1
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Xu J, Wan J, Huang HY, Chen Y, Huang Y, Huang J, Zhang Z, Su C, Zhou Y, Lin X, Lin YCD, Huang HD. miRStart 2.0: enhancing miRNA regulatory insights through deep learning-based TSS identification. Nucleic Acids Res 2024:gkae1086. [PMID: 39578697 DOI: 10.1093/nar/gkae1086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Revised: 10/17/2024] [Accepted: 11/14/2024] [Indexed: 11/24/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by binding to the 3'-untranslated regions of target mRNAs, influencing various biological processes at the post-transcriptional level. Identifying miRNA transcription start sites (TSSs) and transcription factors' (TFs) regulatory roles is crucial for elucidating miRNA function and transcriptional regulation. miRStart 2.0 integrates over 4500 high-throughput datasets across five data types, utilizing a multi-modal approach to annotate 28 828 putative TSSs for 1745 human and 1181 mouse miRNAs, supported by sequencing-based signals. Over 6 million tissue-specific TF-miRNA interactions, integrated from ChIP-seq data, are supplemented by DNase hypersensitivity and UCSC conservation data, with network visualizations. Our deep learning-based model outperforms existing tools in miRNA TSS prediction, achieving the most overlaps with both cell-specific and non-cell-specific validated TSSs. The user-friendly web interface and visualization tools make miRStart 2.0 easily accessible to researchers, enabling efficient identification of miRNA upstream regulatory elements in relation to their TSSs. This updated database provides systems-level insights into gene regulation and disease mechanisms, offering a valuable resource for translational research, facilitating the discovery of novel therapeutic targets and precision medicine strategies. miRStart 2.0 is now accessible at https://awi.cuhk.edu.cn/∼miRStart2.
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Affiliation(s)
- Jiatong Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Jingting Wan
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Guangdong Provincial Key Laboratory of Digital Biology and Drug Development, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Yigang Chen
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Yixian Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Junyang Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Ziyue Zhang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Chang Su
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Yuming Zhou
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Xingqiao Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Yang-Chi-Dung Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Guangdong Provincial Key Laboratory of Digital Biology and Drug Development, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Guangdong Provincial Key Laboratory of Digital Biology and Drug Development, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P.R. China
- Department of Endocrinology, Key Laboratory of Endocrinology of National Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.9 Dongdansantiao Street, Dongcheng District, Beijing 100730, P.R. China
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2
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Nieland L, Vrijmoet AB, Jetten IW, Rufino-Ramos D, de Reus AJEM, Breyne K, Kleinstiver BP, Maguire CA, Broekman MLD, Breakefield XO, Abels ER. CRISPR targeting of mmu-miR-21a through a single adeno-associated virus vector prolongs survival of glioblastoma-bearing mice. Mol Ther 2024:S1525-0016(24)00750-0. [PMID: 39563028 DOI: 10.1016/j.ymthe.2024.11.023] [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: 05/23/2024] [Revised: 09/23/2024] [Accepted: 11/15/2024] [Indexed: 11/21/2024] Open
Abstract
Glioblastoma (GB), the most aggressive tumor of the central nervous system (CNS), has poor patient outcomes with limited effective treatments available. MicroRNA-21 (miR-21(a)) is a known oncogene, abundantly expressed in many cancer types. miR-21(a) promotes GB progression, and lack of miR-21(a) reduces the tumorigenic potential. Here, we propose a single adeno-associated virus (AAV) vector strategy targeting mmu-miR-21a using the Staphylococcus aureus Cas9 ortholog (SaCas9) guided by a single-guide RNA (sgRNA). Our results demonstrate that AAV8 is a well-suited AAV serotype to express SaCas9-KKH/sgRNA at the tumor site in an orthotopic GB model. The SaCas9-KKH induced a genomic deletion, resulting in lowered mmu-miR-21a levels in the brain, leading to reduced tumor growth and improved overall survival. In this study, we demonstrated that disruption of genomic mmu-miR-21a with a single AAV vector influenced glioma development, resulting in beneficial anti-tumor outcomes in GB-bearing mice.
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Affiliation(s)
- Lisa Nieland
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA; Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Anne B Vrijmoet
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Isabelle W Jetten
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - David Rufino-Ramos
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra J E M de Reus
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Koen Breyne
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Casey A Maguire
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Marike L D Broekman
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA; Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Department of Neurosurgery, Haaglanden Medical Center, 2512 VA The Hague, the Netherlands; Department of Neurosurgery, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Xandra O Breakefield
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Erik R Abels
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands.
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3
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Kim EH, Ryu Y, Choi J, Park D, Lee JW, Chi SG, Kim SH, Yang Y. Targeting miR-21 to Overcome P-glycoprotein Drug Efflux in Doxorubicin-Resistant 4T1 Breast Cancer. Biomater Res 2024; 28:0095. [PMID: 39434899 PMCID: PMC11491560 DOI: 10.34133/bmr.0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/17/2024] [Accepted: 09/24/2024] [Indexed: 10/23/2024] Open
Abstract
Acquired resistance to chemotherapy is a major challenge in the treatment of triple-negative breast cancer (TNBC). Despite accumulated evidence showing microRNA-21 (miR-21) as a vital regulator of tumor progression, the role of miR-21 in modulating the multidrug resistance of TNBC remains obscure. In this study, we demonstrate that miR-21 affects chemoresistance in 4T1 TNBC cells in response to doxorubicin (DOX) by regulating the P-glycoprotein (P-gp) drug efflux pump. Overexpression of miR-21 in the 4T1 cells markedly reduced their sensitivity to DOX, impeding DOX-promoted cell death. We employed anti-miR-21 oligonucleotide conjugated with a PD-L1-binding peptide (P21) for targeted delivery to 4T1 tumor cells. The selective down-regulation of miR-21 in 4T1 TNBC led to the reversal of P-gp-mediated DOX resistance by up-regulating phosphatase and tensin homolog (PTEN). Our study highlights that miR-21 is a key regulator of drug efflux pumps in TNBC, and targeting miR-21 could enhance DOX sensitivity, offering a potential therapeutic option for patients with DOX-resistant TNBC.
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Affiliation(s)
- Eun Hye Kim
- Medicinal Materials Research Center, Biomedical Research Division,
Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Life Sciences,
Korea University, Seoul 02841, Republic of Korea
| | - Youngri Ryu
- Medicinal Materials Research Center, Biomedical Research Division,
Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Life Sciences,
Korea University, Seoul 02841, Republic of Korea
| | - Jiwoong Choi
- Medicinal Materials Research Center, Biomedical Research Division,
Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Daeho Park
- Medicinal Materials Research Center, Biomedical Research Division,
Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Life Sciences,
Korea University, Seoul 02841, Republic of Korea
| | - Jong Won Lee
- Medicinal Materials Research Center, Biomedical Research Division,
Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology,
Korea University, Seoul 02841, Republic of Korea
| | - Sung-Gil Chi
- Department of Life Sciences,
Korea University, Seoul 02841, Republic of Korea
| | - Sun Hwa Kim
- Medicinal Materials Research Center, Biomedical Research Division,
Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology,
Korea University, Seoul 02841, Republic of Korea
| | - Yoosoo Yang
- Medicinal Materials Research Center, Biomedical Research Division,
Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School,
University of Science and Technology, Seoul 02792, Republic of Korea
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4
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Wilczyński B, Dąbrowska A, Kulbacka J, Baczyńska D. Chemoresistance and the tumor microenvironment: the critical role of cell-cell communication. Cell Commun Signal 2024; 22:486. [PMID: 39390572 PMCID: PMC11468187 DOI: 10.1186/s12964-024-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 09/27/2024] [Indexed: 10/12/2024] Open
Abstract
Resistance of cancer cells to anticancer drugs remains a major challenge in modern medicine. Understanding the mechanisms behind the development of chemoresistance is key to developing appropriate therapies to counteract it. Nowadays, with advances in technology, we are paying more and more attention to the role of the tumor microenvironment (TME) and intercellular interactions in this process. We also know that important elements of the TME are not only the tumor cells themselves but also other cell types, such as mesenchymal stem cells, cancer-associated fibroblasts, stromal cells, and macrophages. TME elements can communicate with each other indirectly (via cytokines, chemokines, growth factors, and extracellular vesicles [EVs]) and directly (via gap junctions, ligand-receptor pairs, cell adhesion, and tunnel nanotubes). This communication appears to be critical for the development of chemoresistance. EVs seem to be particularly interesting structures in this regard. Within these structures, lipids, proteins, and nucleic acids can be transported, acting as signaling molecules that interact with numerous biochemical pathways, thereby contributing to chemoresistance. Moreover, drug efflux pumps, which are responsible for removing drugs from cancer cells, can also be transported via EVs.
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Affiliation(s)
- Bartosz Wilczyński
- Faculty of Medicine, Wroclaw Medical University, Pasteura 1, Wroclaw, 50-367, Poland
| | - Alicja Dąbrowska
- Faculty of Medicine, Wroclaw Medical University, Pasteura 1, Wroclaw, 50-367, Poland
| | - Julita Kulbacka
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, Wroclaw, 50-556, Poland.
- Department of Immunology and Bioelectrochemistry, State Research Institute Centre for Innovative Medicine, Santariškių g. 5, Vilnius, LT-08406, Lithuania.
| | - Dagmara Baczyńska
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, Wroclaw, 50-556, Poland
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5
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Zai H, Wu X, Zhou Y, Hu Y, Zhu Q. Lnc NBAT1 Inhibits the Proliferation and Migration of Liver Cancer Cells Through the miR-21/PDCD4/AP-1 Signaling Axis. Appl Biochem Biotechnol 2024:10.1007/s12010-024-05008-z. [PMID: 39093348 DOI: 10.1007/s12010-024-05008-z] [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] [Accepted: 07/23/2024] [Indexed: 08/04/2024]
Abstract
Long non-coding RNAs (Lnc RNAs) are proven to participate in liver cancer (LC) regulation. The regulation of miR-21 by lnc NBAT1 has been studied in other cancers. However, the effect of this regulation on LC and its specific mechanism remains unclear. Lnc NBAT1 and miR-21 expressions in clinical tissues were measured by RT-qPCR. PDCD4, AP-1, p-c-Fos, p-c-Jun, and cyclin D1 expressions were analyzed by Western blot. Overexpression of lnc NBAT1 was studied to explore its influence on malignant behaviors of Bel7402 cells and the development of LC in the xenograft mouse model (XMM). The regulation mechanism of lnc NBAT1 in LC was explored by lnc NBAT1 overexpression, miR-21 mimic treatment, or PDCD4 silencing in Bel7402 cells. Lnc NBAT1 expression was downregulated while miR-21 expression was upregulated in LC tissues and cell lines. In comparison with LX-2 cells, the expressions of PDCD4 and AP-1 were downregulated in Bel7402 cells, while those of p-c-Fos, p-c-Jun, and cyclin D1 were upregulated. Further, lnc NBAT1 was found to localize primarily in the cytoplasm of Bel7402 cells. Overexpression of lnc NBAT1 enhanced cell apoptosis, blocked the cell cycle, suppressed malignant behaviors of Bel7402 cells, and inhibited tumor progression in the XMM. Mechanistically, lnc NBAT1 functioned as a competing endogenous RNA (ceRNA) by binding to the downstream target miR-21 to stabilize the expressions of PDCD4 and AP-1, thereby inhibiting malignant behaviors of Bel7402 cells. Lnc NBAT1 suppressed malignant behaviors of LC cells through the miR-21/PDCD4/AP-1 axis. Lnc NBAT1 might be a promising biomarker for LC treatment.
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Affiliation(s)
- Hongyan Zai
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yifan Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu Hu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qin Zhu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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6
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Abrishami A, Bahrami AR, Saljooghi AS, Matin MM. Enhanced theranostic efficacy of epirubicin-loaded SPION@MSN through co-delivery of an anti-miR-21-expressing plasmid and ZIF-8 hybridization to target colon adenocarcinoma. NANOSCALE 2024; 16:6215-6240. [PMID: 38446130 DOI: 10.1039/d3nr06642h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Using targeted drug delivery systems has emerged as a promising approach to increase the efficacy of chemotherapy, particularly in combination with gene therapy. The overexpression of miR-21 plays a crucial role in colorectal cancer (CRC) progression, and targeted inhibition of miR-21 offers significant potential for enhancing CRC chemotherapy outcomes. In this study, a theranostic system based on mesoporous silica and superparamagnetic iron oxide nanoparticles (SPION@MSNs) was synthesized as a core-shell structure. After loading epirubicin (EPI) in the open pores of MSN, the plasmid expressing anti-miR-21 (pDNA) covered the outer surface with the help of a ZIF-8 (zeolitic imidazolate framework-8) film. Afterward, polyethylene glycol (PEG) and AS1411 aptamer were conjugated to the surface to improve the protective, biocompatibility, and targeting abilities of the nanocarrier. Moreover, the physicochemical characteristics as well as the loading capacity and release profile of EPI and pDNA were fully evaluated. The uptake of the nanoparticles by CRC and normal cell lines in addition to the anticancer effects related to targeted combinational therapy were investigated in vitro. Finally, in vivo tests were performed on BALB/c mice bearing colorectal tumors to evaluate the effectiveness of the targeted nanoparticles, their possible side effects, and also their application in fluorescence and magnetic imaging in vivo. The successful synthesis of SPION@MSN-EPI/pDNA-ZIF-8-PEG-Apt nanoparticles (∼68 nm) and good loading efficiency and controlled release of EPI and pDNA were confirmed. Moreover, hemolysis and gel retardation assays demonstrated the biocompatibility and plasmid protection. Cellular uptake and expression of copGFP illustrated selective entry and transient transfection of targeted nanoparticles, consistent with the cytotoxicity results that indicated the synergistic effects of chemo-gene therapy. The results of animal studies proved the high antitumor efficiency of targeted nanoparticles with minimal tissue damage, which was in line with fluorescence and magnetic imaging results. The novel synthesized nanoparticles containing SPION@MSN-ZIF-8 were suitable for CRC theranostics, and the combined approach of chemo-gene therapy suppressed the tumor more effectively.
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Affiliation(s)
- Amir Abrishami
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Ahmad Reza Bahrami
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amir Sh Saljooghi
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
- Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
- Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
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7
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Vahabi M, Xu G, Avan A, Peters GJ, Giovannetti E. Pharmacological mechanisms underlying the interaction of the nucleoside analogue gemcitabine with the c-MET inhibitor tivantinib in pancreatic cancer. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024; 43:837-850. [PMID: 38420938 DOI: 10.1080/15257770.2024.2319215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/06/2024] [Accepted: 02/11/2024] [Indexed: 03/02/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy with limited treatment options, highlighting the urgent need for innovative approaches. A promising target for new anticancer therapies across various tumor types is the receptor tyrosine kinase c-MET. Here, we examined the impact of the c-MET inhibitor tivantinib in combination with gemcitabine on both primary and immortalized PDAC cells, and we investigated the mechanism underlying this combined treatment's effects. Our findings demonstrate that tivantinib is synergistic with gemcitabine, which is not related to cytidine deaminase but to inhibition of the polymerization of tubulin. Moreover, these drugs affected the expression of microRNAs miR-21 and miR-34, which regulate key oncogenic pathways. These findings might have an impact on the selection of patients for future trials.
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Affiliation(s)
- Mahrou Vahabi
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Geng Xu
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Godefridus J Peters
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Fondazione Pisana per la Scienza, Pisa, Italy
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8
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Maleki EH, Bahrami AR, Matin MM. Cancer cell cycle heterogeneity as a critical determinant of therapeutic resistance. Genes Dis 2024; 11:189-204. [PMID: 37588236 PMCID: PMC10425754 DOI: 10.1016/j.gendis.2022.11.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/20/2022] [Accepted: 11/16/2022] [Indexed: 01/15/2023] Open
Abstract
Intra-tumor heterogeneity is now arguably one of the most-studied topics in tumor biology, as it represents a major obstacle to effective cancer treatment. Since tumor cells are highly diverse at genetic, epigenetic, and phenotypic levels, intra-tumor heterogeneity can be assumed as an important contributing factor to the nullification of chemotherapeutic effects, and recurrence of the tumor. Based on the role of heterogeneous subpopulations of cancer cells with varying cell-cycle dynamics and behavior during cancer progression and treatment; herein, we aim to establish a comprehensive definition for adaptation of neoplastic cells against therapy. We discuss two parallel and yet distinct subpopulations of tumor cells that play pivotal roles in reducing the effects of chemotherapy: "resistant" and "tolerant" populations. Furthermore, this review also highlights the impact of the quiescent phase of the cell cycle as a survival mechanism for cancer cells. Beyond understanding the mechanisms underlying the quiescence, it provides an insightful perspective on cancer stem cells (CSCs) and their dual and intertwined functions based on their cell cycle state in response to treatment. Moreover, CSCs, epithelial-mesenchymal transformed cells, circulating tumor cells (CTCs), and disseminated tumor cells (DTCs), which are mostly in a quiescent state of the cell cycle are proved to have multiple biological links and can be implicated in our viewpoint of cell cycle heterogeneity in tumors. Overall, increasing our knowledge of cell cycle heterogeneity is a key to identifying new therapeutic solutions, and this emerging concept may provide us with new opportunities to prevent the dreadful cancer recurrence.
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Affiliation(s)
- Ebrahim H. Maleki
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, 9177948974 Mashhad, Iran
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 31-007 Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348 Krakow, Poland
| | - Ahmad Reza Bahrami
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, 9177948974 Mashhad, Iran
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, 9177948974 Mashhad, Iran
| | - Maryam M. Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, 9177948974 Mashhad, Iran
- Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, 9177948974 Mashhad, Iran
- Stem Cell and Regenerative Medicine Research Group, Iranian Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi Branch, 917751376 Mashhad, Iran
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9
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Sun G, Ni K, Shen J, Liu D, Wang H. microRNA-486-5p Regulates DNA Damage Inhibition and Cisplatin Resistance in Lung Adenocarcinoma by Targeting AURKB. Crit Rev Eukaryot Gene Expr 2024; 34:13-23. [PMID: 38505869 DOI: 10.1615/critreveukaryotgeneexpr.v34.i4.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Lung adenocarcinoma (LUAD) severely affects human health, and cisplatin (DDP) resistance is the main obstacle in LUAD treatment, the mechanism of which is unknown. Bioinformatics methods were utilized to predict expression and related pathways of AURKB in LUAD tissues, as well as the upstream regulated microRNAs. qRT-PCR assayed expression of AURKB and microRNA-486-5p. RIP and dual-luciferase experiments verified the binding and interaction between the two genes. CCK-8 was used to detect cell proliferation ability and IC50 values. Flow cytometry was utilized to assess the cell cycle. Comet assay and western blot tested DNA damage and γ-H2AX protein expression, respectively. In LUAD, AURKB was upregulated, but microRNA-486-5p was downregulated. The targeted relationship between the two was confirmed by RIP and dual-luciferase experiments. Cell experiments showed that AURKB knock-down inhibited cell proliferation, reduced IC50 values, induced cell cycle arrest, and caused DNA damage. The rescue experiment presented that high expression of microRNA-486-5p could weaken the impact of AURKB overexpression on LUAD cell behavior and DDP resistance. microRNA-486-5p regulated DNA damage to inhibit DDP resistance in LUAD by targeting AURKB, implying that microRNA-486-5p/AURKB axis may be a possible therapeutic target for DDP resistance in LUAD patients.
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Affiliation(s)
- Gaozhong Sun
- Department of Thoracic Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, China
| | - Kewei Ni
- Department of Thoracic Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, China
| | - Jian Shen
- Department of Thoracic Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, China
| | - Dongdong Liu
- Department of Thoracic Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, China
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Ma C, Zhou Q, Shi J, Gao H, Huang D, Xue H, Wang H, Zhang Z, Yang S, Zhang J, Zhang K. CRISPR-empowered electrochemical biosensor for target amplification-free and sensitive detection of miRNA. Talanta 2024; 266:125125. [PMID: 37651913 DOI: 10.1016/j.talanta.2023.125125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system provides a new molecular diagnostic tool for construction of biosensor platforms due to its high programmability and target specificity. Herein, we developed a CRISPR-empowered electrochemical biosensor by combining the advantages of CRISPR/Cas13a and primer exchange reaction (PER), named PER-E-CRISPR, for target amplification-free and sensitive detection of miR-21. Dual-signal amplification procedures involve the binding of target miR-21 induced by CRISPR-based amplification, along with the hybridization of multiple short single-stranded DNA strands with PER concatemers. When target miR-21 is present, CRISPR/Cas13a specifically recognizes the target miRNA, triggering the trans-cleavage activity of CRISPR/Cas13a. Then Cas13a/crRNA/miRNA cleaved the predesigned ribonucleotide site in hairpin 1 (HP1) and released trigger to open hairpin 2 (HP2) modified on the electrode surface. Then PER bridge sequence contained in HP2 is exposed and hybridized with PER concatemers, following multiple short single-stranded DNA tagged with methylene blue (ssDNA-MB) bond with the PER concatemers. Under optimized conditions, PER-E-CRISPR assay for detecting miR-21 exhibits linearity in dynamic range from 10-13 to 10-7 M, and we obtained a limit of detection (LOD) of 30.2 fM. The established PER-E-CRISPR biosensor shows perfect practical performance in actual plasma, which may have great promising prospects for miRNA detection in the field of molecular diagnosis.
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Affiliation(s)
- Chihong Ma
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Qin Zhou
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Hua Gao
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Di Huang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Huimin Xue
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Han Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China
| | - Sen Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China.
| | - Junli Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China.
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, 450001, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, 450052, China.
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Ziegler JN, Tian C. Engineered Extracellular Vesicles: Emerging Therapeutic Strategies for Translational Applications. Int J Mol Sci 2023; 24:15206. [PMID: 37894887 PMCID: PMC10607082 DOI: 10.3390/ijms242015206] [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: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Extracellular vesicles (EVs) are small, membrane-bound vesicles used by cells to deliver biological cargo such as proteins, mRNA, and other biomolecules from one cell to another, thus inducing a specific response in the target cell and are a powerful method of cell to cell and organ to organ communication, especially during the pathogenesis of human disease. Thus, EVs may be utilized as prognostic and diagnostic biomarkers, but they also hold therapeutic potential just as mesenchymal stem cells have been used in therapeutics. However, unmodified EVs exhibit poor targeting efficacy, leading to the necessity of engineered EVS. To highlight the advantages and therapeutic promises of engineered EVs, in this review, we summarized the research progress on engineered EVs in the past ten years, especially in the past five years, and highlighted their potential applications in therapeutic development for human diseases. Compared to the existing stem cell-derived EV-based therapeutic strategies, engineered EVs show greater promise in clinical applications: First, engineered EVs mediate good targeting efficacy by exhibiting a targeting peptide that allows them to specifically target a specific organ or even cell type, thus avoiding accumulation in undesired locations and increasing the potency of the treatment. Second, engineered EVs can be artificially pre-loaded with any necessary biomolecular cargo or even therapeutic drugs to treat a variety of human diseases such as cancers, neurological diseases, and cardiovascular ailments. Further research is necessary to improve logistical challenges in large-scale engineered EV manufacturing, but current developments in engineered EVs prove promising to greatly improve therapeutic treatment for traditionally difficult to treat diseases.
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Affiliation(s)
| | - Changhai Tian
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA;
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Király J, Szabó E, Fodor P, Fejes Z, Nagy B, Juhász É, Vass A, Choudhury M, Kónya G, Halmos G, Szabó Z. Shikonin Causes an Apoptotic Effect on Human Kidney Cancer Cells through Ras/MAPK and PI3K/AKT Pathways. Molecules 2023; 28:6725. [PMID: 37764501 PMCID: PMC10534756 DOI: 10.3390/molecules28186725] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
(1) Background: Shikonin, the main ingredient in Chinese herbal medicine, is described as a novel angiogenesis inhibitor, and its anticancer effects have already been studied. Shikonin and its derivatives induce apoptosis and suppress metastasis, which further enhance the effectiveness of chemotherapy. However, their mechanism of function has not been completely elucidated on human renal cancer cells. (2) Methods: In our study, CAKI-2 and A-498 cells were treated with increasing concentrations (2.5-40 µM) of shikonin, when colony formation ability and cytotoxic activity were tested. The changes in the expression of the main targets of apoptotic pathways were measured by RT-qPCR and Western blot. The intracellular levels of miR-21 and miR-155 were quantified by RT-qPCR. (3) Results: Shikonin exerted a dose-dependent effect on the proliferation of the cell lines examined. In 5 µM concentration of shikonin in vitro elevated caspase-3 and -7 levels, the proteins of the Ras/MAPK and PI3K/AKT pathways were activated. However, no significant changes were detected in the miR-21 and miR-155 expressions. (4) Conclusions: Our findings indicated that shikonin causes apoptosis of renal cancer cells by activating the Ras/MAPK and PI3K/AKT pathways. These effects of shikonin on renal cancer cells may bear important potential therapeutic implications for the treatment of renal cancer.
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Affiliation(s)
- József Király
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary; (J.K.); (P.F.); (A.V.); (G.K.); (G.H.)
| | - Erzsébet Szabó
- Department of Pharmacology, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary;
- HUN-RE-DE Pharmamodul Research Group, University of Debrecen, 4032 Debrecen, Hungary
| | - Petra Fodor
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary; (J.K.); (P.F.); (A.V.); (G.K.); (G.H.)
| | - Zsolt Fejes
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.F.); (B.N.J.)
| | - Béla Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.F.); (B.N.J.)
| | - Éva Juhász
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Anna Vass
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary; (J.K.); (P.F.); (A.V.); (G.K.); (G.H.)
| | - Mahua Choudhury
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M Health Science Center, College Station, TX 77845, USA;
| | - Gábor Kónya
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary; (J.K.); (P.F.); (A.V.); (G.K.); (G.H.)
| | - Gábor Halmos
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary; (J.K.); (P.F.); (A.V.); (G.K.); (G.H.)
| | - Zsuzsanna Szabó
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary; (J.K.); (P.F.); (A.V.); (G.K.); (G.H.)
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Ebrahimi A, Bakhshaei Shahrebabaki P, Fouladi H, Mansoori Derakhshan S. The impact of microRNAs on the resistance of breast cancer subtypes to chemotherapy. Pathol Res Pract 2023; 249:154702. [PMID: 37562283 DOI: 10.1016/j.prp.2023.154702] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Breast cancer (BC) formation is primarily influenced by genetics, epigenetics and environmental factors. Aberrant Genetics and epigenetics leads to a condition known as heterogeneity. The heterogeneity of BC can be divided into several subtypes. Among the epigenetic factors, microRNAs (miRNAs) have been shown to play a crucial role in the development and progression of malignancies. These small non-coding RNAs regulate gene expression through a variety of mechanisms, resulting in either mRNA degradation or translation repression. As miRNAs directly control many proteins, genetic anomalies affect tumor metastasis, apoptosis, proliferation, and cell transportation. Consequently, miRNA dysregulations contribute not only in cancer development but also in invasiveness, proliferation rate and more importantly, drug response. Findings mostly indicate subtype-specified identical miRNA profile in BC. Among the BC subtypes, TNBC, HER2 + and luminal are the most resistant to therapy, respectively. Therapy resistance is greatly associated with miRNA expression profile. Hence, concentration of miRNA is the first marker of its role in chemotherapy response. Overexpressed miRNAs may disrupt drug efflux transporters and decrease the drug accumulation in cell. While down-regulated miRNAs which mediate drug resistance processes are mostly correlated with poor treatment response. Moreover, other mechanisms in which miRNAs play crucial roles in chemoresistance such as cell receptor mediations, dysregulation by environmental factors, DNA defects, etc. Recently, several miRNA-based treatments have shown promising results in cancer treatment. Inhibition of up-regulated miRNAs is one of these therapeutic approaches whilst transfecting cell with down-regulated miRNAs also show promising results. Moreover, drug-resistance could also be determined while in the pre-treatment phase via expression levels of miRNAs. Therefore, miRNAs provide intriguing insights and challenges in overcoming chemoresistance. In this article, we have discussed how miRNAs regulate breast cancer subtypes-specific chemoresistance.
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Affiliation(s)
- Amir Ebrahimi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Genetics, Tabriz, Iran
| | - Peyman Bakhshaei Shahrebabaki
- Department of Vascular and Endovascular Surgery, Ayatollah Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Fouladi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Genetics, Tabriz, Iran
| | - Sima Mansoori Derakhshan
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Genetics, Tabriz, Iran.
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