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Pathania AS, Chava H, Balusu R, Pasupulati AK, Coulter DW, Challagundla KB. The crosstalk between non-coding RNAs and cell-cycle events: A new frontier in cancer therapy. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200785. [PMID: 38595981 PMCID: PMC10973673 DOI: 10.1016/j.omton.2024.200785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The cell cycle comprises sequential events during which a cell duplicates its genome and divides it into two daughter cells. This process is tightly regulated to ensure that the daughter cell receives identical copied chromosomal DNA and that any errors in the DNA during replication are correctly repaired. Cyclins and their enzyme partners, cyclin-dependent kinases (CDKs), are critical regulators of G- to M-phase transitions during the cell cycle. Mitogenic signals induce the formation of the cyclin/CDK complexes, resulting in phosphorylation and activation of the CDKs. Once activated, cyclin/CDK complexes phosphorylate specific substrates that drive the cell cycle forward. The sequential activation and inactivation of cyclin-CDK complexes are tightly controlled by activating and inactivating phosphorylation events induced by cell-cycle proteins. The non-coding RNAs (ncRNAs), which do not code for proteins, regulate cell-cycle proteins at the transcriptional and translational levels, thereby controlling their expression at different cell-cycle phases. Deregulation of ncRNAs can cause abnormal expression patterns of cell-cycle-regulating proteins, resulting in abnormalities in cell-cycle regulation and cancer development. This review explores how ncRNA dysregulation can disrupt cell division balance and discusses potential therapeutic approaches targeting these ncRNAs to control cell-cycle events in cancer treatment.
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Affiliation(s)
- Anup S. Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Haritha Chava
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ramesh Balusu
- Department of Hematologic Malignancies and Cellular Therapeutics, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Anil K. Pasupulati
- Department of Biochemistry, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Don W. Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishore B. Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- The Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
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2
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Towle R, Dickman CTD, MacLellan SA, Chen J, Prisman E, Guillaud M, Garnis C. Identification of a serum-based microRNA signature that detects recurrent oral squamous cell carcinoma before it is clinically evident. Br J Cancer 2023; 129:1810-1817. [PMID: 37798371 PMCID: PMC10667517 DOI: 10.1038/s41416-023-02405-9] [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: 11/21/2022] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Survival rates for oral squamous cell carcinoma (OSCC) have remained poor for decades, a fact largely attributable to late-stage diagnoses and high recurrence rates. We report analysis of serum miRNA expression in samples from patients with high-risk oral lesions (HRL, including OSCC/carcinoma in situ lesions) and healthy non-cancer controls, with the aim of non-invasively detecting primary or recurrent disease before it is clinically evident. METHODS Discovery, test, and validation sets were defined from a total of 468 serum samples (305 HRL and 163 control samples). Samples were analysed using multiple qRT-PCR platforms. RESULTS A two-miRNA classifier comprised of miR-125b-5p and miR-342-3p was defined following discovery and test analyses. Analysis in an independent validation cohort reported sensitivity and specificity of ~74% for this classifier. Significantly, when this classifier was applied to serial serum samples taken from patients both before treatment and during post-treatment surveillance, it identified recurrence an average of 15 months prior to clinical presentation. CONCLUSIONS These results indicate this serum miRNA classifier is effective as a simple, non-invasive monitoring tool for earlier detection of recurrent disease when lesions are typically smaller and amenable to a wider array of treatment options to improve survival.
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Affiliation(s)
- Rebecca Towle
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Christopher T D Dickman
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Sara A MacLellan
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Jiahua Chen
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
| | - Eitan Prisman
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Martial Guillaud
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Cathie Garnis
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, BC, Canada.
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3
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Deng X, Chen X, Luo Y, Que J, Chen L. Intratumor microbiome derived glycolysis-lactate signatures depicts immune heterogeneity in lung adenocarcinoma by integration of microbiomic, transcriptomic, proteomic and single-cell data. Front Microbiol 2023; 14:1202454. [PMID: 37664112 PMCID: PMC10469687 DOI: 10.3389/fmicb.2023.1202454] [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: 04/08/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Microbiome plays roles in lung adenocarcinoma (LUAD) development and anti-tumor treatment efficacy. Aberrant glycolysis in tumor might promote lactate production that alter tumor microenvironment, affecting microbiome, cancer cells and immune cells. We aimed to construct intratumor microbiome score to predict prognosis of LUAD patients and thoroughly investigate glycolysis and lactate signature's association with LUAD immune cell infiltration. Methods The Cancer Genome Atlas-LUAD (TCGA-LUAD) microbiome data was downloaded from cBioPortal and analyzed to examine its association with overall survival to create a prognostic scoring model. Gene Set Enrichment Analysis (GSEA) was used to find each group's major mechanisms involved. Our study then investigated the glycolysis and lactate pattern in LUAD patients based on 19 genes, which were correlated with the tumor microenvironment (TME) phenotypes and immunotherapy outcomes. We developed a glycolysis-lactate risk score and signature to accurately predict TME phenotypes, prognosis, and response to immunotherapy. Results Using the univariate Cox regression analysis, the abundance of 38 genera were identified with prognostic values and a lung-resident microbial score (LMS) was then developed from the TCGA-LUAD-microbiome dataset. Glycolysis hallmark pathway was significantly enriched in high-LMS group and three distinct glycolysis-lactate patterns were generated. Patients in Cluster1 exhibited unfavorable outcomes and might be insensitive to immunotherapy. Glycolysis-lactate score was constructed for predicting prognosis with high accuracy and validated in external cohorts. Gene signature was developed and this signature was elevated in epithelial cells especially in tumor mass on single-cell level. Finally, we found that the glycolysis-lactate signature levels were consistent with the malignancy of histological subtypes. Discussion Our study demonstrated that an 18-microbe prognostic score and a 19-gene glycolysis-lactate signature for predicting prognosis of LUAD patients. Our LMS, glycolysis-lactate score and glycolysis-lactate signature have potential roles in precision therapy of LUAD patients.
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Affiliation(s)
| | | | | | - Jun Que
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liang Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Hsu CC, Yang Y, Kannisto E, Zeng X, Yu G, Patnaik SK, Dy GK, Reid ME, Gan Q, Wu Y. Simultaneous Detection of Tumor Derived Exosomal Protein-MicroRNA Pairs with an Exo-PROS Biosensor for Cancer Diagnosis. ACS NANO 2023; 17:8108-8122. [PMID: 37129374 DOI: 10.1021/acsnano.2c10970] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Tumor derived exosomes (TEXs) have emerged as promising biomarkers for cancer liquid biopsy. Conventional methods (such as ELISA and qRT-PCR) and emerging biosensing technologies mainly detect a single type of exosomal biomarker due to the distinct properties of different biomolecules. Sensitive detection of two different types of TEX biomarkers, i.e., protein and microRNA combined biomarkers, may greatly improve cancer diagnostic accuracy. We developed an exosome protein microRNA one-stop (Exo-PROS) biosensor that not only selectively captured TEXs but also enabled in situ, simultaneous detection of TEX protein-microRNA pairs via a surface plasmon resonance mechanism. Exo-PROS assay is a fast, reliable, low sample consumption, and user-friendly test. With a total of 175 cancer patients and normal controls, we demonstrated that TEX protein-microRNA pairs measured by Exo-PROS assay detected lung cancer and breast cancer with 99% and 96% accuracy, respectively. Exo-PROS assay also showed superior diagnostic performance to conventional ELISA and qRT-PCR methods. Our results demonstrated that Exo-PROS assay is a potent liquid biopsy assay for cancer diagnosis.
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Affiliation(s)
- Chang-Chieh Hsu
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Yunchen Yang
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Eric Kannisto
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Elm and Carlton Street, Buffalo, New York 14263, United States
| | - Xie Zeng
- Department of Electrical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Guan Yu
- Department of Biostatistics, University at Buffalo, The State University of New York, Buffalo, New York 14263, United States
| | - Santosh K Patnaik
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Elm and Carlton Street, Buffalo, New York 14263, United States
| | - Grace K Dy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Street, Buffalo, New York 14263, United States
| | - Mary E Reid
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Street, Buffalo, New York 14263, United States
| | - Qiaoqiang Gan
- Department of Electrical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
- Materials Science Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Yun Wu
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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Siqueira IR, Batabyal RA, Freishtat R, Cechinel LR. Potential involvement of circulating extracellular vesicles and particles on exercise effects in malignancies. Front Endocrinol (Lausanne) 2023; 14:1121390. [PMID: 36936170 PMCID: PMC10020195 DOI: 10.3389/fendo.2023.1121390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
Physical activity and exercise have been widely related to prevention, treatment, and control for several non-communicable diseases. In this context, there are innumerous pre-clinical and clinical evidence indicating the potential role of exercise, beyond cancer prevention and survival, improved quality of life, including on psychological components, bone health and cachexia, from cancer survivors is described as well. This mini-review raises the potential role of circulating extracellular and particles vesicles (EVPs) cargo, as exerkines, conducting several positive effects on adjacent and/or distant tissues such as tumor, immune, bone and muscle cells. We highlighted new perspectives about microRNAs into EVPs changes induced by exercise and its benefits on malignancies, since microRNAs can be implicated with intricated physiopathological processes. Potential microRNAs into EVPs were pointed out here as players spreading beneficial effects of exercise, such as miR-150-5p, miR-124, miR-486, and miRNA-320a, which have previous findings on involvement with clinical outcomes and as well as tumor microenvironment, regulating intercellular communication and tumor growth. For example, high-intensity interval aerobic exercise program seems to increase miR-150 contents in circulating EVPs obtained from women with normal weight or overweight. In accordance circulating EVPs miR-150-5p content is correlated with prognosis colorectal cancer, and ectopic expression of miR-150 may reduce cell proliferation, invasion and metastasis. Beyond the involvement of bioactive miRNAs into circulating EVPs and their pathways related to clinical and preclinical findings, this mini review intends to support further studies on EVPs cargo and exercise effects in oncology.
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Affiliation(s)
- Ionara Rodrigues Siqueira
- Graduate Program in Biological Sciences: Pharmacology and Therapeutics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Graduate Program in Biological Sciences: Physiology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- *Correspondence: Ionara Rodrigues Siqueira,
| | - Rachael A. Batabyal
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, United States
- Division of Emergency Medicine, Children’s National Hospital, Washington, DC, United States
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Robert Freishtat
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, United States
| | - Laura Reck Cechinel
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, United States
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Functional Screen for microRNAs Suppressing Anchorage-Independent Growth in Human Cervical Cancer Cells. Int J Mol Sci 2022; 23:ijms23094791. [PMID: 35563182 PMCID: PMC9100801 DOI: 10.3390/ijms23094791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
The progression of anchorage-dependent epithelial cells to anchorage-independent growth represents a critical hallmark of malignant transformation. Using an in vitro model of human papillomavirus (HPV)-induced transformation, we previously showed that acquisition of anchorage-independent growth is associated with marked (epi)genetic changes, including altered expression of microRNAs. However, the laborious nature of the conventional growth method in soft agar to measure this phenotype hampers a high-throughput analysis. We developed alternative functional screening methods using 96- and 384-well ultra-low attachment plates to systematically investigate microRNAs regulating anchorage-independent growth. SiHa cervical cancer cells were transfected with a microRNA mimic library (n = 2019) and evaluated for cell viability. We identified 84 microRNAs that consistently suppressed growth in three independent experiments. Further validation in three cell lines and comparison of growth in adherent and ultra-low attachment plates yielded 40 microRNAs that specifically reduced anchorage-independent growth. In conclusion, ultra-low attachment plates are a promising alternative for soft-agar assays to study anchorage-independent growth and are suitable for high-throughput functional screening. Anchorage independence suppressing microRNAs identified through our screen were successfully validated in three cell lines. These microRNAs may provide specific biomarkers for detecting and treating HPV-induced precancerous lesions progressing to invasive cancer, the most critical stage during cervical cancer development.
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Elkady G, Chen Y, Hu C, Chen J, Chen X, Guo A. MicroRNA Profile of MA-104 Cell Line Associated With the Pathogenesis of Bovine Rotavirus Strain Circulated in Chinese Calves. Front Microbiol 2022; 13:854348. [PMID: 35516441 PMCID: PMC9062783 DOI: 10.3389/fmicb.2022.854348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Bovine rotavirus (BRV) causes massive economic losses in the livestock industry worldwide. Elucidating the pathogenesis of BRV would help in the development of more effective measures to control BRV infection. The MA-104 cell line is sensitive to BRV and is thereby a convenient tool for determining BRV–host interactions. Thus far, the role of the microRNAs (miRNAs) of MA-104 cells during BRV infection is still ambiguous. We performed Illumina RNA sequencing analysis of the miRNA libraries of BRV-infected and mock-infected MA-104 cells at different time points: at 0 h post-infection (hpi) (just after 90 min of adsorption) and at 6, 12, 24, 36, and 48 hpi. The total clean reads obtained from BRV-infected and uninfected cells were 74,701,041 and 74,184,124, respectively. Based on these, 579 were categorized as known miRNAs and 144 as novel miRNAs. One hundred and sixty differentially expressed (DE) miRNAs in BRV-infected cells in comparison with uninfected MA-104 cells were successfully investigated, 95 of which were upregulated and 65 were downregulated. The target messenger RNAs (mRNAs) of the DE miRNAs were examined by bioinformatics analysis. Functional annotation of the target genes with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) suggested that these genes mainly contributed to biological pathways, endocytosis, apoptotic process, trans-Golgi membrane, and lysosome. Pathways such as the mammalian target of rapamycin (mTOR) (mml-miR-486-3p and mml-miR-197-3p), nuclear factor kappa B (NF-κB) (mml-miR-204-3p and novel_366), Rap1 (mml-miR-127-3p), cAMP (mml-miR-106b-3p), mitogen-activated protein kinase (MAPK) (mml-miR-342-5p), T-cell receptor signaling (mml-miR-369-5p), RIG-I-like receptor signaling (mml-miR-504-5p), AMP-activated protein kinase (AMPK) (mml-miR-365-1-5p), and phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling (mml-miR-299-3p) were enriched. Moreover, real-time quantitative PCR (qPCR) verified the expression profiles of 23 selected DE miRNAs, which were consistent with the results of deep sequencing, and the 28 corresponding target mRNAs were mainly of regulatory pathways of the cellular machinery and immune importance, according to the bioinformatics analysis. Our study is the first to report a novel approach that uncovers the impact of BRV infection on the miRNA expressions of MA-104 cells, and it offers clues for identifying potential candidates for antiviral or vaccine strategies.
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Affiliation(s)
- Gehad Elkady
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Benha University, Benha, Egypt
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Aizhen Guo,
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Zhang Y, Chen R, Deng L, Shuai Z, Chen M. The Effect of Metformin on the Proliferation, Apoptosis and CD133 mRNA Expression of Colon Cancer Stem Cells by Upregulation of miR 342-3p. Drug Des Devel Ther 2021; 15:4633-4647. [PMID: 34815662 PMCID: PMC8602950 DOI: 10.2147/dddt.s336490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/30/2021] [Indexed: 01/01/2023] Open
Abstract
Objective To explore whether metformin (MET) can affect the biological behaviour and CD133 mRNA expression of CD133+ colon cancer stem cells (CCSCs) through miR-342-3p. Methods The direct immunomagnetic bead method was used to select CD133+ CCSCs from the SW480 and HCT116 cell lines, and miRNA-tailing qRT-PCR was used to detect the expression changes of tumor suppressor-related miRNAs (miR-34a, miR-126, miR-143, miR-145, miR-342-3p, miR-342-5p) after MET intervention. Then, miR-342-3p with markedly significant differential expression was selected as the target miRNA. The lentiviruses LV16-hsa-miR-342-3p inhibitor and LV16-NC were used for the transfection inhibition test. CCK-8, flow cytometry, and qRT-PCR were used to detect the cell viability, apoptosis rate, and CD133 mRNA expression of CD133+ CCSCs. Results Under the high-glucose environment, the expression of tumor suppressor-related miRNAs in CCSCs changed differently (p <0.05), MET also had different effects on the expression of tumor suppressor-related miRNA under different glucose concentrations (p<0.05). Among them, MET upregulates the expression of miR-342-3p in CCSCs for the first time. The results of the lentiviruses transfection inhibition test showed that after miR-342-3p was inhibited, the cell viability and apoptosis rate of CD133+ CCSCs did not change significantly compared with before inhibition (p>0.05), but the expression of CD133 mRNA markedly increased (p<0.05). Meanwhile, after MET intervention, the apoptosis rate and the expression of CD133 mRNA of CD133+ CCSCs was significantly increased, and the proliferation of CD133+ CCSCs was obviously inhibited (p<0.05). Conclusion MET upregulating the expression of miR-342-3p may not have a significant effect on the proliferation and apoptosis of CD133+ CCSCs, but it can reduce the expression of CD133 mRNA in CD133+ CCSCs.
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Affiliation(s)
- Yaqin Zhang
- Department of Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People's Republic of China
| | - Ruofei Chen
- Department of Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People's Republic of China
| | - Lili Deng
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People's Republic of China
| | - Zongwen Shuai
- Department of Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People's Republic of China
| | - Mingwei Chen
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People's Republic of China
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Human microRNA similarity in breast cancer. Biosci Rep 2021; 41:229885. [PMID: 34612484 PMCID: PMC8529337 DOI: 10.1042/bsr20211123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in a variety of human diseases, including breast cancer. A number of miRNAs are up- and down-regulated in breast cancer. However, little is known about miRNA similarity and similarity network in breast cancer. Here, a collection of 272 breast cancer-associated miRNA precursors (pre-miRNAs) were utilized to calculate similarities of sequences, target genes, pathways and functions and construct a combined similarity network. Well-characterized miRNAs and their similarity network were highlighted. Interestingly, miRNA sequence-dependent similarity networks were not identified in spite of sequence–target gene association. Similarity networks with minimum and maximum number of miRNAs originate from pathway and mature sequence, respectively. The breast cancer-associated miRNAs were divided into seven functional classes (classes I–VII) followed by disease enrichment analysis and novel miRNA-based disease similarities were found. The finding would provide insight into miRNA similarity, similarity network and disease heterogeneity in breast cancer.
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10
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Hosseinalizadeh H, Mahmoodpour M, Ebrahimi A. Circulating non-coding RNAs as a diagnostic and management biomarker for breast cancer: current insights. Mol Biol Rep 2021; 49:705-715. [PMID: 34677714 DOI: 10.1007/s11033-021-06847-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
Cancer biomarkers can be used to determine the molecular status of a tumor or its metastases, which either release them directly into body fluids or indirectly through disruption of tumor/metastatic tissue. New minimally invasive and repeatable sample collection methods, such as liquid biopsy, have been developed in the last decade to apply cancer knowledge and track its progression. Circulating non-coding RNAs, which include microRNAs, long non-coding RNAs, and PIWI-interacting RNAs, are increasingly being recognized as potential cancer biomarkers. The growing understanding of cancer's molecular pathogenesis, combined with the rapid development of new molecular techniques, encourages the study of early molecular alterations associated with cancer development in body fluids. Specific genetic and epigenetic changes in circulating free RNA (cf-RNA) in plasma, serum, and urine could be used as diagnostic biomarkers for a variety of cancers. Only a subset of these cf-RNAs have been studied in breast cancer, with the most extensive research focusing on cf-miRNA in plasma. These findings pave the way for immediate use of selected cf-RNAs as biomarkers in breast cancer liquid biopsy, as well as additional research into other cf-RNAs to advance.
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Affiliation(s)
- Hamed Hosseinalizadeh
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, 41376, Rasht, Iran
| | - Mehrdad Mahmoodpour
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, 41376, Rasht, Iran
| | - Ammar Ebrahimi
- Department of Biomedical Sciences, University of Lausanne, Rue Du Bugnon 7, 1005, Lausanne, Switzerland.
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11
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Wu YY, Lai HF, Huang TC, Chen YG, Ye RH, Chang PY, Lai SW, Chen YC, Lee CH, Liu WN, Dai MS, Chen JH, Ho CL, Chiu YL. Aberrantly reduced expression of miR-342-5p contributes to CCND1-associated chronic myeloid leukemia progression and imatinib resistance. Cell Death Dis 2021; 12:908. [PMID: 34611140 PMCID: PMC8492784 DOI: 10.1038/s41419-021-04209-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/08/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022]
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disorder associated with the Philadelphia chromosome, and the current standard of care is the use of tyrosine kinase inhibitors (TKI). However, some patients will not achieve a molecular response and may progress to blast crisis, and the underlying mechanisms remain to be clarified. In this study, next-generation sequencing was used to explore endogenous miRNAs in CML patients versus healthy volunteers, and miR-342-5p was identified as the primary target. We found that miR-342-5p was downregulated in CML patients and had a significant inhibitory effect on cell proliferation in CML. Through a luciferase reporter system, miR-342-5p was reported to target the 3'-UTR domain of CCND1 and downregulated its expression. Furthermore, overexpression of miR-342-5p enhanced imatinib-induced DNA double-strand breaks and apoptosis. Finally, by analyzing clinical databases, we further confirmed that miR-342-5p was associated with predicted molecular responses in CML patients. In conclusion, we found that both in vivo and in vitro experiments and database cohorts showed that miR-342-5p plays a key role in CML patients, indicating that miR-342-5p may be a potential target for future CML treatment or prognostic evaluation.
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MESH Headings
- 3' Untranslated Regions/genetics
- Animals
- Apoptosis/drug effects
- Apoptosis/genetics
- Base Sequence
- Cell Line, Tumor
- Cell Proliferation/genetics
- Cell Survival/genetics
- Cyclin D1/genetics
- Cyclin D1/metabolism
- DNA Breaks, Double-Stranded
- Disease Models, Animal
- Disease Progression
- Down-Regulation/genetics
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Gene Expression Regulation, Leukemic
- Gene Ontology
- Humans
- Imatinib Mesylate/pharmacology
- Imatinib Mesylate/therapeutic use
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/blood
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukocytes/pathology
- Mice, Inbred C57BL
- MicroRNAs/genetics
- MicroRNAs/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Up-Regulation/genetics
- Mice
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Affiliation(s)
- Yi-Ying Wu
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Hsing-Fan Lai
- Department of Biochemistry, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
- Graduate Institute of Life Sciences, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Tzu-Chuan Huang
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Yu-Guang Chen
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Ren-Hua Ye
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Ping-Ying Chang
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Shiue-Wei Lai
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Yeu-Chin Chen
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Cho-Hao Lee
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Wei-Nung Liu
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Ming-Shen Dai
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Jia-Hong Chen
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Ching-Liang Ho
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, 11490, Taipei, Taiwan, ROC
| | - Yi-Lin Chiu
- Department of Biochemistry, National Defense Medical Center, 11490, Taipei, Taiwan, ROC.
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12
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Isca C, Piacentini F, Mastrolia I, Masciale V, Caggia F, Toss A, Piombino C, Moscetti L, Barbolini M, Maur M, Dominici M, Omarini C. Circulating and Intracellular miRNAs as Prognostic and Predictive Factors in HER2-Positive Early Breast Cancer Treated with Neoadjuvant Chemotherapy: A Review of the Literature. Cancers (Basel) 2021; 13:cancers13194894. [PMID: 34638377 PMCID: PMC8508299 DOI: 10.3390/cancers13194894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNA) are small noncoding RNAs that can act as both oncogene and tumor suppressors. Deregulated miRNA expression has been detected in human cancers, including breast cancer (BC). Considering their important roles in tumorigenesis, miRNAs have been investigated as potential prognostic and diagnostic biomarkers. Neoadjuvant setting is an optimal model to investigate in vivo the mechanism of treatment resistance. In the management of human epidermal growth factor receptor-2 (HER2)-positive early BC, the anti-HER2-targeted therapies have drastically changed the survival outcomes. Despite this, growing drug resistance due to the pressure of therapy is relatively frequent. In the present review, we focused on the main miRNAs involved in HER2-positive BC tumorigenesis and discussed the recent evidence on their predictive and prognostic value.
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Affiliation(s)
- Chrystel Isca
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41124 Modena, Italy; (C.I.); (F.P.); (F.C.); (A.T.); (C.P.); (M.B.); (M.D.)
| | - Federico Piacentini
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41124 Modena, Italy; (C.I.); (F.P.); (F.C.); (A.T.); (C.P.); (M.B.); (M.D.)
| | - Ilenia Mastrolia
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy; (I.M.); (V.M.)
| | - Valentina Masciale
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy; (I.M.); (V.M.)
| | - Federica Caggia
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41124 Modena, Italy; (C.I.); (F.P.); (F.C.); (A.T.); (C.P.); (M.B.); (M.D.)
| | - Angela Toss
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41124 Modena, Italy; (C.I.); (F.P.); (F.C.); (A.T.); (C.P.); (M.B.); (M.D.)
| | - Claudia Piombino
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41124 Modena, Italy; (C.I.); (F.P.); (F.C.); (A.T.); (C.P.); (M.B.); (M.D.)
| | - Luca Moscetti
- Division of Medical Oncology, Department of Oncology-Hematology, University Hospital of Modena, 41124 Modena, Italy; (L.M.); (M.M.)
| | - Monica Barbolini
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41124 Modena, Italy; (C.I.); (F.P.); (F.C.); (A.T.); (C.P.); (M.B.); (M.D.)
| | - Michela Maur
- Division of Medical Oncology, Department of Oncology-Hematology, University Hospital of Modena, 41124 Modena, Italy; (L.M.); (M.M.)
| | - Massimo Dominici
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41124 Modena, Italy; (C.I.); (F.P.); (F.C.); (A.T.); (C.P.); (M.B.); (M.D.)
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy; (I.M.); (V.M.)
| | - Claudia Omarini
- Division of Medical Oncology, Department of Oncology-Hematology, University Hospital of Modena, 41124 Modena, Italy; (L.M.); (M.M.)
- Correspondence: ; Tel.: +39-059-4222845
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13
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Wen X, Zhang H, Xiang B, Zhang W, Gong F, Li S, Chen H, Luo X, Deng J, You Y, Hu Z, Jiang C. Hyperoxia-induced miR-342-5p down-regulation exacerbates neonatal bronchopulmonary dysplasia via the Raf1 regulator Spred3. Br J Pharmacol 2021; 178:2266-2283. [PMID: 33434946 DOI: 10.1111/bph.15371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 12/10/2020] [Accepted: 01/01/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND AND PURPOSE Bronchopulmonary dysplasia (BPD) is the most prevalent chronic paediatric lung disease and is linked to the development of chronic obstructive pulmonary disease. MicroRNA-based regulation of type II alveolar epithelial cell (T2AEC) proliferation and apoptosis is an important factor in the pathogenesis of BPD and warrants further investigation. EXPERIMENTAL APPROACH Two murine models of hyperoxic lung injury (with or without miR-342-5p or Sprouty-related, EVH1 domain-containing protein 3 [Spred3] modulation) were employed: a hyperoxia-induced acute lung injury model (100% O2 on postnatal days 1-7) and the BPD model (100% O2 on postnatal days 1-4, followed by room air for 10 days). Tracheal aspirate pellets from healthy control and moderate/severe BPD neonates were randomly selected for clinical miR-342-5p analysis. KEY RESULTS Hyperoxia decreased miR-342-5p levels in primary T2AECs, MLE12 cells and neonatal mouse lungs. Transgenic miR-342 overexpression in neonatal mice ameliorated survival rates and improved the BPD phenotype and BPD-associated pulmonary arterial hypertension (PAH). T2AEC-specific miR-342 transgenic overexpression, as well as miR-342-5p mimic therapy, also ameliorated the BPD phenotype and associated PAH. miR-342-5p targets the 3'UTR of the Raf1 regulator Spred3, inhibiting Spred3 expression. Treatment with recombinant Spred3 exacerbated the BPD phenotype and associated PAH. Notably, miR-342-5p inhibition under room air conditions did not mimic the BPD phenotype. Moderate/severe BPD tracheal aspirate pellets exhibited decreased miR-342-5p levels relative to healthy control pellets. CONCLUSION AND IMPLICATIONS These findings suggest that miR-342-5p mimic therapy may show promise in the treatment or prevention of BPD.
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Affiliation(s)
- Xin Wen
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Zhang
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Bo Xiang
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Weiyu Zhang
- Department of Pediatrics, Chongqing Jiulongpo District Maternity Child Health Care Hospital, Chongqing, China
| | - Fang Gong
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Shiling Li
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Hongyan Chen
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Xuan Luo
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Deng
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Yaoyao You
- Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Zhangxue Hu
- Department of Pediatrics, Army Medical Center, Army Medical University, Chongqing, China
| | - Changke Jiang
- Department of Pediatrics, Chongqing Yongchuan District Maternity Child Health Care Hospital, Chongqing, China.,Department of Pediatrics, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
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14
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Rao AKDM, Arvinden VR, Ramasamy D, Patel K, Meenakumari B, Ramanathan P, Sundersingh S, Sridevi V, Rajkumar T, Herceg Z, Gowda H, Mani S. Identification of novel dysregulated circular RNAs in early-stage breast cancer. J Cell Mol Med 2021; 25:3912-3921. [PMID: 33544410 PMCID: PMC8051735 DOI: 10.1111/jcmm.16324] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 12/29/2020] [Accepted: 01/09/2021] [Indexed: 01/04/2023] Open
Abstract
Breast cancer is a major cause of cancer-related death in women worldwide. Non-coding RNAs are a potential resource to be used as an early diagnostic biomarker for breast cancer. Circular RNAs are a recently identified group of non-coding RNA with a significant role in disease development with potential utility in diagnosis/prognosis in cancer. In this study, we identified 26 differentially expressed circular RNAs associated with early-stage breast cancer. RNA sequencing and two circRNA detection tools (find_circ and DCC) were used to understand the circRNA expression signature in breast cancer. We identified hsa_circ_0006743 (circJMJD1C) and hsa_circ_0002496 (circAPPBP1) to be significantly up-regulated in early-stage breast cancer tissues. Co-expression analysis identified four pairs of circRNA-miRNA (hsa_circ_0023990 : hsa-miR-548b-3p, hsa_circ_0016601 : hsa_miR-1246, hsa_circ_0001946 : hsa-miR-1299 and hsa_circ_0000117:hsa-miR-502-5p) having potential interaction. The miRNA target prediction and network analysis revealed mRNA possibly regulated by circRNAs. We have thus identified circRNAs of diagnostic implications in breast cancer and also observed circRNA-miRNA interaction which could be involved in breast cancer development.
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Affiliation(s)
| | | | - Deepa Ramasamy
- Department of Molecular OncologyCancer Institute (WIA)ChennaiIndia
| | - Krishna Patel
- Institute of BioinformaticsITPLBangaloreIndia
- Amrita School of BiotechnologyAmrita Vishwa VidyapeethamKollamIndia
| | | | - Priya Ramanathan
- Department of Molecular OncologyCancer Institute (WIA)ChennaiIndia
| | | | - Velusami Sridevi
- Department of Surgical OncologyCancer Institute (WIA)ChennaiIndia
| | | | - Zdenko Herceg
- Epigenetics GroupInternational Agency for Research on Cancer (IARC)LyonFrance
| | - Harsha Gowda
- Institute of BioinformaticsITPLBangaloreIndia
- Amrita School of BiotechnologyAmrita Vishwa VidyapeethamKollamIndia
- Manipal Academy of Higher Education (MAHE)ManipalIndia
- QIMR BerghoferRoyal Brisbane Hospital QLDBrisbaneQldAustralia
| | - Samson Mani
- Department of Molecular OncologyCancer Institute (WIA)ChennaiIndia
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15
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Pham VVH, Liu L, Bracken CP, Goodall GJ, Li J, Le TD. DriverGroup: a novel method for identifying driver gene groups. Bioinformatics 2021; 36:i583-i591. [PMID: 33381812 DOI: 10.1093/bioinformatics/btaa797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION Identifying cancer driver genes is a key task in cancer informatics. Most existing methods are focused on individual cancer drivers which regulate biological processes leading to cancer. However, the effect of a single gene may not be sufficient to drive cancer progression. Here, we hypothesize that there are driver gene groups that work in concert to regulate cancer, and we develop a novel computational method to detect those driver gene groups. RESULTS We develop a novel method named DriverGroup to detect driver gene groups by using gene expression and gene interaction data. The proposed method has three stages: (i) constructing the gene network, (ii) discovering critical nodes of the constructed network and (iii) identifying driver gene groups based on the discovered critical nodes. Before evaluating the performance of DriverGroup in detecting cancer driver groups, we firstly assess its performance in detecting the influence of gene groups, a key step of DriverGroup. The application of DriverGroup to DREAM4 data demonstrates that it is more effective than other methods in detecting the regulation of gene groups. We then apply DriverGroup to the BRCA dataset to identify driver groups for breast cancer. The identified driver groups are promising as several group members are confirmed to be related to cancer in literature. We further use the predicted driver groups in survival analysis and the results show that the survival curves of patient subpopulations classified using the predicted driver groups are significantly differentiated, indicating the usefulness of DriverGroup. AVAILABILITY AND IMPLEMENTATION DriverGroup is available at https://github.com/pvvhoang/DriverGroup. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vu V H Pham
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.,Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.,Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Thuc D Le
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
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16
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Long Noncoding RNA OIP5-AS1 Promotes the Disease Progression in Nasopharyngeal Carcinoma by Targeting miR-203. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9850928. [PMID: 33628831 PMCID: PMC7884132 DOI: 10.1155/2021/9850928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/02/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a kind of malignancy generated from the nasopharyngeal epithelium. Recently, long noncoding RNA (lncRNA) has been shown to be involved in the regulation of many signaling pathways and is closely associated with carcinogenesis and tumor progression. However, the precise role of lncRNA Opa-interacting protein 5 antisense RNA 1 (OIP5-AS1) in NPC is not well understood. Here, we find that OIP5-AS1 is overexpressed in NPC patient specimens and NPC cell lines. Further investigations reveal that knockdown of OIP5-AS1 significantly inhibits the proliferation, migration, and invasion and accelerates the apoptosis of NPC cells in vitro. Consistent with these findings, NPC progression is significantly slowed in mice when OIP5-AS1 is knocked down. Interestingly, there is a functional link between OIP5-AS1 and microRNA-203 (miR-203), a tumor suppressor, in NPC cells. In conclusion, our data demonstrate that OIP5-AS1 plays an important role in the development and progression of NPC by targeting miR-203 and therefore provide a promising target for the treatment of NPC.
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17
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Zhao Y, Tao Z, Chen X. Identification of the miRNA-mRNA regulatory pathways and a miR-21-5p based nomogram model in clear cell renal cell carcinoma. PeerJ 2020; 8:e10292. [PMID: 33194441 PMCID: PMC7648458 DOI: 10.7717/peerj.10292] [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: 04/09/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background The purpose of this study was to determine the key microRNAs (miRNAs) and their regulatory networks in clear cell renal cell carcinoma (ccRCC). Methods Five mRNA and three microRNA microarray datasets were downloaded from the Gene Expression Omnibus database and used to screen the differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs). Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed with Metascape. A miRNA-mRNA network was mapped with the Cytoscape tool. The results were validated with data from The Cancer Genome Atlas (TCGA) and qRT-PCR. A nomogram model based on independent prognostic key DEMs, stage and grade was constructed for further investigation. Results A total of 26 key DEMs and 307 DEGs were identified. Dysregulation of four key DEMs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) was identified to correlate with overall survival. The results were validated with TCGA data and qRT-PCR. The nomogram model showed high accuracy in predicting the prognosis of patients with ccRCC. Conclusion We identified 26 DEMs that may play vital roles in the regulatory networks of ccRCC. Four miRNAs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) were considered as potential biomarkers in the prognosis of ccRCC, among which only miR-21-5p was found to be an independent prognostic factor. A nomogram model was then created on the basis of independent factors for better prediction of prognosis for patients with ccRCC. Our results suggest a need for further experimental validation studies.
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Affiliation(s)
- Yiqiao Zhao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zijia Tao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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18
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Ji B, Chen L, Cai Q, Guo Q, Chen Z, He D. Identification of an 8-miRNA signature as a potential prognostic biomarker for glioma. PeerJ 2020; 8:e9943. [PMID: 33062427 PMCID: PMC7528815 DOI: 10.7717/peerj.9943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background Glioma is the most common form of primary malignant intracranial tumor. Methods In the current study, miRNA matrix were obtained from the Chinese Glioma Genome Atlas (CGGA), and then univariate Cox regression analysis and Lasso regression analysis were utilized to select candidate miRNAs and multivariate Cox regression analysis was applied to establish a miRNA signature for predicting overall survival (OS) of glioma. The signature was assessed with the area under the curve (AUC) of the receiver operating characteristic curve (ROC) and validated by data from Gene Expression Omnibus (GEO). Results Eight miRNAs (miR-1246, miR-148a, miR-150, miR-196a, miR-338-3p, miR-342-5p, miR-548h and miR-645) were included in the miRNA signature. The AUC of ROC analysis for 1- and 3-year OS in the CGGA dataset was 0.747 and 0.905, respectively. In the GEO dataset, The AUC for 1- and 3-year was 0.736 and 0.809, respectively. The AUC in both the CGGA and GEO datasets was similar to that based on WHO 2007 classification (0.736 and 0.799) and WHO 2016 classification (0.663 and 0.807). Additionally, Kaplan–Meier plot revealed that high-risk score patients had a poorer clinical outcome. Multivariate Cox regression analysis suggested that the miRNA signature was an independent prognosis-related factor [HR: 6.579, 95% CI [1.227−35.268], p = 0.028]. Conclusion On the whole, in the present study, based on eight miRNAs, a novel prognostic signature was developed for predicting the 1- and 3- year survival rate in glioma. The results may be conducive to predict the precise prognosis of glioma and to elucidate the underlying molecular mechanisms. However, further experimental researches of miRNAs are needed to validate the findings of this study.
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Affiliation(s)
- Baowei Ji
- Department of Neurosurgery, Wuhan University, Renmin Hospital, Wuhan, China
| | - Lihua Chen
- Department of Anesthesiology, Wuhan University, Renmin Hospital, Wuhan, China
| | - Qiang Cai
- Department of Neurosurgery, Wuhan University, Renmin Hospital, Wuhan, China
| | - Qiao Guo
- Department of Neurosurgery, Wuhan University, Renmin Hospital, Wuhan, China
| | - Zhibiao Chen
- Department of Neurosurgery, Wuhan University, Renmin Hospital, Wuhan, China
| | - Du He
- Department of Oncology, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
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19
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Cui Z, Pu T, Zhang Y, Wang J, Zhao Y. Long non-coding RNA LINC00346 contributes to cisplatin resistance in nasopharyngeal carcinoma by repressing miR-342-5p. Open Biol 2020; 10:190286. [PMID: 32397872 PMCID: PMC7276527 DOI: 10.1098/rsob.190286] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/25/2020] [Indexed: 12/28/2022] Open
Abstract
Cisplatin has been used as the first-line chemotherapy to treat advanced nasopharyngeal carcinoma (NPC), while acquired cisplatin resistance resulting from epigenetic regulation is not well understood. The relative expression of LINC00346 was detected in healthy persons, cisplatin-sensitive (CS) patients and cisplatin-resistant (CR) patients. The regulatory effect of LINC00346 on the proliferation was detected by cell-counting kit-8. Apoptosis was assayed by histone/DNA ELISA and Caspase-3 activity. Clonal formation and cisplatin resistance were also deciphered. Luciferase reporter and RNA immunoprecipitation assay were adopted to study the interaction between LINC00346 and miR-342-5p. LINC00346 was highly expressed in NPC patients, especially in CR patients, which was associated with cisplatin resistance and poor prognosis. Inhibition of LINC00346 expression promoted cisplatin sensitivity of NPC cells, while LINC00346 over-expression promoted cisplatin resistance of NPC cells. miR-342-5p expression was negatively correlated with cisplatin resistance, and microRNA-342-5p siRNAs treatment could rescue the cisplatin resistance diminished by LINC00346 inhibition. It was further found that miR-342-5p was negatively regulated by LINC00346. In conclusion, LINC00346 regulates the cisplatin resistance of NPC cells by inhibiting miR-342-5p, which could provide a potential target for chemotherapy resistance.
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Affiliation(s)
- Zheqing Cui
- Department of Rhinology, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, Henan 450052, People's Republic of China
| | - Tian Pu
- Department of Gastroenterology, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, Henan 450052, People's Republic of China
| | - Yujie Zhang
- Department of Rhinology, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, Henan 450052, People's Republic of China
| | - Jia Wang
- Department of Rhinology, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, Henan 450052, People's Republic of China
| | - Yulin Zhao
- Department of Rhinology, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, Henan 450052, People's Republic of China
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20
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Bialkowski K, Kasprzak KS. A profile of 8-oxo-dGTPase activities in the NCI-60 human cancer panel: Meta-analytic insight into the regulation and role of MTH1 (NUDT1) gene expression in carcinogenesis. Free Radic Biol Med 2020; 148:1-21. [PMID: 31883466 DOI: 10.1016/j.freeradbiomed.2019.12.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 01/15/2023]
Abstract
We measured the specific 8-oxo-dGTPase activity profile of the NCI-60 panel of malignant cell lines, and MTH1 protein levels in a subset of 16 lines. Their 8-oxo-dGTPase activity was compared to twelve publicly accessible MTH1 mRNA expression data bases and their cross-consistency was analyzed. 8-oxo-dGTPase and MTH1 protein levels in these cell lines are generally, but not always, mainly determined by MTH1 mRNA expression levels. The aneuploidy number of MTH1 gene copies only slightly affects its mRNA expression levels. By using the data mining platforms Compare and CellMiner, our 8-oxo-dGTPase profile was compared to five global gene expression datasets to identify genes whose expression levels are directly or inversely associated with 8-oxo-dGTPase. We analyzed effects of SNP within MTH1 on MTH1 mRNA level and enzyme activity. Similar association analysis was performed for five microRNA expression datasets. We identified several proteins and microRNA which might be involved in the regulation of MTH1 expression and we discuss potential mechanisms. Comparison of chemical and natural products sensitivities of the NCI-60 panel suggests seven compounds which are directly or inversely associated with 8-oxo-dGTPase. We provide an integrated picture of MTH1 expression combined from eleven consistent MTH1 mRNA and our 8-oxo-dGTPase activity NCI-60 profiles.
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Affiliation(s)
- Karol Bialkowski
- Department of Clinical Biochemistry, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, 85-092, Poland.
| | - Kazimierz S Kasprzak
- Scientist Emeritus, Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
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Bitaraf A, Babashah S, Garshasbi M. Aberrant expression of a five-microRNA signature in breast carcinoma as a promising biomarker for diagnosis. J Clin Lab Anal 2020; 34:e23063. [PMID: 31595567 PMCID: PMC7031575 DOI: 10.1002/jcla.23063] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most common malignancy among females with dismal quality of life in patients. It has been proven that epigenetic factors, especially microRNAs, are involved in breast carcinogenesis and progression. This study aimed to assess the expression and clinical performances of a five-microRNA signature (miR-127-3p, miR-133a-3p, miR-155-5p, miR-199b-5p, and miR-342-5p) in breast cancer and adjacent normal tissues to identify a potential biomarker for BC and investigate the relationship between their expression and clinicopathological features of BC patients as well. METHODS In this case-control investigation, we recruited 50 pairs of tumor and matched non-tumor surgical specimens from patients diagnosed with BC. Expression levels of miR-127-3p, miR-133a-3p, miR-155-5p, miR-199b-5p, and miR-342-5p were measured in BC and adjacent normal tissues by RT-qPCR. RESULTS We found that miR-127-3p, miR-133a-3p, miR-199b-5p, and miR-342-5p were significantly down-regulated, while miR-155-5p was significantly up-regulated in BC tumor tissues compared with the corresponding adjacent normal tissues. The decreased expression of miR-127-3p, miR-133a-3p, miR-342-5p, and up-regulation of miR-155-5p showed a significant correlation with disease stage. We also found a significant down-regulation of miR-127-3p, miR-199b-5p, and miR-342-5p compared in HER-2-negative patients. Our results indicated that miR-155-5p had a higher expression level in HER-2-positive patients. Receiver operating characteristic (ROC) curve analysis demonstrated that all these five microRNAs can serve as potential biomarkers to distinguish between tumor and non-tumor breast tissue samples. CONCLUSIONS The present findings suggested that dysregulation of this five-miRNA signature might be considered as a promising and functional biomarker for BC diagnosis.
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Affiliation(s)
- Amirreza Bitaraf
- Department of Molecular GeneticsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Sadegh Babashah
- Department of Molecular GeneticsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Masoud Garshasbi
- Department of Medical GeneticsFaculty of Medical SciencesTarbiat Modares UniversityTehranIran
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Pham VVH, Liu L, Bracken CP, Goodall GJ, Long Q, Li J, Le TD. CBNA: A control theory based method for identifying coding and non-coding cancer drivers. PLoS Comput Biol 2019; 15:e1007538. [PMID: 31790386 PMCID: PMC6907873 DOI: 10.1371/journal.pcbi.1007538] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 12/12/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023] Open
Abstract
A key task in cancer genomics research is to identify cancer driver genes. As these genes initialise and progress cancer, understanding them is critical in designing effective cancer interventions. Although there are several methods developed to discover cancer drivers, most of them only identify coding drivers. However, non-coding RNAs can regulate driver mutations to develop cancer. Hence, novel methods are required to reveal both coding and non-coding cancer drivers. In this paper, we develop a novel framework named Controllability based Biological Network Analysis (CBNA) to uncover coding and non-coding cancer drivers (i.e. miRNA cancer drivers). CBNA integrates different genomic data types, including gene expression, gene network, mutation data, and contains a two-stage process: (1) Building a network for a condition (e.g. cancer condition) and (2) Identifying drivers. The application of CBNA to the BRCA dataset demonstrates that it is more effective than the existing methods in detecting coding cancer drivers. In addition, CBNA also predicts 17 miRNA drivers for breast cancer. Some of these predicted miRNA drivers have been validated by literature and the rest can be good candidates for wet-lab validation. We further use CBNA to detect subtype-specific cancer drivers and several predicted drivers have been confirmed to be related to breast cancer subtypes. Another application of CBNA is to discover epithelial-mesenchymal transition (EMT) drivers. Of the predicted EMT drivers, 7 coding and 6 miRNA drivers are in the known EMT gene lists. Cancer is a disease of cells in human body and it causes a high rate of deaths worldwide. There has been evidence that coding and non-coding RNAs are key players in the initialisation and progression of cancer. These coding and non-coding RNAs are considered as cancer drivers. To design better diagnostic and therapeutic plans for cancer patients, we need to know the roles of cancer drivers in cancer development as well as their regulatory mechanisms in the human body. In this study, we propose a novel framework to identify coding and non-coding cancer drivers (i.e. miRNA cancer drivers). The proposed framework is applied to the breast cancer dataset for identifying drivers of breast cancer. Comparing our method with existing methods in predicting coding cancer drivers, our method shows a better performance. Several miRNA cancer drivers predicted by our method have already been validated by literature. The predicted cancer drivers by our method could be a potential source for further wet-lab experiments to discover the causes of cancer. In addition, the proposed method can be used to detect drivers of cancer subtypes and drivers of the epithelial-mesenchymal transition in cancer.
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Affiliation(s)
- Vu V. H. Pham
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, Australia
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, Australia
| | - Cameron P. Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine, The University of Adelaide, Adelaide, Australia
| | - Gregory J. Goodall
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine, The University of Adelaide, Adelaide, Australia
| | - Qi Long
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, Australia
- * E-mail: (JL); (TL)
| | - Thuc D. Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, Australia
- * E-mail: (JL); (TL)
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Downregulation of miR-302b is associated with poor prognosis and tumor progression of breast cancer. Breast Cancer 2019; 27:291-298. [PMID: 31721061 DOI: 10.1007/s12282-019-01022-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) are well known to play crucial role in various types of cancers, including breast cancer (BC). METHODS The present study aimed to investigate the expression, clinical value, and functional role of miR-302b in BC. The expression level of miR-302b was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The clinical value of miR-302b in BC prognosis was calculated via Kaplan-Meier survival analysis and Cox regression analysis. Cell experiments were applied to investigate the functional role of miR-302b in BC. RESULTS miR-302b was significantly downregulated in BC tissues and cell lines compared to the corresponding controls (all P < 0.01). Notably, the expression of miR-302b was significantly associated with lymph node metastasis and TNM stage (all P < 0.05). Patients with lower miR-302b expression had shorter survival time than those with higher miR-302b expression (log-rank P = 0.002). Furthermore, miR-302b expression and TNM stage were proven to be independent prognostic factors for BC. Overexpression of miR-302b inhibited BC cell proliferation, migration, and invasion in BT549 and MCF-7 cell lines, while silence of miR-302b exhibited an opposite effects on BC cells (all P < 0.05). RUNX2 was determined to be the target gene of miR-302b. CONCLUSIONS The present study suggests that miR-302b functions as a tumor suppressor in BC and inhibits the tumor progression of BC via targeting RUNX2. Downregulation of miR-302b might be a significant prognostic factor for poor survival in BC patients.
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Liu Q, Wang Z, Zhou X, Tang M, Tan W, Sun T, Deng Y. miR-342-5p inhibits osteosarcoma cell growth, migration, invasion, and sensitivity to Doxorubicin through targeting Wnt7b. Cell Cycle 2019; 18:3325-3336. [PMID: 31601147 DOI: 10.1080/15384101.2019.1676087] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Osteosarcoma (OS) accounts for 9 percent of cancer-related deaths in young people. The PI3K/Akt signaling, a well-known carcinogenic signaling pathway in human cancer, cooperates with other signaling pathways such as Wnt signaling to promote cancer progression. Wnt7b, as a transforming member of the Wnt family, could activate mTORC1 through PI3K-AKT signaling and is upregulated in OS. In the present study, we found that miR-342-5p inhibits Wnt7b expression via direct binding to Wnt7b 3'-UTR. miR-342-5p overexpression remarkably suppressed the viability and invasion while enhanced the apoptosis of OS cells; meanwhile, Wnt7b, β-catenin, c-myc, and cyclin D1 proteins were reduced while E-cadherin protein showed to be increased. Consistent with its expression pattern, Wnt7b exerted oncogenic effects on OS cells. Wnt7b could significantly attenuate the impacts of miR-342-5p. In conclusion, we demonstrated a miR-342-5p/Wnt7b axis that regulates the capacity of OS cells to proliferate and to invade through Wnt/β-catenin signaling. The miR-342-5p/Wnt7b axis might be novel targets for OS targeted therapy, which needs further in vivo and clinical investigations.
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Affiliation(s)
- Qing Liu
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenting Wang
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaohua Zhou
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingying Tang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Tan
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tianshi Sun
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Youwen Deng
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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