conventional chemical drugs, monoclonal antibodies, and immunotherapeutic drugs known as immune checkpoint inhibitors (ICI), many patients resist various approaches. In recent years, the relationship between gene expression profiles and drug resistance phenotypes has attracted much attention. Non-coding RNAs (ncRNAs) are regulatory molecules that have been shown to regulate gene expression and cell transcriptome. Two categories, microRNAs and long non-coding RNAs have been more considered and studied among these ncRNAs. Studying the role of different ncRNAs in chemical drug resistance and ICI resistance together can be beneficial in selecting more effective treatments for breast cancer. Changing the expression and action mechanism of these regulatory molecules on drug resistance phenotypes is the main topic of this review article.
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12
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Zheng W, Ye W, Wu Z, Huang X, Xu Y, Chen Q, Lin Z, Chen Y, Bai P, Chen C. Identification of potential plasma biomarkers in early-stage nasopharyngeal carcinoma-derived exosomes based on RNA sequencing. Cancer Cell Int 2021; 21:185. [PMID: 33789676 PMCID: PMC8011216 DOI: 10.1186/s12935-021-01881-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Early diagnosis of nasopharyngeal carcinoma (NPC) is vital to improve the prognosis of these patients. However, early diagnosis of NPC is typically challenging. Therefore, we explored the pathogenetic roles and associated mechanisms of exosomes in plasma of patients with early-stage NPC. METHODS Exosomes in plasma were extracted by ultra-high-speed centrifugation. Western blot and transmission electron microscopy (TEM) were used to verify the purity of exosomes. The sequencing data (6 plasma samples from healthy volunteers vs. 6 NPC plasma samples) were analyzed by principal component analysis (PCA), DESeq2, gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and TargetScan. The differentially expressed miRNAs (DEmiRNAs) were obtained from the dataset (GSE118720) downloaded from the Gene Expression Omnibus (GEO) repository. Additionally, the datasets downloaded from the GEO database (GSE12452, GSE13597, GSE53819, GSE64634) were used to predict the target genes and functions of hsa-miR-1301-3p. qPCR was applied to verify the differences in the expressions of hsa-miR-1301-3p between 10 normal plasma and 10 NPC plasma samples. RESULTS Western blot, TEM, and Nanoparticle Tracking Analysis showed adequate purity of the extracted exosomes. RNA-seq analysis revealed 21 upregulated miRNAs, and 10 downregulated miRNAs in plasma exosomes of early-stage NPC patients. GO analysis showed that the target genes of DEmiRNAs were mainly enriched in DNA synthesis and transcription regulation. KEGG analysis revealed that DEmiRNAs were mainly enriched in PI3K-Akt and MAPK signaling pathways. Moreover, the expression of hsa-mir-1301-3p was verified to be significantly upregulated in enlarged samples of plasma exosomes. CONCLUSIONS We identified several DEmiRNAs extracted from tumor-derived exosomes between normal plasma and early-stage NPC plasma. Bioinformatics analyses indicated that these DEmiRNAs may be related to NPC development. Our study may provide novel insights into underlying biomarkers and mechanisms of plasma exosomes in early-stage NPC.
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Affiliation(s)
- Wei Zheng
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Wangzhong Ye
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
- Fujian Medical University, Fuzhou, Fujian, People's Republic of China
| | - Zijie Wu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
- Fujian Medical University, Fuzhou, Fujian, People's Republic of China
| | - Xinyi Huang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
- Fujian Medical University, Fuzhou, Fujian, People's Republic of China
| | - Yuanji Xu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Qinyan Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
- Fujian Medical University, Fuzhou, Fujian, People's Republic of China
| | - Zhizhong Lin
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Yanyu Chen
- School of Nuclear Science and Technology, University of South China, Hengyang, Hunan, China
| | - Penggang Bai
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Chuanben Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China.
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Abstract
Despite the decline in death rate from breast cancer and recent advances in targeted therapies and combinations for the treatment of metastatic disease, metastatic breast cancer remains the second leading cause of cancer-associated death in U.S. women. The invasion-metastasis cascade involves a number of steps and multitudes of proteins and signaling molecules. The pathways include invasion, intravasation, circulation, extravasation, infiltration into a distant site to form a metastatic niche, and micrometastasis formation in a new environment. Each of these processes is regulated by changes in gene expression. Noncoding RNAs including microRNAs (miRNAs) are involved in breast cancer tumorigenesis, progression, and metastasis by post-transcriptional regulation of target gene expression. miRNAs can stimulate oncogenesis (oncomiRs), inhibit tumor growth (tumor suppressors or miRsupps), and regulate gene targets in metastasis (metastamiRs). The goal of this review is to summarize some of the key miRNAs that regulate genes and pathways involved in metastatic breast cancer with an emphasis on estrogen receptor α (ERα+) breast cancer. We reviewed the identity, regulation, human breast tumor expression, and reported prognostic significance of miRNAs that have been documented to directly target key genes in pathways, including epithelial-to-mesenchymal transition (EMT) contributing to the metastatic cascade. We critically evaluated the evidence for metastamiRs and their targets and miRNA regulation of metastasis suppressor genes in breast cancer progression and metastasis. It is clear that our understanding of miRNA regulation of targets in metastasis is incomplete.
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Affiliation(s)
- Belinda J Petri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40292, USA.
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14
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Li G, Chen Y, Jin W, Zhai B, Li Y, Sun G, Li H, Kang X, Tian Y. Effects of miR-125b-5p on Preadipocyte Proliferation and Differentiation in Chicken. Mol Biol Rep 2021; 48:491-502. [PMID: 33398680 DOI: 10.1007/s11033-020-06080-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/10/2020] [Indexed: 12/21/2022]
Abstract
Our previous studies have shown that miR-125b-5p was highly expressed and significantly upregulated during abdominal fat deposition in chickens. However, the role of miR-125b in the regulation of adipogenesis is not clear in chickens. Therefore, we evaluated the effects of miR-125b-5p on preadipocyte proliferation and differentiation and the interaction between miR-125b-5p and the acyl-CoA synthetase bubblegum family member 2 (ACSBG2) gene in adipogenesis in chicken abdominal adipose tissue. Here, transfection tests of miR-125b-5p mimic/inhibitor were performed in preadipocytes, and the effects of miR-125b-5p on preadipocytes proliferation and differentiation were analyzed. The target site of miR-125b-5p in the 3'UTR (untranslated region) of ACSBG2 were verified by a luciferase reporter assay. Our results showed that miR-125b-5p overexpression inhibited proliferation and reduced the number of cells in S phase and G2/M phase in preadipocytes; conversely, miR-125b-5p inhibition promoted the proliferation and increased the number of cells in S phase and G2/M phase. In adipocytes after induction, miR-125b-5p overexpression led to a notable increase in the accumulation of lipid droplets as well as in the concentration of triglycerides, while miR-125b-5p inhibition had the opposite effect. Furthermore, miR-125b-5p could directly bind to the 3'UTR of ACSBG2, and its overexpression could significantly repress the mRNA and protein expression of ACSBG2. These results indicate that miR-125b-5p can inhibit preadipocyte proliferation and can promote preadipocyte differentiation to affect adipogenesis in chicken abdominal adipose tissues, at least partially by downregulating ACSBG2.
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Affiliation(s)
- Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China.
| | - Yi Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China
| | - Wenjiao Jin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China
| | - Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China
| | - Yuanfang Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450002, P. R. China.
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15
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Pofali P, Mondal A, Londhe V. Exosome as a Natural Gene Delivery Vector for Cancer Treatment. Curr Cancer Drug Targets 2020; 20:821-830. [DOI: 10.2174/1568009620666200924154149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022]
Abstract
Background:
Current gene therapy vectors such as viral, non-viral, and bacterial vectors,
which are used for cancer treatment, but there are certain safety concerns and stability issues
of these conventional vectors. Exosomes are the vesicles of size 40-100 nm secreted from multivesicular
bodies into the extracellular environment by most of the cell types in-vivo and in-vitro.
As a natural nanocarrier, exosomes are immunologically inert, biocompatible, and can cross biological
barriers like the blood-brain barrier, intestinal barrier, and placental barrier.
Objective:
This review focusses on the role of exosome as a carrier to efficiently deliver a gene for
cancer treatment and diagnosis. The methods for loading of nucleic acids onto the exosomes, advantages
of exosomes as a smart intercellular shuttle for gene delivery and therapeutic applications as
a gene delivery vector for siRNA, miRNA and Clustered Regularly Interspaced Short Palindromic
Repeats (CRISPR) and also the limitations of exosomes as a gene carrier are all reviewed in this article.
Methods:
Mostly, electroporation and chemical transfection are used to prepare gene loaded exosomes.
Results:
Exosome-mediated delivery is highly promising and advantageous in comparison to the
current delivery methods for systemic gene therapy. Targeted exosomes, loaded with therapeutic
nucleic acids, can efficiently promote the reduction of tumor proliferation without any adverse effects.
Conclusion:
In the near future, exosomes can become an efficient gene carrier for delivery and a
biomarker for the diagnosis and treatment of cancer.
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Affiliation(s)
- Prasad Pofali
- National Institute of Immunohematology, Parel, Mumbai 400012, India
| | - Adrita Mondal
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM’s NMIMS, Vile Parle West, Mumbai 400056, Maharashtra, India
| | - Vaishali Londhe
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM’s NMIMS, Vile Parle West, Mumbai 400056, Maharashtra, India
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16
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Kudela E, Samec M, Koklesova L, Liskova A, Kubatka P, Kozubik E, Rokos T, Pribulova T, Gabonova E, Smolar M, Biringer K. miRNA Expression Profiles in Luminal A Breast Cancer-Implications in Biology, Prognosis, and Prediction of Response to Hormonal Treatment. Int J Mol Sci 2020; 21:ijms21207691. [PMID: 33080858 PMCID: PMC7589921 DOI: 10.3390/ijms21207691] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/25/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer, which is the most common malignancy in women, does not form a uniform nosological unit but represents a group of malignant diseases with specific clinical, histopathological, and molecular characteristics. The increasing knowledge of the complex pathophysiological web of processes connected with breast cancercarcinogenesis allows the development of predictive and prognostic gene expressionand molecular classification systems with improved risk assessment, which could be used for individualized treatment. In our review article, we present the up-to-date knowledge about the role of miRNAs and their prognostic and predictive value in luminal A breast cancer. Indeed, an altered expression profile of miRNAs can distinguish not only between cancer and healthy samples, but they can classify specific molecular subtypes of breast cancer including HER2, Luminal A, Luminal B, and TNBC. Early identification and classification of breast cancer subtypes using miRNA expression profilescharacterize a promising approach in the field of personalized medicine. A detection of sensitive and specific biomarkers to distinguish between healthy and early breast cancer patients can be achieved by an evaluation of the different expression of several miRNAs. Consequently, miRNAs represent a potential as good diagnostic, prognostic, predictive, and therapeutic biomarkers for patients with luminal A in the early stage of BC.
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Affiliation(s)
- Erik Kudela
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University of Bratislava, 03601 Martin, Slovakia; (M.S.); (L.K.); (A.L.); (E.K.); (T.R.); (T.P.); (K.B.)
- Correspondence: ; Tel.: +421-9-0230-0017
| | - Marek Samec
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University of Bratislava, 03601 Martin, Slovakia; (M.S.); (L.K.); (A.L.); (E.K.); (T.R.); (T.P.); (K.B.)
| | - Lenka Koklesova
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University of Bratislava, 03601 Martin, Slovakia; (M.S.); (L.K.); (A.L.); (E.K.); (T.R.); (T.P.); (K.B.)
| | - Alena Liskova
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University of Bratislava, 03601 Martin, Slovakia; (M.S.); (L.K.); (A.L.); (E.K.); (T.R.); (T.P.); (K.B.)
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Erik Kozubik
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University of Bratislava, 03601 Martin, Slovakia; (M.S.); (L.K.); (A.L.); (E.K.); (T.R.); (T.P.); (K.B.)
| | - Tomas Rokos
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University of Bratislava, 03601 Martin, Slovakia; (M.S.); (L.K.); (A.L.); (E.K.); (T.R.); (T.P.); (K.B.)
| | - Terezia Pribulova
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University of Bratislava, 03601 Martin, Slovakia; (M.S.); (L.K.); (A.L.); (E.K.); (T.R.); (T.P.); (K.B.)
| | - Eva Gabonova
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia; (E.G.); (M.S.)
| | - Marek Smolar
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia; (E.G.); (M.S.)
| | - Kamil Biringer
- Department of Obstetrics and Gynecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University of Bratislava, 03601 Martin, Slovakia; (M.S.); (L.K.); (A.L.); (E.K.); (T.R.); (T.P.); (K.B.)
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17
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Khalife H, Skafi N, Fayyad-Kazan M, Badran B. MicroRNAs in breast cancer: New maestros defining the melody. Cancer Genet 2020; 246-247:18-40. [PMID: 32805688 DOI: 10.1016/j.cancergen.2020.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/07/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
MicroRNAs, short non-coding single-stranded RNAs, are important regulators and gatekeepers of the coding genes in the human genome. MicroRNAs are highly conserved among species and expressed in different tissues and cell types. They are involved in almost all the biological processes as apoptosis, proliferation, cell cycle arrest and differentiation. Playing all these roles, it is not surprising that the deregulation of the microRNA profile causes a number of diseases including cancer. Breast cancer, the most commonly diagnosed malignancy in women, accounts for the highest cancer-related deaths worldwide. Different microRNAs were shown to be up or down regulated in breast cancer. MicroRNAs can function as oncogenes or tumor suppressors according to their targets. In this review, the most common microRNAs implicated in breast cancer are fully illustrated with their targets. Besides, the review highlights the effect of exosomal microRNA on breast cancer and the effect of microRNAs on drug and therapies resistance as well as the miRNA-based therapeutic strategies used until today.
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Affiliation(s)
- Hoda Khalife
- Laboratory of Cancer biology and Molecular Immunology, Faculty of Sciences-I, Lebanese University, Hadath, Beirut, Lebanon.
| | - Najwa Skafi
- Laboratory of Cancer biology and Molecular Immunology, Faculty of Sciences-I, Lebanese University, Hadath, Beirut, Lebanon.
| | - Mohammad Fayyad-Kazan
- Laboratory of Cancer biology and Molecular Immunology, Faculty of Sciences-I, Lebanese University, Hadath, Beirut, Lebanon; Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Bassam Badran
- Laboratory of Cancer biology and Molecular Immunology, Faculty of Sciences-I, Lebanese University, Hadath, Beirut, Lebanon.
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18
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The Emerging Role of MicroRNAs in Breast Cancer. JOURNAL OF ONCOLOGY 2020; 2020:9160905. [PMID: 32714393 PMCID: PMC7354667 DOI: 10.1155/2020/9160905] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/10/2020] [Indexed: 12/24/2022]
Abstract
Breast cancer (BC) is the most common malignancy in women. Due to BC heterogeneity, complexity, and metastasis, many BC patients do not successfully respond to therapies. The effective management of BC depends on early diagnosis and monitoring of drug response. Therefore, identifying new biomarkers for the diagnosis, prognosis, and development of new drugs is urgently required. Dysregulation of microRNAs (miRNAs) participates in the tumorigenesis and progression of cancers, especially breast cancer (BC). Several studies demonstrated that miRNAs could perform their function as oncogenes or tumor suppressors. This review describes recent progress on the role of microRNAs in the diagnosis, prognosis, hallmark, and treatment of BC. According to a recent literature survey, miRNAs play a pivotal role in the regulation of hallmarks of cancer, such as proliferation, apoptosis, invasion, metastasis, and tumor stemness. Many miRNAs are potential biomarkers for BC for diagnosis, and some are indicators of prognosis. Moreover, circulating miRNA profiles, as minimally invasive, diagnostic, and prognostic markers, are broadly used in BC therapy, and some miRNAs are good predictors of therapeutic outcomes. Other miRNAs are involved in overcoming chemoresistance and in increasing BC drug sensitivity.
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19
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He J, He Y, Yu B, Wang X, Chen D. Transcriptome Characterization of Repressed Embryonic Myogenesis Due to Maternal Calorie Restriction. Front Cell Dev Biol 2020; 8:527. [PMID: 32671071 PMCID: PMC7332729 DOI: 10.3389/fcell.2020.00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/04/2020] [Indexed: 11/13/2022] Open
Abstract
Fetal malnutrition decreases skeletal myofiber number and muscle mass in neonatal mammals, which increases the risk of developing obesity and diabetes in adult life. However, the associated molecular mechanisms remain unclear. Here, we investigated how the nutrient (calorie) availability affects embryonic myogenesis using a porcine model. Sows were given a normal or calorie restricted diet, following which skeletal muscle was harvested from the fetuses at 35, 55, and 90 days of gestation (dg) and used for histochemical analysis and high-throughput sequencing. We observed abrupt repression of primary myofiber formation following maternal calorie restriction (MCR). Transcriptome profiling of prenatal muscles revealed that critical genes and muscle-specific miRNAs associated with increased proliferation and myoblast differentiation were downregulated during MCR-induced repression of myogenesis. Moreover, we identified several novel miRNA-mRNA interactions through an integrative analysis of their expression profiles, devising a putative molecular network involved in the regulation of myogenesis. Interestingly, NC_010454.3_1179 was identified as a novel myogenic miRNA that can base-pair with sequences in the 3'-UTR of myogenic differentiation protein 1 (MyoD1). And we found that this UTR inhibited the expression of a linked reporter gene encoding a key myogenic regulatory factor, resulting in suppression of myogenesis. Our results greatly increase our understanding of the mechanisms underlying the nutrient-modulated myogenesis, and may also serve as a valuable resource for further investigation of fundamental developmental processes or assist in rational target selection ameliorating repressed myogenesis under fetal malnutrition.
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Affiliation(s)
- Jun He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
| | - Ying He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
| | - Bing Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
| | | | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
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20
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Shafi S, Khan S, Hoda F, Fayaz F, Singh A, Khan MA, Ali R, Pottoo FH, Tariq S, Najmi AK. Decoding Novel Mechanisms and Emerging Therapeutic Strategies in Breast Cancer Resistance. Curr Drug Metab 2020; 21:199-210. [DOI: 10.2174/1389200221666200303124946] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/12/2019] [Accepted: 12/30/2019] [Indexed: 12/24/2022]
Abstract
Breast cancer (BC), an intricate and highly heterogeneous disorder, has presently afflicted 2.09 million females globally. Chemoresistance remains a paramount challenge in the treatment of BC. Owing to its assorted nature, the chemoresistant mechanisms of BC still need intensive research. Accumulating evidence suggests that abnormalities related to the biogenesis of cancer stem cells (CSCs) and microRNAs (miRNAs) are associated with BC progression and chemoresistance. The presently available interventions are inadequate to target chemoresistance, therefore more efficient alternatives are urgently needed to improvise existing therapeutic regimens. A myriad of strategies is being explored, such as immunotherapy, gene therapy, and combination treatment to surmount chemoresistance. Additionally, nanoparticles as chemotherapeutic carriers put forward the options to encapsulate numerous drugs, alone as well as in combination for cancer theranostics. This review summarizes the chemoresistance mechanisms of miRNAs and CSCs as well as the most recently documented therapeutic approaches for the treatment of chemoresistance in BC. By unraveling the underpinning mechanism of BC chemoresistance, researchers could possibly develop more efficient treatment strategies towards BC.
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Affiliation(s)
- Sadat Shafi
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Sana Khan
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Farazul Hoda
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Faizana Fayaz
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research, Sector-3, MB Road, Pushp Vihar, New Delhi 110017, India
| | - Archu Singh
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Mohammad Ahmed Khan
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Ruhi Ali
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research, Sector-3, MB Road, Pushp Vihar, New Delhi 110017, India
| | - Faheem Hyder Pottoo
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Sana Tariq
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research, Sector-3, MB Road, Pushp Vihar, New Delhi 110017, India
| | - Abul Kalam Najmi
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
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21
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Oh M, Park S, Kim S, Chae H. Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. Brief Bioinform 2020; 22:66-76. [PMID: 32227074 DOI: 10.1093/bib/bbaa032] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
Gene expressions are subtly regulated by quantifiable measures of genetic molecules such as interaction with other genes, methylation, mutations, transcription factor and histone modifications. Integrative analysis of multi-omics data can help scientists understand the condition or patient-specific gene regulation mechanisms. However, analysis of multi-omics data is challenging since it requires not only the analysis of multiple omics data sets but also mining complex relations among different genetic molecules by using state-of-the-art machine learning methods. In addition, analysis of multi-omics data needs quite large computing infrastructure. Moreover, interpretation of the analysis results requires collaboration among many scientists, often requiring reperforming analysis from different perspectives. Many of the aforementioned technical issues can be nicely handled when machine learning tools are deployed on the cloud. In this survey article, we first survey machine learning methods that can be used for gene regulation study, and we categorize them according to five different goals: gene regulatory subnetwork discovery, disease subtype analysis, survival analysis, clinical prediction and visualization. We also summarize the methods in terms of multi-omics input types. Then, we explain why the cloud is potentially a good solution for the analysis of multi-omics data, followed by a survey of two state-of-the-art cloud systems, Galaxy and BioVLAB. Finally, we discuss important issues when the cloud is used for the analysis of multi-omics data for the gene regulation study.
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Affiliation(s)
- Minsik Oh
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Korea
| | - Sungjoon Park
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea.,Bioinformatics Institute, Seoul National University, Seoul, 08826, Korea
| | - Heejoon Chae
- Division of Computer Science, Sookmyung Women's University, Seoul, 04310,Korea
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22
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Najminejad H, Kalantar SM, Abdollahpour‐Alitappeh M, Karimi MH, Seifalian AM, Gholipourmalekabadi M, Sheikhha MH. Emerging roles of exosomal miRNAs in breast cancer drug resistance. IUBMB Life 2019; 71:1672-1684. [DOI: 10.1002/iub.2116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Hamid Najminejad
- Department of Medical GeneticsShahid Sadoughi University of Medical Sciences Yazd Iran
| | - Seyed Mehdi Kalantar
- Research and Clinical Center for InfertilityShahid Sadoughi University of Medical Sciences Yazd Iran
| | | | | | - Alexander M. Seifalian
- Nanotechnology & Regenerative Medicine Commercialization Centre (Ltd)The London BioScience Innovation Centre London UK
| | - Mazaher Gholipourmalekabadi
- Cellular and Molecular Research CentreIran University of Medical Sciences Tehran Iran
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in MedicineIran University of Medical Sciences Tehran Iran
| | - Mohammad Hasan Sheikhha
- Research and Clinical Center for InfertilityShahid Sadoughi University of Medical Sciences Yazd Iran
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23
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Zhao Y, Chen X, Yin J. Adaptive boosting-based computational model for predicting potential miRNA-disease associations. Bioinformatics 2019; 35:4730-4738. [DOI: 10.1093/bioinformatics/btz297] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 03/19/2019] [Accepted: 04/18/2019] [Indexed: 12/24/2022] Open
Abstract
AbstractMotivationRecent studies have shown that microRNAs (miRNAs) play a critical part in several biological processes and dysregulation of miRNAs is related with numerous complex human diseases. Thus, in-depth research of miRNAs and their association with human diseases can help us to solve many problems.ResultsDue to the high cost of traditional experimental methods, revealing disease-related miRNAs through computational models is a more economical and efficient way. Considering the disadvantages of previous models, in this paper, we developed adaptive boosting for miRNA-disease association prediction (ABMDA) to predict potential associations between diseases and miRNAs. We balanced the positive and negative samples by performing random sampling based on k-means clustering on negative samples, whose process was quick and easy, and our model had higher efficiency and scalability for large datasets than previous methods. As a boosting technology, ABMDA was able to improve the accuracy of given learning algorithm by integrating weak classifiers that could score samples to form a strong classifier based on corresponding weights. Here, we used decision tree as our weak classifier. As a result, the area under the curve (AUC) of global and local leave-one-out cross validation reached 0.9170 and 0.8220, respectively. What is more, the mean and the standard deviation of AUCs achieved 0.9023 and 0.0016, respectively in 5-fold cross validation. Besides, in the case studies of three important human cancers, 49, 50 and 50 out of the top 50 predicted miRNAs for colon neoplasms, hepatocellular carcinoma and breast neoplasms were confirmed by the databases and experimental literatures.Availability and implementationThe code and dataset of ABMDA are freely available at https://github.com/githubcode007/ABMDA.Supplementary informationSupplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yan Zhao
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Jun Yin
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
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24
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Guo J, He K, Zeng H, Shi Y, Ye P, Zhou Q, Pan Z, Long X. Differential microRNA expression profiles determined by next-generation sequencing in three fulvestrant-resistant human breast cancer cell lines. Oncol Lett 2019; 17:3765-3776. [PMID: 30930984 PMCID: PMC6425361 DOI: 10.3892/ol.2019.10061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/06/2019] [Indexed: 12/19/2022] Open
Abstract
Fulvestrant resistance is a major clinical issue in the treatment of endocrine-based breast cancer. MicroRNAs (miRNAs) are known to serve an important role in tumor chemoresistance. In the present study, the association between miRNA expression profiles and fulvestrant resistance was investigated in human breast cancer cell lines. Three fulvestrant-resistant breast cancer cell lines, namely MCF-7-CC, MCF-7-TT and MCF-7-21, were established using the human breast cancer cell line MCF-7 as the parental cell line and fulvestrant as the screening drug in vitro. Next-generation sequencing was used to determine the miRNA expression profiles in these cell lines. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to determine the biological functions of differentially expressed miRNAs. In total, 1,536 miRNAs were detected in all the samples, including 1,240 known miRNAs and 296 predicted miRNAs. It was observed that the differential miRNA expression profiles varied among the three fulvestrant-resistant cell lines (MCF-7-CC, MCF-7-TT and MCF-7-21), and certain differentially expressed miRNAs were only detected in one or two of the cell lines. A total of 257 miRNAs that were differentially expressed between MCF-7-CC and MCF-7 cells were detected, among which 69 miRNAs were upregulated and 188 miRNAs were downregulated. In addition, 270 miRNAs with significantly different expression between MCF-7-TT and MCF-7 cells were observed, including 180 upregulated and 90 downregulated miRNAs. Between MCF-7-21 and MCF-7 cells, a total of 227 miRNAs were differentially expressed, among which 52 miRNAs were upregulated and 175 miRNAs were downregulated. The miRNAs that were differentially expressed in the three fulvestrant-resistant cell lines as compared with the parental MCF-7 cell line were primarily involved in the following biological processes: Biological regulation, extracellular matrix-receptor interaction, the Notch signaling pathway and focal adhesion. Taken together, the results suggested that miR-143, miR-145, miR-137, miR-424 and miR-21 may serve important roles in fulvestrant resistance in breast cancer. The study findings may provide a basis for further research on the treatment of fulvestrant-resistant breast cancer.
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Affiliation(s)
- Juan Guo
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Keli He
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Hui Zeng
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yu Shi
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Peng Ye
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Qian Zhou
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Zhongya Pan
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xinghua Long
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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Bharti A, Agnihotri N, Prabhakar N. A voltammetric hybridization assay for microRNA-21 using carboxylated graphene oxide decorated with gold-platinum bimetallic nanoparticles. Mikrochim Acta 2019; 186:185. [DOI: 10.1007/s00604-019-3302-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/03/2019] [Indexed: 12/21/2022]
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26
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Yang S, Lee JY, Hur H, Oh JH, Kim MH. Up-regulation of HOXB cluster genes are epigenetically regulated in tamoxifen-resistant MCF7 breast cancer cells. BMB Rep 2018; 51:450-455. [PMID: 29804556 PMCID: PMC6177504 DOI: 10.5483/bmbrep.2018.51.9.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Indexed: 12/17/2022] Open
Abstract
Tamoxifen (TAM) is commonly used to treat estrogen receptor (ER)-positive breast cancer. Despite the remarkable benefits, resistance to TAM presents a serious therapeutic challenge. Since several HOX transcription factors have been proposed as strong candidates in the development of resistance to TAM therapy in breast cancer, we generated an in vitro model of acquired TAM resistance using ER-positive MCF7 breast cancer cells (MCF7-TAMR), and analyzed the expression pattern and epigenetic states of HOX genes. HOXB cluster genes were uniquely up-regulated in MCF7-TAMR cells. Survival analysis of in slico data showed the correlation of high expression of HOXB genes with poor response to TAM in ER-positive breast cancer patients treated with TAM. Gain- and loss-of-function experiments showed that the overexpression of multi HOXB genes in MCF7 renders cancer cells more resistant to TAM, whereas the knockdown restores TAM sensitivity. Furthermore, activation of HOXB genes in MCF7-TAMR was associated with histone modifications, particularly the gain of H3K9ac. These findings imply that the activation of HOXB genes mediate the development of TAM resistance, and represent a target for development of new strategies to prevent or reverse TAM resistance.
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Affiliation(s)
- Seoyeon Yang
- Department of Anatomy, Embryology Laboratory, and 2Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Laboratory, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ho Hur
- Department of Surgery, National Health Insurance Service Ilsan Hospital, Goyang 10444, Korea
| | - Ji Hoon Oh
- Department of Anatomy, Embryology Laboratory, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Laboratory, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
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27
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Li H, Wei X, Ding T, Chu D. Genome-Wide Profiling of Cardinium-Responsive MicroRNAs in the Exotic Whitefly, Bemisia tabaci (Gennadius) Biotype Q. Front Physiol 2018; 9:1580. [PMID: 30483149 PMCID: PMC6241202 DOI: 10.3389/fphys.2018.01580] [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: 07/05/2018] [Accepted: 10/23/2018] [Indexed: 12/15/2022] Open
Abstract
Although the bacterial symbiont Cardinium has profound effects on the ecological adaptation of its host, the whitefly Bemisia tabaci (Gennadius) biotype Q (hereafter referred to as B. tabaci Q), the molecular mechanism underlying interactions between these two organisms is not yet fully understood. In this study, sRNA libraries were constructed, amplified, and sequenced for Cardinium-infected (C+) and uninfected (C∗−) B. tabaci Q with identical genetic backgrounds. Subsequently, the genes targeted by the differentially expressed miRNAs were predicted by integrating the B. tabaci Q genome data. A total of 125 known and 100 novel miRNAs were identified, among which 23 significant differentially expressed miRNAs were identified in both libraries. It is noteworthy that an analysis of target genes showed that Cardinium-responsive miRNA-regulated genes were functional in apoptosis, reproduction, development, immune response, thermotolerance and insecticide resistance. GO and KEGG pathway analysis revealed that some miRNA-target genes are closely associated with energy metabolism. A major finding of this study was the identification of several miRNAs that may be involved in physiological processes in response to environmental stress, i.e., insecticides and high temperatures. This information will provide a foundation to help further elucidate the functions of Cardinium in B. tabaci Q.
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Affiliation(s)
- Hongran Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiaoying Wei
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Tianbo Ding
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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Xiong H, Zhao W, Wang J, Seifer BJ, Ye C, Chen Y, Jia Y, Chen C, Shen J, Wang L, Sui X, Zhou J. Oncogenic mechanisms of Lin28 in breast cancer: new functions and therapeutic opportunities. Oncotarget 2018; 8:25721-25735. [PMID: 28147339 PMCID: PMC5421965 DOI: 10.18632/oncotarget.14891] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/11/2017] [Indexed: 12/25/2022] Open
Abstract
The RNA binding protein Lin28 is best known for the critical role in cell development, recent researches also have implied its oncogenic function in various human cancers, including breast cancer. Specifically, aberrant Lin28 participates in multiple pathological processes, such as proliferation, metastasis, radiotherapy and chemotherapy resistance, metabolism, immunity and inflammation as well as stemness. In this review, we summarize the let-7-dependent and let-7-independent mechanism regulated by Lin28, focusing on its relation with tumor hallmarks in breast cancer, and subsequently discuss our present knowledge of Lin28 to develop a molecular-based therapeutic strategy against breast cancer.
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Affiliation(s)
- Hanchu Xiong
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Wenhe Zhao
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Ji Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | | | - Chenyang Ye
- Cancer Institute (Key Laboratory of Cancer Prevention & Intervention, National Ministry of Education), Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yongxia Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yunlu Jia
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Cong Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jianguo Shen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Linbo Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xinbing Sui
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China.,Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jichun Zhou
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
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Han J, Liu S, Zhang Y, Xu Y, Jiang Y, Zhang C, Li C, Li X. MiRSEA: Discovering the pathways regulated by dysfunctional MicroRNAs. Oncotarget 2018; 7:55012-55025. [PMID: 27474169 PMCID: PMC5342398 DOI: 10.18632/oncotarget.10839] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/10/2016] [Indexed: 12/17/2022] Open
Abstract
Recent studies have shown that dysfunctional microRNAs (miRNAs) are involved in the progression of various cancers. Dysfunctional miRNAs may jointly regulate their target genes and further alter the activities of canonical biological pathways. Identification of the pathways regulated by a group of dysfunctional miRNAs could help uncover the pathogenic mechanisms of cancer and facilitate development of new drug targets. Current miRNA-pathway analyses mainly use differentially-expressed miRNAs to predict the shared pathways on which they act. However, these methods fail to consider the level of differential expression level, which could improve our understanding of miRNA function. We propose a novel computational method, MicroRNA Set Enrichment Analysis (MiRSEA), to identify the pathways regulated by dysfunctional miRNAs. MiRSEA integrates the differential expression levels of miRNAs with the strength of miRNA pathway associations to perform direct enrichment analysis using miRNA expression data. We describe the MiRSEA methodology and illustrate its effectiveness through analysis of data from hepatocellular cancer, gastric cancer and lung cancer. With these analyses, we show that MiRSEA can successfully detect latent biological pathways regulated by dysfunctional miRNAs. We have implemented MiRSEA as a freely available R-based package on CRAN (https://cran.r-project.org/web/packages/MiRSEA/).
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Affiliation(s)
- Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Siyao Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Ying Jiang
- College of Basic Medical Science, Heilongjiang University of Chinese Medicine, Harbin 150040, PR China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Harbin, 150081, PR China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
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30
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Romano G, Veneziano D, Acunzo M, Croce CM. Small non-coding RNA and cancer. Carcinogenesis 2017; 38:485-491. [PMID: 28449079 DOI: 10.1093/carcin/bgx026] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/09/2017] [Indexed: 12/14/2022] Open
Abstract
The ENCODE project has reported that at least 80% of the human genome is biologically active, yet only a small part of human DNA encodes for protein. The massive amount of RNA transcribed but not translated into protein can be classified as housekeeping RNA (such as rRNA, tRNA) and regulatory RNA (such as miRNA, piRNA, lncRNA). Small non-coding RNAs, in particular, have been the focus of many studies in the last 20 years and their fundamental role in many human diseases is currently well established. Inter alia, their role in cancer development and progression, as well as in drug resistance, is being increasingly investigated. In this review, focusing our attention on recent research results, we provide an overview of the four large classes of small non-coding RNAs, namely, miRNAs, piRNAs, snoRNA and the new class of tRNA-derived fragments, highlighting their fundamental role in cancer and their potential as diagnostic and prognostic biomarkers.
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Affiliation(s)
- Giulia Romano
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Dario Veneziano
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Mario Acunzo
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
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31
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Liu Y, Zeng X, He Z, Zou Q. Inferring microRNA-disease associations by random walk on a heterogeneous network with multiple data sources. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:905-915. [PMID: 27076459 DOI: 10.1109/tcbb.2016.2550432] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Since the discovery of the regulatory function of microRNA (miRNA), increased attention has focused on identifying the relationship between miRNA and disease. It has been suggested that computational method are an efficient way to identify potential disease-related miRNAs for further confirmation using biological experiments. In this paper, we first highlighted three limitations commonly associated with previous computational methods. To resolve these limitations, we established disease similarity subnetwork and miRNA similarity subnetwork by integrating multiple data sources, where the disease similarity is composed of disease semantic similarity and disease functional similarity, and the miRNA similarity is calculated using the miRNA-target gene and miRNA-lncRNA (long non-coding RNA) associations. Then, a heterogeneous network was constructed by connecting the disease similarity subnetwork and the miRNA similarity subnetwork using the known miRNA-disease associations. We extended random walk with restart to predict miRNA-disease associations in the heterogeneous network. The leave-one-out cross-validation achieved an average area under the curve (AUC) of 0:8049 across 341 diseases and 476 miRNAs. For five-fold cross-validation, our method achieved an AUC from 0:7970 to 0:9249 for 15 human diseases. Case studies further demonstrated the feasibility of our method to discover potential miRNA-disease associations. An online service for prediction is freely available at http://ifmda.aliapp.com.
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32
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Bach DH, Hong JY, Park HJ, Lee SK. The role of exosomes and miRNAs in drug-resistance of cancer cells. Int J Cancer 2017; 141:220-230. [PMID: 28240776 DOI: 10.1002/ijc.30669] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/08/2017] [Accepted: 02/20/2017] [Indexed: 12/14/2022]
Abstract
Chemotherapy, one of the principal approaches for cancer patients, plays a crucial role in controlling tumor progression. Clinically, tumors reveal a satisfactory response following the first exposure to the chemotherapeutic drugs in treatment. However, most tumors sooner or later become resistant to even chemically unrelated anticancer agents after repeated treatment. The reduced drug accumulation in tumor cells is considered one of the significant mechanisms by decreasing drug permeability and/or increasing active efflux (pumping out) of the drugs across the cell membrane. The mechanisms of treatment failure of chemotherapeutic drugs have been investigated, including drug efflux, which is mediated by extracellular vesicles (EVs). Exosomes, a subset of EVs with a size range of 40-150 nm and a lipid bilayer membrane, can be released by all cell types. They mediate specific cell-to-cell interactions and activate signaling pathways in cells they either fuse with or interact with, including cancer cells. Exosomal RNAs are heterogeneous in size but enriched in small RNAs, such as miRNAs. In the primary tumor microenvironment, cancer-secreted exosomes and miRNAs can be internalized by other cell types. MiRNAs loaded in these exosomes might be transferred to recipient niche cells to exert genome-wide regulation of gene expression. How exosomal miRNAs contribute to the development of drug resistance in the context of the tumor microenvironment has not been fully described. In this review, we will highlight recent studies regarding EV-mediated microRNA delivery in formatting drug resistance. We also suggest the use of EVs as an advancing method in antiresistance treatment.
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Affiliation(s)
- Duc-Hiep Bach
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Ji-Young Hong
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Hyen Joo Park
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Sang Kook Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Republic of Korea
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33
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Cheng X, Xi QY, Wei S, Wu D, Ye RS, Chen T, Qi QE, Jiang QY, Wang SB, Wang LN, Zhu XT, Zhang YL. Critical role of miR-125b in lipogenesis by targeting stearoyl-CoA desaturase-1 (SCD-1). J Anim Sci 2016; 94:65-76. [PMID: 26812313 DOI: 10.2527/jas.2015-9456] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Alteration of gene expression tightly regulates lipogenesis. Stearoyl-CoA desaturase-1 (SCD-1), a key enzyme in lipogenesis, catalyzes the conversion of SFA to MUFA, and inhibition of its activity impairs lipid synthesis. As posttranscriptional regulators, microRNAs are involved in many pathways of lipid metabolism; however, their effect on SCD-1 has not been reported. In this study, miR-125b was identified as a potential regulator of SCD-1 using bioinformatics analysis. Here, we validated SCD-1 as the target of miR-125b using a dual luciferase assay. During adipogenesis, a synthetic mimic or inhibitor was used to overexpress or reduce the expression of miR-125b in porcine adipocytes. Overexpression of miR-125b reduced the accumulation of lipid droplets and triglycerides concentration and repressed SCD-1 protein expression and MUFA composition. The inhibitor had the reverse effect. Small interfering RNA against tested in adipocytes further proved the direct correlation between miR-125b and SCD-1. Moreover, in vivo experiments in mice showed that injection of miR-125b expression vector decreased the hepatic triglycerides concentration relative to saline. This study indicated that miR-125b regulates lipogenesis by targeting SCD-1; therefore, miR-125b might be applied in therapy of lipid metabolism disorders.
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Liu P, Sun M, Jiang W, Zhao J, Liang C, Zhang H. Identification of targets of miRNA-221 and miRNA-222 in fulvestrant-resistant breast cancer. Oncol Lett 2016; 12:3882-3888. [PMID: 27895744 PMCID: PMC5104194 DOI: 10.3892/ol.2016.5180] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/10/2016] [Indexed: 12/13/2022] Open
Abstract
The present study aimed to identify the differentially expressed genes (DEGs) regulated by microRNA (miRNA)-221 and miRNA-222 that are associated with the resistance of breast cancer to fulvestrant. The GSE19777 transcription profile was downloaded from the Gene Expression Omnibus database, and includes data from three samples of antisense miRNA-221-transfected fulvestrant-resistant MCF7-FR breast cancer cells, three samples of antisense miRNA-222-transfected fulvestrant-resistant MCF7-FR cells and three samples of control inhibitor (green fluorescent protein)-treated fulvestrant-resistant MCF7-FR cells. The linear models for microarray data package in R/Bioconductor was employed to screen for DEGs in the miRNA-transfected cells, and the pheatmap package in R was used to perform two-way clustering. Pathway enrichment was conducted using the Gene Set Enrichment Analysis tool. Furthermore, a miRNA-messenger (m) RNA regulatory network depicting interactions between miRNA-targeted upregulated DEGs was constructed and visualized using Cytoscape. In total, 492 and 404 DEGs were identified for the antisense miRNA-221-transfected MCF7-FR cells and the antisense miRNA-222-transfected MCF7-FR cells, respectively. Genes of the pentose phosphate pathway (PPP) were significantly enriched in the antisense miRNA-221-transfected MCF7-FR cells. In addition, components of the Wnt signaling pathway and cell adhesion molecules (CAMs) were significantly enriched in the antisense miRNA-222-transfected MCF7-FR cells. In the miRNA-mRNA regulatory network, miRNA-222 was demonstrated to target protocadherin 10 (PCDH10). The results of the present study suggested that the PPP and Wnt signaling pathways, as well as CAMs and PCDH10, may be associated with the resistance of breast cancer to fulvestrant.
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Affiliation(s)
- Pengfei Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China; Tianjin's Clinical Research Center for Cancer, Sino-US Center of Lymphoma and Leukemia, Tianjin 300060, P.R. China
| | - Manna Sun
- School of Material Science and Engineering, Heibei University of Technology, Tianjin 300322, P.R. China
| | - Wenhua Jiang
- Department of Radiotherapy, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Jinkun Zhao
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Chunyong Liang
- School of Material Science and Engineering, Heibei University of Technology, Tianjin 300322, P.R. China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China; Tianjin's Clinical Research Center for Cancer, Sino-US Center of Lymphoma and Leukemia, Tianjin 300060, P.R. China
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35
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Lee CJ, Ahn H, Lee SB, Shin JY, Park WY, Kim JI, Lee J, Ryu H, Kim S. Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of Ews/Ewsr1 KO mice. BMC Med Genomics 2016; 9 Suppl 1:33. [PMID: 27534535 PMCID: PMC4989891 DOI: 10.1186/s12920-016-0195-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Multifunctional transcription factor (TF) gene EWS/EWSR1 is involved in various cellular processes such as transcription regulation, noncoding RNA regulation, splicing regulation, genotoxic stress response, and cancer generation. Role of a TF gene can be effectively studied by measuring genome-wide gene expression, i.e., transcriptome, in an animal model of Ews/Ewsr1 knockout (KO). However, when a TF gene has complex multi-functions, conventional approaches such as differentially expressed genes (DEGs) analysis are not successful to characterize the role of the EWS gene. In this regard, network-based analyses that consider associations among genes are the most promising approach. Methods Networks are constructed and used to show associations among biological entities at various levels, thus different networks represent association at different levels. Taken together, in this paper, we report contributions on both computational and biological sides. Results Contribution on the computational side is to develop a novel computational framework that combines miRNA-gene network and protein-protein interaction network information to characterize the multifunctional role of EWS gene. On the biological side, we report that EWS regulates G-protein, Gnai1, in the spinal cord of Ews/Ewsr1 KO mice using the two biological network integrated analysis method. Neighbor proteins of Gnai1, G-protein complex subunits Gnb1, Gnb2 and Gnb4 were also down-regulated at their gene expression level. Interestingly, up-regulated genes, such as Rgs1 and Rgs19, are linked to the inhibition of Gnai1 activities. We further verified the altered expression of Gnai1 by qRT-PCR in Ews/Ewsr1 KO mice. Conclusions Our integrated analysis of miRNA-transcriptome network and PPI network combined with qRT-PCR verifies that Gnai1 function is impaired in the spinal cord of Ews/Ewsr1 KO mice. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0195-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chai-Jin Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Hongryul Ahn
- Department of Computer Science and Engineering, Seoul National University, Seoul, 151-744, Republic of Korea
| | - Sean Bong Lee
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Jong-Yeon Shin
- Genome Medicine Institute and Department of Biochemistry, Seoul National University College of Medicine, Seoul, 110-799, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center and Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 135-710, Republic of Korea
| | - Jong-Il Kim
- Genome Medicine Institute and Department of Biochemistry, Seoul National University College of Medicine, Seoul, 110-799, Republic of Korea
| | - Junghee Lee
- VA Boston Healthcare System, Boston, MA, 02130, USA.,Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Hoon Ryu
- VA Boston Healthcare System, Boston, MA, 02130, USA. .,Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA. .,Center for Neuromedicine, Brain Science Institute, Korea Institute of Science and Technology, Seoul, 136-791, Republic of Korea.
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea. .,Department of Computer Science and Engineering, Seoul National University, Seoul, 151-744, Republic of Korea. .,Bioinformatics Institute, Seoul National University, Seoul, 151-747, Republic of Korea.
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36
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Tormo E, Pineda B, Serna E, Guijarro A, Ribas G, Fores J, Chirivella E, Climent J, Lluch A, Eroles P. MicroRNA Profile in Response to Doxorubicin Treatment in Breast Cancer. J Cell Biochem 2016; 116:2061-73. [PMID: 25802200 DOI: 10.1002/jcb.25162] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 12/16/2022]
Abstract
UNLABELLED Chemotherapy treatment is the standard in triple negative breast cancers, a cancer subgroup which lacks a specific target. The mechanisms leading to the response, as well as any markers that allow the differentiation between responder and non-responder groups prior to treatment are unknown. In parallel, miRNAs can act as oncogenes or tumor suppressors and there is evidence of their involvement in promoting resistance to anticancer drugs. Therefore we hypothesized that changes in miRNA expression after doxorubicin treatment may also be relevant in treatment response. OBJECTIVE To study miRNAs that are differentially expressed in response to doxorubicin treatment. METHODS One luminal-A and two triple negative, breast cancer cell lines were exposed to doxorubicin. Microarray analysis was performed to identify the common and differentially modified miRNAs. Genes and pathways that are theoretically regulated by these miRNAs were analyzed. RESULTS Thirteen miRNAs common to all three lines were modified, in addition to 25 that were specific to triple negative cell lines, and 69 that changed only in the luminal-A cell line. This altered expression pattern seemed to be more strongly related to the breast cancer subgroup than to the treatment. The analysis of target genes revealed that cancer related pathways were the most affected by these miRNAs, moreover many of them had been previously related to chemotherapy resistance; thus suggesting follow-up studies. Additionally, through functional assays, we showed that miR-548c-3p is implicated in doxorubicin-treated MCF-7 cell viability, suggesting a role for this miRNA in resistance.
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Affiliation(s)
- Eduardo Tormo
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Begoña Pineda
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Eva Serna
- Unidad Central de, Investigación en Medicina-INCLIVA, Universitat de Valencia, Valencia, Spain
| | - Alba Guijarro
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Gloria Ribas
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Jaume Fores
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | | | - Joan Climent
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Ana Lluch
- INCLIVA Biomedical Research Institute, Valencia, Spain.,Department of Hematology and Medical Oncology, Hospital Clínico Universitario de, Valencia, Spain
| | - Pilar Eroles
- INCLIVA Biomedical Research Institute, Valencia, Spain
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Chen X. miREFRWR: a novel disease-related microRNA-environmental factor interactions prediction method. MOLECULAR BIOSYSTEMS 2016; 12:624-33. [DOI: 10.1039/c5mb00697j] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
miREFRWR was developed to uncover the hidden disease-related miRNA–EF interactions by implementing random walks on an miRNA similarity network and EF similarity network, respectively.
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Affiliation(s)
- Xing Chen
- National Center for Mathematics and Interdisciplinary Sciences
- Chinese Academy of Sciences
- Beijing 100190
- China
- Academy of Mathematics and Systems Science
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38
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Mukhadi S, Hull R, Mbita Z, Dlamini Z. The Role of MicroRNAs in Kidney Disease. Noncoding RNA 2015; 1:192-221. [PMID: 29861424 PMCID: PMC5932548 DOI: 10.3390/ncrna1030192] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/28/2015] [Accepted: 11/08/2015] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that regulate pathophysiological processes that suppress gene expression by binding to messenger RNAs. These biomolecules can be used to study gene regulation and protein expression, which will allow better understanding of many biological processes such as cell cycle progression and apoptosis that control the fate of cells. Several pathways have also been implicated to be involved in kidney diseases such as Transforming Growth Factor-β, Mitogen-Activated Protein Kinase signaling, and Wnt signaling pathways. The discovery of miRNAs has provided new insights into kidney pathologies and may provide new innovative and effective therapeutic strategies. Research has demonstrated the role of miRNAs in a variety of kidney diseases including renal cell carcinoma, diabetic nephropathy, nephritic syndrome, renal fibrosis, lupus nephritis and acute pyelonephritis. MiRNAs are implicated as playing a role in these diseases due to their role in apoptosis, cell proliferation, differentiation and development. As miRNAs have been detected in a stable condition in different biological fluids, they have the potential to be tools to study the pathogenesis of human diseases with a great potential to be used in disease prognosis and diagnosis. The purpose of this review is to examine the role of miRNA in kidney disease.
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Affiliation(s)
- Sydwell Mukhadi
- Forensic Science Laboratory, 730 Pretorius street, Arcadia 0083, South Africa.
| | - Rodney Hull
- College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X6, Florida 1709, Johannesburg 1709, South Africa.
| | - Zukile Mbita
- Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Private Bag x1106, Sovenga 0727, South Africa.
| | - Zodwa Dlamini
- Research, Innovation & Engagements Portfolio, Mangosuthu University of Technology, Durban 4031, South Africa.
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Karami F, Mohammadi-Yeganeh S, Abedi N, Koochaki A, Kia V, Paryan M. Bioinformatics Prediction andIn VitroAnalysis Revealed That miR-17 Targets Cyclin D1 mRNA in Triple Negative Breast Cancer Cells. Chem Biol Drug Des 2015; 87:317-20. [DOI: 10.1111/cbdd.12671] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/07/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Fariba Karami
- Tehran Medical Branch; Islamic Azad University; khaghani st, shariati Ave PO Box 19395/1495 Tehran Iran
| | - Samira Mohammadi-Yeganeh
- Cellular and Molecular Biology Research Center; Shahid Beheshti University of Medical Sciences; Velenjak, Shahid Chamran Freeway Tehran Iran
- Department of Biotechnology; School of Advanced Technologies in Medicine; Shahid Beheshti University of Medical Sciences; Taleghani Hospital, Velenjak, Shahid Chamran Freeway Tehran Iran
| | - Nairi Abedi
- Tehran Medical Branch; Islamic Azad University; khaghani st, shariati Ave PO Box 19395/1495 Tehran Iran
| | - Ameneh Koochaki
- Department of Biotechnology; School of Advanced Technologies in Medicine; Shahid Beheshti University of Medical Sciences; Taleghani Hospital, Velenjak, Shahid Chamran Freeway Tehran Iran
| | - Vahid Kia
- Department of Medical Biotechnology; Faculty of Medicine; Zanjan University of Medical Sciences; Azadi Sq., Jomhoori Slami Blv. Zanjan Iran
| | - Mahdi Paryan
- Department of Research and Development; Production and Research Complex; Pasteur Institute of Iran; 25th km of Tehran-karaj highway PO Box 3159915111 Tehran Iran
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40
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Di Leva G, Cheung DG, Croce CM. miRNA clusters as therapeutic targets for hormone-resistant breast cancer. Expert Rev Endocrinol Metab 2015; 10:607-617. [PMID: 27721895 PMCID: PMC5053393 DOI: 10.1586/17446651.2015.1099430] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNAs are small non coding RNAs that typically inhibit the translation and stability of messenger RNAs, controlling genes involved in cellular processes such as inflammation, cell cycle regulation, stress response, differentiation, apoptosis, and migration. Not surprisingly, microRNAs are also aberrantly expressed in cancer and promote tumorigenesis by disrupting these vital cellular functions. In this review, we first broadly summarize the role of microRNAs in breast cancer and Estrogen Receptor alpha signaling. Then we focus on what is currently known about the role of microRNAs in anti-hormonal therapy or resistance to endocrine agents. Specifically, we will discuss key miRNAs involved in tamoxifen (miR-221/222, 181, 101, 519a, 301, 375, 342, 451, and the let-7 family), fulvestrant (miR-221/222, miR-200 family), and aromatase inhibitor (miR-128 and the let-7 family) resistance.
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Affiliation(s)
- Gianpiero Di Leva
- Department of Molecular Virology Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Douglas G Cheung
- Department of Molecular Virology Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlo M Croce
- Department of Molecular Virology Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
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Abstract
Therapies targeting estrogen receptor alpha (ERα), including selective ER modulators such as tamoxifen, selective ER downregulators such as fulvestrant (ICI 182 780), and aromatase inhibitors such as letrozole, are successfully used in treating breast cancer patients whose initial tumor expresses ERα. Unfortunately, the effectiveness of endocrine therapies is limited by acquired resistance. The role of microRNAs (miRNAs) in the progression of endocrine-resistant breast cancer is of keen interest in developing biomarkers and therapies to counter metastatic disease. This review focuses on miRNAs implicated as disruptors of antiestrogen therapies, their bona fide gene targets and associated pathways promoting endocrine resistance.
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Affiliation(s)
- Penn Muluhngwi
- Department of Biochemistry and Molecular GeneticsCenter for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, Kentucky 40292, USA
| | - Carolyn M Klinge
- Department of Biochemistry and Molecular GeneticsCenter for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, Kentucky 40292, USA
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42
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Abedi N, Mohammadi-Yeganeh S, Koochaki A, Karami F, Paryan M. miR-141 as potential suppressor of β-catenin in breast cancer. Tumour Biol 2015; 36:9895-901. [PMID: 26164002 DOI: 10.1007/s13277-015-3738-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 06/29/2015] [Indexed: 12/14/2022] Open
Abstract
Triple negative breast cancer (TNBC) is well known for its heterogeneous features and lack of targeted therapy. A variety of cell signaling pathways have been linked to the initiation and progression of these tumors where canonical Wnt signaling is one of the main candidate pathways. Considering past literatures on this matter and negative reports regarding mutations in β-catenin gene (CTNNB1), we focus our attention to another level of gene expression control level, microRNAs (miRNAs). For proper miRNA target detection, we utilized bioinformatics as a relatively new and reliable tool for miRNA: mRNA prediction. MDA-MB-231 (invasive breast cancer) and MCF-10A (normal breast) cell lines were chosen as models. We used different bioinformatic tools such as TargetScan, miRanda, etc. For miRNA targeting CTNNB1-3´UTR confirmation, luciferase assay was carried out. miRNA expression was induced in cell lines through viral constructs expressing desired miRNA. Quantitative real-time PCR was performed for the measurement of expression levels of selected miRNA and target gene. miR-141 was selected via expanded search among various bioinformatic tools. miR-141 expression level was downregulated in MDA-MB-231 cell line, and CTNNB1 gene expression was upregulated. After transduction with viral construct, miR-141 expression was elevated in both cell lines, and gene expression was notably decreased. β-Catenin can be considered as one of the main players in these tumors' pathogenesis. Also, it is the potential target of miR-141, in which its downregulation was detected in cell lines, and can be considered as a promising new targeted approach toward TNBC.
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Affiliation(s)
- Nairi Abedi
- Department of New Sciences, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ameneh Koochaki
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fariba Karami
- Department of New Sciences, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Mahdi Paryan
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran.
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Song Z, Wang Y, Li C, Zhang D, Wang X. Molecular Modification of Metadherin/MTDH Impacts the Sensitivity of Breast Cancer to Doxorubicin. PLoS One 2015; 10:e0127599. [PMID: 25993398 PMCID: PMC4437901 DOI: 10.1371/journal.pone.0127599] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 04/16/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Breast cancer is a leading cause of death in women and with an increasing worldwide incidence. Doxorubicin, as a first-line anthracycline-based drug is conventional used on breast cancer clinical chemotherapy. However, the drug resistances limited the curative effect of the doxorubicin therapy in breast cancer patients, but the molecular mechanism determinants of breast cancer resistance to doxorubicin chemotherapy are not fully understood. In order to explore the association between metadherin (MTDH) and doxorubicin sensitivity, the differential expressions of MTDH in breast cancer cell lines and the sensitivity to doxorubicin of breast cancer cell lines were investigated. METHODS The mRNA and protein expression of MTDH were determined by real-time PCR and Western blot in breast cancer cells such as MDA-MB-231, MCF-7, MDA-MB-435S, MCF-7/ADR cells. Once MTDH gene was knocked down by siRNA in MCF-7/ADR cells and overexpressed by MTDH plasmid transfection in MDA-MB-231 cells, the cell growth and therapeutic sensitivity of doxorubicin were evaluated using MTT and the Cell cycle assay and apoptosis rate was determined by flow cytometry. RESULTS MCF-7/ADR cells revealed highly expressed MTDH and MDA-MB-231 cells had the lowest expression of MTDH. After MTDH gene was knocked down, the cell proliferation was inhibited, and the inhibitory rate of cell growth and apoptosis rate were enhanced, and the cell cycle arrest during the G0/G1 phase in the presence of doxorubicin treatment. On the other hand, the opposite results were observed in MDA-MB-231 cells with overexpressed MTDH gene. CONCLUSION MTDH gene plays a promoting role in the proliferation of breast cancer cells and its high expression may be associated with doxorubicin sensitivity of breast cancer.
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Affiliation(s)
- Zhenchuan Song
- Department of Breast Center, Fourth Hospital of Hebei Medical University No. 169 Tian Shan Street, Shijiazhuang, 050035, China
| | - Yong Wang
- Department of Breast Center, Fourth Hospital of Hebei Medical University No. 169 Tian Shan Street, Shijiazhuang, 050035, China
| | - Chao Li
- Department of Breast Center, Fourth Hospital of Hebei Medical University No. 169 Tian Shan Street, Shijiazhuang, 050035, China
| | - Donghong Zhang
- Department of Breast Center, Fourth Hospital of Hebei Medical University No. 169 Tian Shan Street, Shijiazhuang, 050035, China
| | - Xinle Wang
- Department of Breast Center, Fourth Hospital of Hebei Medical University No. 169 Tian Shan Street, Shijiazhuang, 050035, China
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Rhee S, Chae H, Kim S. PlantMirnaT: miRNA and mRNA integrated analysis fully utilizing characteristics of plant sequencing data. Methods 2015; 83:80-7. [PMID: 25863133 DOI: 10.1016/j.ymeth.2015.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 11/29/2022] Open
Abstract
miRNA is known to regulate up to several hundreds coding genes, thus the integrated analysis of miRNA and mRNA expression data is an important problem. Unfortunately, the integrated analysis is challenging since it needs to consider expression data of two different types, miRNA and mRNA, and target relationship between miRNA and mRNA is not clear, especially when microarray data is used. Fortunately, due to the low sequencing cost, small RNA and RNA sequencing are routinely processed and we may be able to infer regulation relationships between miRNAs and mRNAs more accurately by using sequencing data. However, no method is developed specifically for sequencing data. Thus we developed PlantMirnaT, a new miRNA-mRNA integrated analysis system. To fully leverage the power of sequencing data, three major features are developed and implemented in PlantMirnaT. First, we implemented a plant-specific short read mapping tool based on recent discoveries on miRNA target relationship in plant. Second, we designed and implemented an algorithm considering miRNA targets in the full intragenic region, not just 3' UTR. Lastly but most importantly, our algorithm is designed to consider quantity of miRNA expression and its distribution on target mRNAs. The new algorithm was used to characterize rice under drought condition using our proprietary data. Our algorithm successfully discovered that two miRNAs, miRNA1425-5p, miRNA 398b, that are involved in suppression of glucose pathway in a naturally drought resistant rice, Vandana. The system can be downloaded at https://sites.google.com/site/biohealthinformaticslab/resources.
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Affiliation(s)
- S Rhee
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - H Chae
- School of Informatics and Computing, Computer Science Department, Indiana University, Bloomington, IN, USA
| | - S Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea; Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
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45
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Jin D, Lee H. A computational approach to identifying gene-microRNA modules in cancer. PLoS Comput Biol 2015; 11:e1004042. [PMID: 25611546 PMCID: PMC4303261 DOI: 10.1371/journal.pcbi.1004042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 11/16/2014] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) play key roles in the initiation and progression of various cancers by regulating genes. Regulatory interactions between genes and miRNAs are complex, as multiple miRNAs can regulate multiple genes. In addtion, these interactions vary from patient to patient and even among patients with the same cancer type, as cancer development is a heterogeneous process. These relationships are more complicated because transcription factors and other regulatory molecules can also regulate miRNAs and genes. Hence, it is important to identify the complex relationships between genes and miRNAs in cancer. In this study, we propose a computational approach to constructing modules that represent these relationships by integrating the expression data of genes and miRNAs with gene-gene interaction data. First, we used a biclustering algorithm to construct modules consisting of a subset of genes and a subset of samples to incorporate the heterogeneity of cancer cells. Second, we combined gene-gene interactions to include genes that play important roles in cancer-related pathways. Then, we selected miRNAs that are closely associated with genes in the modules based on a Gaussian Bayesian network and Bayesian Information Criteria. When we applied our approach to ovarian cancer and glioblastoma (GBM) data sets, 33 and 54 modules were constructed, respectively. In these modules, 91% and 94% of ovarian cancer and GBM modules, respectively, were explained either by direct regulation between genes and miRNAs or by indirect relationships via transcription factors. In addition, 48.4% and 74.0% of modules from ovarian cancer and GBM, respectively, were enriched with cancer-related pathways, and 51.7% and 71.7% of miRNAs in modules were ovarian cancer-related miRNAs and GBM-related miRNAs, respectively. Finally, we extensively analyzed significant modules and showed that most genes in these modules were related to ovarian cancer and GBM. A microRNA (miRNA) is a small RNA molecule that regulates the expression of mRNA genes. A miRNA can regulate multiple genes, and a gene can be regulated by multiple miRNAs. The regulation of genes by miRNAs may vary from patient to patient, even if they suffer from the same type of cancer. In this study, we identify the relationships between genes and miRNAs in cancer patients using expression data. Because these relationships are complicated by the involvement of transcription factors, which are among the most influential regulators of genes, we also attempt to explain the triple relationship among genes, miRNAs, and transcription factors. We constructed modules consisting of a set of genes and miRNAs, in which the expression levels are highly correlated. In most of these modules, genes and miRNAs are related to specific cancer types; their relationships are explained both by direct regulation of genes by miRNAs and by indirect relationships via transcription factors.
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Affiliation(s)
- Daeyong Jin
- School of Information and Communications, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Hyunju Lee
- School of Information and Communications, Gwangju Institute of Science and Technology, Gwangju, South Korea
- * E-mail:
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46
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Yu H, Lee H, Herrmann A, Buettner R, Jove R. Revisiting STAT3 signalling in cancer: new and unexpected biological functions. Nat Rev Cancer 2014; 14:736-46. [PMID: 25342631 DOI: 10.1038/nrc3818] [Citation(s) in RCA: 1558] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Janus kinases (JAKs) and signal transducer and activator of transcription (STAT) proteins, particularly STAT3, are among the most promising new targets for cancer therapy. In addition to interleukin-6 (IL-6) and its family members, multiple pathways, including G-protein-coupled receptors (GPCRs), Toll-like receptors (TLRs) and microRNAs were recently identified to regulate JAK-STAT signalling in cancer. Well known for its role in tumour cell proliferation, survival, invasion and immunosuppression, JAK-STAT3 signalling also promotes cancer through inflammation, obesity, stem cells and the pre-metastatic niche. In addition to its established role as a transcription factor in cancer, STAT3 regulates mitochondrion functions, as well as gene expression through epigenetic mechanisms. Newly identified regulators and functions of JAK-STAT3 in tumours are important targets for potential therapeutic strategies in the treatment of cancer.
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Affiliation(s)
- Hua Yu
- Department of Cancer Immunotherapeutics and Tumor Immunology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Heehyoung Lee
- Department of Cancer Immunotherapeutics and Tumor Immunology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Andreas Herrmann
- Department of Cancer Immunotherapeutics and Tumor Immunology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Ralf Buettner
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Richard Jove
- Vaccine and Gene Therapy Institute of Florida, Port St. Lucie, Florida 34987, USA
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47
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Chae H, Rhee S, Nephew KP, Kim S. BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data. Bioinformatics 2014; 31:265-7. [DOI: 10.1093/bioinformatics/btu614] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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48
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Semi-supervised learning for potential human microRNA-disease associations inference. Sci Rep 2014; 4:5501. [PMID: 24975600 PMCID: PMC4074792 DOI: 10.1038/srep05501] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/13/2014] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs play critical role in the development and progression of various diseases. Predicting potential miRNA-disease associations from vast amount of biological data is an important problem in the biomedical research. Considering the limitations in previous methods, we developed Regularized Least Squares for MiRNA-Disease Association (RLSMDA) to uncover the relationship between diseases and miRNAs. RLSMDA can work for diseases without known related miRNAs. Furthermore, it is a semi-supervised (does not need negative samples) and global method (prioritize associations for all the diseases simultaneously). Based on leave-one-out cross validation, reliable AUC have demonstrated the reliable performance of RLSMDA. We also applied RLSMDA to Hepatocellular cancer and Lung cancer and implemented global prediction for all the diseases simultaneously. As a result, 80% (Hepatocellular cancer) and 84% (Lung cancer) of top 50 predicted miRNAs and 75% of top 20 potential associations based on global prediction have been confirmed by biological experiments. We also applied RLSMDA to diseases without known related miRNAs in golden standard dataset. As a result, in the top 3 potential related miRNA list predicted by RLSMDA for 32 diseases, 34 disease-miRNA associations were successfully confirmed by experiments. It is anticipated that RLSMDA would be a useful bioinformatics resource for biomedical researches.
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49
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Girardi C, De Pittà C, Casara S, Calura E, Romualdi C, Celotti L, Mognato M. Integration analysis of microRNA and mRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity. BIOMED RESEARCH INTERNATIONAL 2014; 2014:296747. [PMID: 25045661 PMCID: PMC4090438 DOI: 10.1155/2014/296747] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 01/07/2023]
Abstract
We analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition, simulated by a ground-based rotating wall vessel (RWV) bioreactor. Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1 g incubated ones. Among these, miR-9-5p, miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs, we performed gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichment in the biological processes of immune/inflammatory response, signal transduction, regulation of response to stress, regulation of programmed cell death, and regulation of cell proliferation. We identified the correlation of miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p expression with that of genes involved in immune/inflammatory response (e.g., IFNG and IL17F), apoptosis (e.g., PDCD4 and PTEN), and cell proliferation (e.g., NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation.
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Affiliation(s)
- C. Girardi
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - C. De Pittà
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - S. Casara
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - E. Calura
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - C. Romualdi
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - L. Celotti
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
- Laboratori Nazionali di Legnaro, INFN, Viale dell'Università 2, Legnaro, 35020 Padova, Italy
| | - M. Mognato
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
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50
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Viedma-Rodríguez R, Baiza-Gutman L, Salamanca-Gómez F, Diaz-Zaragoza M, Martínez-Hernández G, Ruiz Esparza-Garrido R, Velázquez-Flores MA, Arenas-Aranda D. Mechanisms associated with resistance to tamoxifen in estrogen receptor-positive breast cancer (review). Oncol Rep 2014; 32:3-15. [PMID: 24841429 DOI: 10.3892/or.2014.3190] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/03/2014] [Indexed: 11/06/2022] Open
Abstract
Anti-estrogens such as tamoxifen are widely used in the clinic to treat estrogen receptor-positive breast tumors. Patients with estrogen receptor-positive breast cancer initially respond to treatment with anti-hormonal agents such as tamoxifen, but remissions are often followed by the acquisition of resistance and, ultimately, disease relapse. The development of a rationale for the effective treatment of tamoxifen-resistant breast cancer requires an understanding of the complex signal transduction mechanisms. In the present study, we explored some mechanisms associated with resistance to tamoxifen, such as pharmacologic mechanisms, loss or modification in estrogen receptor expression, alterations in co-regulatory proteins and the regulation of the different signaling pathways that participate in different cellular processes such as survival, proliferation, stress, cell cycle, inhibition of apoptosis regulated by the Bcl-2 family, autophagy, altered expression of microRNA, and signaling pathways that regulate the epithelial-mesenchymal transition in the tumor microenvironment. Delineation of the molecular mechanisms underlying the development of resistance may aid in the development of treatment strategies to enhance response and compromise resistance.
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Affiliation(s)
- Rubí Viedma-Rodríguez
- Molecular Genetics Laboratory, Medical Research Unit in Human Genetics, Pediatric Hospital, National Medical Center Century XXI (CMN-SXXI), Mexican Social Security Institute (IMSS), Mexico City, Mexico
| | - Luis Baiza-Gutman
- Unit of Morphology and Function, Faculty of Higher Studies (FES) Iztacala, National Autonomous University of Mexico (UNAM), Los Reyes Iztacala, State of Mexico, Mexico
| | - Fabio Salamanca-Gómez
- Molecular Genetics Laboratory, Medical Research Unit in Human Genetics, Pediatric Hospital, National Medical Center Century XXI (CMN-SXXI), Mexican Social Security Institute (IMSS), Mexico City, Mexico
| | | | - Guadalupe Martínez-Hernández
- Unit of Morphology and Function, Faculty of Higher Studies (FES) Iztacala, National Autonomous University of Mexico (UNAM), Los Reyes Iztacala, State of Mexico, Mexico
| | - Ruth Ruiz Esparza-Garrido
- Molecular Genetics Laboratory, Medical Research Unit in Human Genetics, Pediatric Hospital, National Medical Center Century XXI (CMN-SXXI), Mexican Social Security Institute (IMSS), Mexico City, Mexico
| | - Miguel Angel Velázquez-Flores
- Molecular Genetics Laboratory, Medical Research Unit in Human Genetics, Pediatric Hospital, National Medical Center Century XXI (CMN-SXXI), Mexican Social Security Institute (IMSS), Mexico City, Mexico
| | - Diego Arenas-Aranda
- Molecular Genetics Laboratory, Medical Research Unit in Human Genetics, Pediatric Hospital, National Medical Center Century XXI (CMN-SXXI), Mexican Social Security Institute (IMSS), Mexico City, Mexico
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