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Luo Y, Liu W, Tang P, Jiang D, Gu C, Huang Y, Gong F, Rong Y, Qian D, Chen J, Zhou Z, Zhao S, Wang J, Xu T, Wei Y, Yin G, Fan J, Cai W. miR-624-5p promoted tumorigenesis and metastasis by suppressing hippo signaling through targeting PTPRB in osteosarcoma cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:488. [PMID: 31829261 PMCID: PMC6907337 DOI: 10.1186/s13046-019-1491-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/25/2019] [Indexed: 02/07/2023]
Abstract
Background Accumulating evidence indicates that aberrant microRNA (miRNA) expression contributes to osteosarcoma progression. This study aimed to elucidate the association between miR-624-5p expression and osteosarcoma (OS) development and to investigate its underlying mechanism. Methods We analyzed GSE65071 from the GEO database and found miR-624-5p was the most upregulated miRNA. The expression of miR-624-5p and its specific target gene were determined in human OS specimens and cell lines by RT-PCR and western blot. The effects of miR-624-5p depletion or ectopic expression on OS proliferation, migration and invasion were evaluated in vitro using CCK-8 proliferation assay, colony formation assay, transwell assay, would-healing assay and 3D spheroid BME cell invasion assay respectively. We investigated in vivo effects of miR-624-5p using a mouse tumorigenicity model. Besides, luciferase reporter assays were employed to identify interactions between miR-624-5p and its specific target gene. Results miR-624-5p expression was upregulated in OS cells and tissues, and overexpressing miR-624-5p led to a higher malignant level of OS, including cell proliferation, migration and invasion in vitro and in vivo. Protein tyrosine phosphatase receptor type B (PTPRB) was negatively correlated with miR-624-5p expression in OS tissues. Using the luciferase reporter assay and Western blotting, PTPRB was confirmed as a downstream target of miR-624-5p. PTPRB restored the effects of miR-624-5p on OS migration and invasion. The Hippo signaling pathway was identified as being involved in the miR-624-5p/PTPRB axis. Conclusions In conclusion, our results suggest that miR-624-5p is a negative regulator of PTPRB and a risk factor for tumor metastasis in OS progression.
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Affiliation(s)
- Yongjun Luo
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Wei Liu
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Pengyu Tang
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Dongdong Jiang
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Changjiang Gu
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Yumin Huang
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Fangyi Gong
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Yuluo Rong
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Dingfei Qian
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Jian Chen
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Zheng Zhou
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Shujie Zhao
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Jiaxing Wang
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Tao Xu
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Yongzhong Wei
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Guoyong Yin
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
| | - Jin Fan
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
| | - Weihua Cai
- Department of Orthopaedics, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
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La Ferlita A, Alaimo S, Veneziano D, Nigita G, Balatti V, Croce CM, Ferro A, Pulvirenti A. Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. Database (Oxford) 2019; 2019:baz115. [PMID: 31735953 PMCID: PMC6859256 DOI: 10.1093/database/baz115] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 07/01/2019] [Accepted: 09/02/2019] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing is increasing our understanding and knowledge of non-coding RNAs (ncRNAs), elucidating their roles in molecular mechanisms and processes such as cell growth and development. Within such a class, tRNA-derived ncRNAs have been recently associated with gene expression regulation in cancer progression. In this paper, we characterize, for the first time, tRNA-derived ncRNAs in NCI-60. Furthermore, we assess their expression profile in The Cancer Genome Atlas (TCGA). Our comprehensive analysis allowed us to report 322 distinct tRNA-derived ncRNAs in NCI-60, categorized in tRNA-derived fragments (11 tRF-5s, 55 tRF-3s), tRNA-derived small RNAs (107 tsRNAs) and tRNA 5' leader RNAs (149 sequences identified). In TCGA, we were able to identify 232 distinct tRNA-derived ncRNAs categorized in 53 tRF-5s, 58 tRF-3s, 63 tsRNAs and 58 5' leader RNAs. This latter group represents an additional evidence of tRNA-derived ncRNAs originating from the 5' leader region of precursor tRNA. We developed a public database, tRFexplorer, which provides users with the expression profile of each tRNA-derived ncRNAs in every cell line in NCI-60 as well as for each TCGA tumor type. Moreover, the system allows us to perform differential expression analyses of such fragments in TCGA, as well as correlation analyses of tRNA-derived ncRNAs expression in TCGA and NCI-60 with gene and miRNA expression in TCGA samples, in association with all omics and compound activities data available on CellMiner. Hence, the tool provides an important opportunity to investigate their potential biological roles in absence of any direct experimental evidence. Database URL: https://trfexplorer.cloud/.
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Affiliation(s)
- Alessandro La Ferlita
- Department of Physics and Astronomy, University of Catania, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Dario Veneziano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Veronica Balatti
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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Pashaei E, Pashaei E, Ahmady M, Ozen M, Aydin N. Meta-analysis of miRNA expression profiles for prostate cancer recurrence following radical prostatectomy. PLoS One 2017; 12:e0179543. [PMID: 28651018 PMCID: PMC5484492 DOI: 10.1371/journal.pone.0179543] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 05/31/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) is a leading reason of death in men and the most diagnosed malignancies in the western countries at the present time. After radical prostatectomy (RP), nearly 30% of men develop clinical recurrence with high serum prostate-specific antigen levels. An important challenge in PCa research is to identify effective predictors of tumor recurrence. The molecular alterations in microRNAs are associated with PCa initiation and progression. Several miRNA microarray studies have been conducted in recurrence PCa, but the results vary among different studies. METHODS We conducted a meta-analysis of 6 available miRNA expression datasets to identify a panel of co-deregulated miRNA genes and overlapping biological processes. The meta-analysis was performed using the 'MetaDE' package, based on combined P-value approaches (adaptive weight and Fisher's methods), in R version 3.3.1. RESULTS Meta-analysis of six miRNA datasets revealed miR-125A, miR-199A-3P, miR-28-5P, miR-301B, miR-324-5P, miR-361-5P, miR-363*, miR-449A, miR-484, miR-498, miR-579, miR-637, miR-720, miR-874 and miR-98 are commonly upregulated miRNA genes, while miR-1, miR-133A, miR-133B, miR-137, miR-221, miR-340, miR-370, miR-449B, miR-489, miR-492, miR-496, miR-541, miR-572, miR-583, miR-606, miR-624, miR-636, miR-639, miR-661, miR-760, miR-890, and miR-939 are commonly downregulated miRNA genes in recurrent PCa samples in comparison to non-recurrent PCa samples. The network-based analysis showed that some of these miRNAs have an established prognostic significance in other cancers and can be actively involved in tumor growth. Gene ontology enrichment revealed many target genes of co-deregulated miRNAs are involved in "regulation of epithelial cell proliferation" and "tissue morphogenesis". Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that these miRNAs regulate cancer pathways. The PPI hub proteins analysis identified CTNNB1 as the most highly ranked hub protein. Besides, common pathway analysis showed that TCF3, MAX, MYC, CYP26A1, and SREBF1 significantly interact with those DE miRNA genes. The identified genes have been known as tumor suppressors and biomarkers which are closely related to several cancer types, such as colorectal cancer, breast cancer, PCa, gastric, and hepatocellular carcinomas. Additionally, it was shown that the combination of DE miRNAs can assist in the more specific detection of the PCa and prediction of biochemical recurrence (BCR). CONCLUSION We found that the identified miRNAs through meta-analysis are candidate predictive markers for recurrent PCa after radical prostatectomy.
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Affiliation(s)
- Elnaz Pashaei
- Department of Computer Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Elham Pashaei
- Department of Computer Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Maryam Ahmady
- Department of Computer Engineering and IT, Payame Noor University, Tehran, Iran
| | - Mustafa Ozen
- Department of Pathology & Immunology Baylor College of Medicine, Houston, Texas, United States of America
| | - Nizamettin Aydin
- Department of Computer Engineering, Yildiz Technical University, Istanbul, Turkey
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Shil S, Joshi RS, Joshi CG, Patel AK, Shah RK, Patel N, Jakhesara SJ, Kundu S, Reddy B, Koringa PG, Rank DN. Transcriptomic comparison of primary bovine horn core carcinoma culture and parental tissue at early stage. Vet World 2017; 10:38-55. [PMID: 28246447 PMCID: PMC5301178 DOI: 10.14202/vetworld.2017.38-55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/29/2016] [Indexed: 12/18/2022] Open
Abstract
Aim: Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn’s SCC tissue and its early passage primary culture using next generation sequencing was the aim of this study. Materials and Methods: Whole transcriptome sequencing of horn’s SCC tissue and its early passage cells using Ion Torrent PGM were done. Comparative expression and analysis of different genes and pathways related to cancer and biological processes associated with malignancy, proliferating capacity, differentiation, apoptosis, senescence, adhesion, cohesion, migration, invasion, angiogenesis, and metabolic pathways were identified. Results: Up-regulated genes in SCC of horn’s early passage cells were involved in transporter activity, catalytic activity, nucleic acid binding transcription factor activity, biogenesis, cellular processes, biological regulation and localization and the down-regulated genes mainly were involved in focal adhesion, extracellular matrix receptor interaction and spliceosome activity. Conclusion: The experiment revealed similar transcriptomic nature of horn’s SCC tissue and its early passage cells.
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Affiliation(s)
- Sharadindu Shil
- Veterinary Officer (WBAH & VS), West Bengal Animal Resources Development Department, Bankura - 772 152, West Bengal, India; Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - R S Joshi
- Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - C G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - A K Patel
- Hester Biosciences Limited, Ahmedabad, Gujarat, India
| | - Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Namrata Patel
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Sumana Kundu
- Veterinary Officer, MVC Sarenga, Government of West Bengal, Bankura, West Bengal, India
| | - Bhaskar Reddy
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - P G Koringa
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - D N Rank
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India; Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
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Sossey-Alaoui K, Plow EF. miR-138-Mediated Regulation of KINDLIN-2 Expression Modulates Sensitivity to Chemotherapeutics. Mol Cancer Res 2015; 14:228-38. [PMID: 26474967 DOI: 10.1158/1541-7786.mcr-15-0299] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/12/2015] [Indexed: 01/24/2023]
Abstract
UNLABELLED Prostate cancer is the second leading cause of cancer-related death in men, second only to lung cancer, mainly due to disease reoccurrence as a result to lack of response to androgen deprivation therapies (ADT) after castration. Patients with metastatic castration-resistant prostate cancer (mCRPC) have very limited treatment options, with docetaxel as the first-line standard of care, for which resistance to this chemotherapeutic ultimately develops. Therefore, finding ways to sensitize tumors to chemotherapies and to limit chemoresistance provides a viable strategy to extend the survival of mCRPC patients. This study investigated the role of Kindlin-2 (FERMT2/K2), a member of the Kindlin family of FERM domain proteins and key regulators of the adhesive functions mediated by integrin, in the sensitization of mCRPC to chemotherapeutics. Loss of K2, which is overexpressed in prostate cancer cells derived from mCRPC tumors, compared with those cells derived from androgen-dependent tumors, significantly enhanced apoptosis and cell death of docetaxel-treated PC3 cells. Furthermore, it was determined that K2-mediated sensitization to docetaxel treatment is the result of inhibition of β1-integrin signaling. Finally, miR-138 specifically targeted K2 and inhibited its expression, thereby regulating a miR-138/K2/β1-integrin signaling axis in mCRPC that is critical for the modulation of sensitivity to chemotherapeutics. Thus, these data identify a novel signaling axis where K2 in combination with chemotherapeutics provides a new target for the treatment of mCRPC. IMPLICATIONS Targeted inhibition of Kindlin-2 in combination with chemotherapy represents an effective treatment option for mCRPC.
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Affiliation(s)
- Khalid Sossey-Alaoui
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.
| | - Edward F Plow
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
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