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Rui X, Zhang X, Jia X, Han J, Wang C, Cao Q, Zhong O, Ding J, Zhao C, Zhang J, Ling X, Li H, Ma X, Meng Q, Huo R. Variants in NLRP2 and ZFP36L2, non-core components of the human subcortical maternal complex, cause female infertility with embryonic development arrest. Mol Hum Reprod 2024; 30:gaae031. [PMID: 39178021 DOI: 10.1093/molehr/gaae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
The subcortical maternal complex (SCMC), which is vital in oocyte maturation and embryogenesis, consists of core proteins (NLRP5, TLE6, OOEP), non-core proteins (PADI6, KHDC3L, NLRP2, NLRP7), and other unknown proteins that are encoded by maternal effect genes. Some variants of SCMC genes have been linked to female infertility characterized by embryonic development arrest. However, so far, the candidate non-core SCMC components associated with embryonic development need further exploration and the pathogenic variants that have been identified are still limited. In this study, we discovered two novel variants [p.(Ala131Val) and p.(Met326Val)] of NLRP2 in patients with primary infertility displaying embryonic development arrest from large families. In vitro studies using 293T cells and mouse oocytes, respectively, showed that these variants significantly decreased protein expression and caused the phenotype of embryonic development arrest. Additionally, we combined the 'DevOmics' database with the whole exome sequence data of our cohort and screened out a new candidate non-core SCMC gene ZFP36L2. Its variants [p.(Ala241Pro) and p.(Pro291dup)] were found to be responsible for embryonic development arrest. Co-immunoprecipitation experiments in 293T cells, used to demonstrate the interaction between proteins, verified that ZFP36L2 is one of the human SCMC components, and microinjection of ZFP36L2 complementary RNA variants into mouse oocytes affected embryonic development. Furthermore, the ZFP36L2 variants were associated with disrupted stability of its target mRNAs, which resulted in aberrant H3K4me3 and H3K9me3 levels. These disruptions decreased oocyte quality and further developmental potential. Overall, this is the first report of ZFP36L2 as a non-core component of the human SCMC and we found four novel pathogenic variants in the NLRP2 and ZFP36L2 genes in 4 of 161 patients that caused human embryonic development arrest. These findings contribute to the genetic diagnosis of female infertility and provide new insights into the physiological function of SCMC in female reproduction.
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Affiliation(s)
- Ximan Rui
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Xiaolan Zhang
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xinru Jia
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Jian Han
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Congjing Wang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Qiqi Cao
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Ou Zhong
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Jie Ding
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
- Reproductive Genetic Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Chun Zhao
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Junqiang Zhang
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiufeng Ling
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Hong Li
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
- Reproductive Genetic Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Xiang Ma
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qingxia Meng
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
- Reproductive Genetic Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Ran Huo
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
- Innovation Center of Suzhou, Nanjing Medical University, Suzhou, China
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Wan L, Jia Y, Chen N, Zheng S. Circ_0003789 Knockdown Inhibits Tumor Progression by miR-429/ZFP36L2 Axis in Gastric Cancer. Biochem Genet 2024; 62:2504-2521. [PMID: 37962691 DOI: 10.1007/s10528-023-10535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/22/2023] [Indexed: 11/15/2023]
Abstract
An increasing number of circRNAs have been found to be involved in the development of gastric cancer. However, the function of circ_0003789 in regulating gastric cancer progression is unclear. Here, we aimed to investigate the expression, function and molecular mechanism of circ_0003789 in gastric cancer pathogenesis. Circ_0003789, miR-429 and ZFP36 ring finger protein like 2 (ZFP36L2) mRNA were quantified by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation was illustrated by 5-Ethynyl-2'-deoxyuridine (Edu), cell counting kit-8 (CCK-8) and colony formation assays. Apoptosis was determined by flow cytometry. Protein level was detected by Western blotting assay. Xenograft assays were used for functional analysis of circ_0003789 in vivo. The relationship between miR-429 and circ_0003789 or ZFP36L2 was predicted by starbase3.0 online database and identified by dual luciferase reporter assay. The expression levels of circ_0003789 and ZFP36L2 were significantly upregulated in gastric cancer tissues and cells, while the expression of miR-429 was downregulated. Downregulation of circ_0003789 inhibited gastric cancer cell growth and invasion and promoted apoptosis in vitro. Circ_0003789 acted as a sponge of miR-429. Moreover, miR-429 silencing by miR-429 inhibitors attenuated the effects of circ_0003789 interference on cell growth, apoptosis and invasion. ZFP36L2 was targeted by miR-429, and the effects of miR-429 on cell growth, invasion and apoptosis were attenuated by ZFP36L2 overexpression. Circ_0003789 could enhance ZFP36L2 expression by interacting with miR-429. Silencing of circ_0003789 inhibited tumor growth in vivo. Circ_0003789 regulates tumor progression in gastric cancer through miR-429/ZFP36L2 axis. This finding implies that circ_0003789 may be a therapeutic target for gastric cancer.
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Affiliation(s)
- Lu Wan
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, 265 Yinquan Dadao, Xianning, 437000, Hubei, China
| | - Yu Jia
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, 265 Yinquan Dadao, Xianning, 437000, Hubei, China
| | - Na Chen
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, 265 Yinquan Dadao, Xianning, 437000, Hubei, China.
| | - Sen Zheng
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, 265 Yinquan Dadao, Xianning, 437000, Hubei, China.
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Sun J, Li M, Sun H, Lin Z, Shi B, Jia Z. Genetic association and functional validation of ZFP36L2 in non-syndromic orofacial cleft subtypes. J Hum Genet 2024; 69:139-144. [PMID: 38321215 DOI: 10.1038/s10038-024-01222-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Non-syndromic orofacial cleft (NSOC) is one of the most common craniofacial malformations with complex etiology. This study aimed to explore the role of specific SNPs in ZFP36L2 and its functional relevance in zebrafish models. METHODS We analyzed genetic data of the Chinese Han population from two previous GWAS, comprising of 2512 cases and 2255 controls. Based on the Hardy-Weinberg Equilibrium (HWE) and minor allele frequency (MAF), SNPs in the ZFP36L2 were selected for association analysis. In addition, zebrafish models were used to clarify the in-situ expression pattern of zfp36l2 and the impact of its Morpholino-induced knockdown. RESULTS Via association analysis, rs7933 in ZFP36L2 was significantly associated with various non-syndromic cleft lip-only subtypes, potentially conferring a protective effect. Zebrafish embryos showed elevated expression of zfp36l2 in the craniofacial region during critical stages of oral cavity formation. Furthermore, Morpholino-induced knockdown of zfp36l2 led to craniofacial abnormalities, including cleft lip, which was partially rescued by the addition of zfp36l2 mRNA. CONCLUSION Our findings highlight the significance of ZFP36L2 in the etiology of NSOC, supported by both human genetic association data and functional studies in zebrafish. These results pave the way for further exploration of targeted interventions for craniofacial malformations.
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Affiliation(s)
- Jialin Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Mujia Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Huaqin Sun
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyuan Lin
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
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Huang Y, Huo Y, Huang L, Zhang L, Zheng Y, Zhang N, Yang M. Super-enhancers: Implications in gastric cancer. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108489. [PMID: 38355091 DOI: 10.1016/j.mrrev.2024.108489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Gastric cancer (GC) is the fifth most prevalent malignancy and the third leading cause of cancer-related mortality globally. Despite intensive efforts to enhance the efficiencies of various therapeutics (chemotherapy, surgical interventions, molecular-targeted therapies, immunotherapies), the prognosis for patients with GC remains poor. This might be predominantly due to the limited understanding of the complicated etiology of GC. Importantly, epigenetic modifications and alterations are crucial during GC development. Super-enhancers (SEs) are a large cluster of adjacent enhancers that greatly activate transcription. SEs sustain cell-specific identity by enhancing the transcription of specific oncogenes. In this review, we systematically summarize how SEs are involved in GC development, including the SE landscape in GC, the SE target genes in GC, and the interventions related to SE functions for treating GC.
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Affiliation(s)
- Yizhou Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Yanfei Huo
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Linying Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Long Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Yanxiu Zheng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China.
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China.
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5
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Zhao J, Faryabi RB. Spatial promoter-enhancer hubs in cancer: organization, regulation, and function. Trends Cancer 2023; 9:1069-1084. [PMID: 37599153 PMCID: PMC10840977 DOI: 10.1016/j.trecan.2023.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/14/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
Transcriptional dysregulation is a hallmark of cancer and can be driven by altered enhancer landscapes. Recent studies in genome organization have revealed that multiple enhancers and promoters can spatially coalesce to form dynamic topological assemblies, known as promoter-enhancer hubs, which strongly correlate with elevated gene expression. In this review, we discuss the structure and complexity of promoter-enhancer hubs recently identified in multiple cancer types. We further discuss underlying mechanisms driving dysregulation of promoter-enhancer hubs and speculate on their functional role in pathogenesis. Understanding the role of promoter-enhancer hubs in transcriptional dysregulation can provide insight into new therapeutic approaches to target these complex features of genome organization.
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Affiliation(s)
- Jingru Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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6
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Hung YH, Capeling M, Villanueva JW, Kanke M, Shanahan MT, Huang S, Cubitt R, Rinaldi VD, Schimenti JC, Spence JR, Sethupathy P. Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model. BMC Genomics 2023; 24:641. [PMID: 37884859 PMCID: PMC10601309 DOI: 10.1186/s12864-023-09743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. RESULTS We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development. CONCLUSION The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Meghan Capeling
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan W Villanueva
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Vera D Rinaldi
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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Zhang Y, Tian F, Zhao J. MiR-520d-3p suppresses the proliferation and epithelial-mesenchymal transition of cervical cancer cells by targeting ZFP36L2. Heliyon 2023; 9:e18789. [PMID: 37600385 PMCID: PMC10432607 DOI: 10.1016/j.heliyon.2023.e18789] [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: 03/03/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
MiR-520d-3p has recently been reported to have anti-tumor function in several cancers, including glioma and gastric cancer. However, the biological function and its mechanism of action remain unclear in cervical cancer (CC). In this study, we observed that miR-520d-3p expression was lowly expressed in CC specimens compared with adjacent normal specimens using reverse transcription quantitative PCR. Moreover, low miR-520d-3p expression was correlated with FIGO stage and lymph node metastasis by Chi-square test. Functionally, overexpression of miR-520d-3p suppressed the proliferation and migration and invasion of two CC cell lines (HeLa and SiHa) using CCK-8 assay and wound healing assay. After target prediction, luciferase reporter assay showed that zinc finger protein 36 ring finger protein-like 2 (ZFP36L2) was a direct target of miR-520d-3p in CC cells. The expression levels of ZFP36L2 at protein and mRNA were significantly increased in CC tissues compared with adjacent tissues. The expression of ZFP36L2 was negatively correlated with miR-520d-3p in the patients with CC. Importantly, ZFP36L2 overexpression abolished the effects of miR-520d-3p on cell proliferation, migration and EMT process in CC cells. In conclusion, our findings indicate that targeting miR-520d-3p/ZFP36L2 axis might be a promising therapeutic target for CC treatment.
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Affiliation(s)
- Yuan Zhang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Fei Tian
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Jing Zhao
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, Hebei, China
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Fukuda K, Seki N, Yasudome R, Mitsueda R, Asai S, Kato M, Idichi T, Kurahara H, Ohtsuka T. Coronin 1C, Regulated by Multiple microRNAs, Facilitates Cancer Cell Aggressiveness in Pancreatic Ductal Adenocarcinoma. Genes (Basel) 2023; 14:genes14050995. [PMID: 37239355 DOI: 10.3390/genes14050995] [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: 03/28/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Coronin proteins are actin-related proteins containing WD repeat domains encoded by seven genes (CORO1A, CORO1B, CORO1C, CORO2A, CORO2B, CORO6, and CORO7) in the human genome. Analysis of large cohort data from The Cancer Genome Atlas revealed that expression of CORO1A, CORO1B, CORO1C, CORO2A, and CORO7 was significantly upregulated in pancreatic ductal adenocarcinoma (PDAC) tissues (p < 0.05). Moreover, high expression of CORO1C and CORO2A significantly predicted the 5 year survival rate of patients with PDAC (p = 0.0071 and p = 0.0389, respectively). In this study, we focused on CORO1C and investigated its functional significance and epigenetic regulation in PDAC cells. Knockdown assays using siRNAs targeting CORO1C were performed in PDAC cells. Aggressive cancer cell phenotypes, especially cancer cell migration and invasion, were inhibited by CORO1C knockdown. The involvement of microRNAs (miRNAs) is a molecular mechanism underlying the aberrant expression of cancer-related genes in cancer cells. Our in silico analysis revealed that five miRNAs (miR-26a-5p, miR-29c-3p, miR-130b-5p, miR-148a-5p, and miR-217) are putative candidate miRNAs regulating CORO1C expression in PDAC cells. Importantly, all five miRNAs exhibited tumor-suppressive functions and four miRNAs except miR-130b-5p negatively regulated CORO1C expression in PDAC cells. CORO1C and its downstream signaling molecules are potential therapeutic targets in PDAC.
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Affiliation(s)
- Kosuke Fukuda
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Ryutaro Yasudome
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Reiko Mitsueda
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Shunichi Asai
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Mayuko Kato
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Takao Ohtsuka
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
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Si H, Zhang N, Shi C, Luo Z, Hou S. Tumor-suppressive miR-29c binds to MAPK1 inhibiting the ERK/MAPK pathway in pancreatic cancer. Clin Transl Oncol 2023; 25:803-816. [PMID: 36510038 DOI: 10.1007/s12094-022-02991-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022]
Abstract
INTRODUCTION GEO- and TCGA-based data analysis suggested the differential expression of miR-29c in pancreatic cancer. However, limited data are available on the downstream mechanistic actions of miR-29c, which may fuel the in vitro and in vivo studies of pancreatic cancer. METHODS The downstream target gene of miR-29c and the downstream ERK/MAPK pathway involved in pancreatic cancer were predicted by bioinformatics tools. Next, the expression of miR-29c and MAPK1 was determined in pancreatic cancer tissues and cells. After ectopic expression and depletion experiments in pancreatic cancer cells, oncogenic phenotypes of pancreatic cancer cells were tested by MTS assay, Transwell assay, and flow cytometry. Effects of miR-29c/MAPK1 on tumorigenic ability in vivo were evaluated in pancreatic cancer xenografts in nude mice. RESULTS Through differential analysis, five pancreatic cancer-related miRNAs (hsa-miR-29c, hsa-miR-107, hsa-miR-324-3p, hsa-miR-375, and hsa-miR-210) were screened out, among which miR-29c was selected as the key miRNA related to prognosis of pancreatic cancer patients. miR-29c could target and inhibit MAPK1 to suppress the activation of ERK/MAPK pathway. miR-29c was downregulated in pancreatic cancer, and its high expression was related to the good prognosis of pancreatic cancer patients. Both in vitro and in vivo experiments demonstrated that restoration of miR-29c inhibited oncogenic phenotypes of pancreatic cancer cells, as well as repressed tumorigenic ability of pancreatic cancer cells in nude mice. CONCLUSIONS Taken together, we unveil a novel miR-29c/MAPK1/ERK/MAPK axis that suppresses pancreatic cancer both in vitro and in vivo.
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Affiliation(s)
- Hongtao Si
- Department of Oncology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People's Republic of China
| | - Ning Zhang
- Department of Oncology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People's Republic of China
| | - Chang Shi
- Department of Oncology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People's Republic of China
| | - Zhanjiang Luo
- The Seventh Hospital of Handan, Handan, 056005, People's Republic of China
| | - Senlin Hou
- Ninth Department of General Surgery, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang, 050000, People's Republic of China.
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10
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Secchi M, Lodola C, Garbelli A, Bione S, Maga G. DEAD-Box RNA Helicases DDX3X and DDX5 as Oncogenes or Oncosuppressors: A Network Perspective. Cancers (Basel) 2022; 14:cancers14153820. [PMID: 35954483 PMCID: PMC9367324 DOI: 10.3390/cancers14153820] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The transformation of a normal cell into a cancerous one is caused by the deregulation of different metabolic pathways, involving a complex network of protein–protein interactions. The cellular enzymes DDX3X and DDX5 play important roles in the maintenance of normal cell metabolism, but their deregulation can accelerate tumor transformation. Both DDX3X and DDX5 interact with hundreds of different cellular proteins, and depending on the specific pathways in which they are involved, both proteins can either act as suppressors of cancer or as oncogenes. In this review, we summarize the current knowledge about the roles of DDX3X and DDX5 in different tumors. In addition, we present a list of interacting proteins and discuss the possible contribution of some of these protein–protein interactions in determining the roles of DDX3X and DDX5 in the process of cancer proliferation, also suggesting novel hypotheses for future studies. Abstract RNA helicases of the DEAD-box family are involved in several metabolic pathways, from transcription and translation to cell proliferation, innate immunity and stress response. Given their multiple roles, it is not surprising that their deregulation or mutation is linked to different pathological conditions, including cancer. However, while in some cases the loss of function of a given DEAD-box helicase promotes tumor transformation, indicating an oncosuppressive role, in other contexts the overexpression of the same enzyme favors cancer progression, thus acting as a typical oncogene. The roles of two well-characterized members of this family, DDX3X and DDX5, as both oncogenes and oncosuppressors have been documented in several cancer types. Understanding the interplay of the different cellular contexts, as defined by the molecular interaction networks of DDX3X and DDX5 in different tumors, with the cancer-specific roles played by these proteins could help to explain their apparently conflicting roles as cancer drivers or suppressors.
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11
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Matuszyk J. MALAT1-miRNAs network regulate thymidylate synthase and affect 5FU-based chemotherapy. Mol Med 2022; 28:89. [PMID: 35922756 PMCID: PMC9351108 DOI: 10.1186/s10020-022-00516-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022] Open
Abstract
Background The active metabolite of 5-Fluorouracil (5FU), used in the treatment of several types of cancer, acts by inhibiting the thymidylate synthase encoded by the TYMS gene, which catalyzes the rate-limiting step in DNA replication. The major failure of 5FU-based cancer therapy is the development of drug resistance. High levels of TYMS-encoded protein in cancerous tissues are predictive of poor response to 5FU treatment. Expression of TYMS is regulated by various mechanisms, including involving non-coding RNAs, both miRNAs and long non-coding RNAs (lncRNAs). Aim To delineate the miRNAs and lncRNAs network regulating the level of TYMS-encoded protein. Main body Several miRNAs targeting TYMS mRNA have been identified in colon cancers, the levels of which can be regulated to varying degrees by lncRNAs. Due to their regulation by the MALAT1 lncRNA, these miRNAs can be divided into three groups: (1) miR-197-3p, miR-203a-3p, miR-375-3p which are downregulated by MALAT1 as confirmed experimentally and the levels of these miRNAs are actually reduced in colon and gastric cancers; (2) miR-140-3p, miR-330-3p that could potentially interact with MALAT1, but not yet supported by experimental results; (3) miR-192-5p, miR-215-5p whose seed sequences do not recognize complementary response elements within MALAT1. Considering the putative MALAT1-miRNAs interaction network, attention is drawn to the potential positive feedback loop causing increased expression of MALAT1 in colon cancer and hepatocellular carcinoma, where YAP1 acts as a transcriptional co-factor which, by binding to the TCF4 transcription factor/ β-catenin complex, may increase the activation of the MALAT1 gene whereas the MALAT1 lncRNA can inhibit miR-375-3p which in turn targets YAP1 mRNA. Conclusion The network of non-coding RNAs may reduce the sensitivity of cancer cells to 5FU treatment by upregulating the level of thymidylate synthase.
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Affiliation(s)
- Janusz Matuszyk
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigla Street, 53-114, Wroclaw, Poland.
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12
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Sobolewski C, Dubuquoy L, Legrand N. MicroRNAs, Tristetraprolin Family Members and HuR: A Complex Interplay Controlling Cancer-Related Processes. Cancers (Basel) 2022; 14:cancers14143516. [PMID: 35884580 PMCID: PMC9319505 DOI: 10.3390/cancers14143516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary AU-rich Element Binding Proteins (AUBPs) represent important post-transcriptional regulators of gene expression by regulating mRNA decay and/or translation. Importantly, AUBPs can interfere with microRNA-dependent regulation by (i) competing with the same binding sites on mRNA targets, (ii) sequestering miRNAs, thereby preventing their binding to their specific targets or (iii) promoting miRNA-dependent regulation. These data highlight a new paradigm where both miRNA and RNA binding proteins form a complex regulatory network involved in physiological and pathological processes. However, this interplay is still poorly considered, and our current models do not integrate this level of complexity, thus potentially giving misleading interpretations regarding the role of these regulators in human cancers. This review summarizes the current knowledge regarding the crosstalks existing between HuR, tristetraprolin family members and microRNA-dependent regulation. Abstract MicroRNAs represent the most characterized post-transcriptional regulators of gene expression. Their altered expression importantly contributes to the development of a wide range of metabolic and inflammatory diseases but also cancers. Accordingly, a myriad of studies has suggested novel therapeutic approaches aiming at inhibiting or restoring the expression of miRNAs in human diseases. However, the influence of other trans-acting factors, such as long-noncoding RNAs or RNA-Binding-Proteins, which compete, interfere, or cooperate with miRNAs-dependent functions, indicate that this regulatory mechanism is much more complex than initially thought, thus questioning the current models considering individuals regulators. In this review, we discuss the interplay existing between miRNAs and the AU-Rich Element Binding Proteins (AUBPs), HuR and tristetraprolin family members (TTP, BRF1 and BRF2), which importantly control the fate of mRNA and whose alterations have also been associated with the development of a wide range of chronic disorders and cancers. Deciphering the interplay between these proteins and miRNAs represents an important challenge to fully characterize the post-transcriptional regulation of pro-tumorigenic processes and design new and efficient therapeutic approaches.
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13
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Zhou M, Li J, Chen C. High expression of ZFP36L2 correlates with the prognosis and immune infiltration in lower-grade glioma. Front Genet 2022; 13:914219. [PMID: 35910229 PMCID: PMC9334557 DOI: 10.3389/fgene.2022.914219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The ZFP36 Ring Finger Protein Like 2 (ZFP36L2) is an RNA-binding protein that regulates gene expression at post-transcriptional level. However, the clinical significance and prognostic value of ZFP36L2 in lower-grade glioma (LGG) remain unclear. Method: ZFP36L2 expression was investigated using public datasets and the prognostic merit of ZFP36L2 with LGG patients was further evaluated. The correlation between the genetic alteration of ZFP36L2 and its mRNA expression was accessed via cBioPortal. Additionally, the prognostic value of the ZFP36L2 methylation levels in LGG was evaluated by MethSurv. The potential biological role of ZFP36L2 in LGG was identified by performing functional analyses. We also examined the correlation between ZFP36L2 expression and the immune infiltration. Finally, the predictive value of ZFP36L2 to immunotherapy was assessed. Result: ZFP36L2 was highly expressed in LGG patients and overexpressed ZFP36L2 predicted poor clinical outcomes. We further identified ZFP36L2 as an independent prognostic factor. The methylation level of ZFP36L2 negatively correlated with the ZFP36L2 expression, and patients with low ZFP36L2 methylation had worse overall survival. The results of functional analysis indicated that ZFP36L2 was involved in multiple immune response-related pathways in LGG. Furthermore, high expression of ZFP36L2 was significantly and positively correlated with immune infiltration. Finally, we found that ZFP36L2 expression was positively correlated with the immune checkpoint PD-L1, and ZFP36L2 low expression cohort gained better benefit from immunotherapy. Conclusion: Our findings demonstrate that ZFP36L2 is a potential biomarker for LGG, highlighting its potential as a therapeutic target in immunotherapy.
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Affiliation(s)
- Min Zhou
- College of Medicine, Wuhan University of Science and Technology, Wuhan, China
- *Correspondence: Min Zhou, ; Cheng Chen,
| | - Jinquan Li
- College of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Cheng Chen
- Wuhan Asia Heart Hospital, Wuhan, China
- *Correspondence: Min Zhou, ; Cheng Chen,
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14
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Song X, He H, Zhang Y, Fan J, Wang L. Mechanisms of action of triptolide against colorectal cancer: insights from proteomic and phosphoproteomic analyses. Aging (Albany NY) 2022; 14:3084-3104. [PMID: 35366242 PMCID: PMC9037262 DOI: 10.18632/aging.203992] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/26/2022] [Indexed: 12/09/2022]
Abstract
Triptolide is a potent anti-inflammatory agent that also possesses anticancer activity, including against colorectal cancer (CRC), one of the most frequent cancers around the world. In order to clarify how triptolide may be effective against CRC, we analyzed the proteome and phosphoproteome of CRC cell line HCT116 after incubation for 48 h with the drug (40 nM) or vehicle. Tandem mass tagging led to the identification of 403 proteins whose levels increased and 559 whose levels decreased in the presence of triptolide. We also identified 3,110 sites in proteins that were phosphorylated at higher levels and 3,161 sites phosphorylated at lower levels in the presence of the drug. Analysis of these differentially expressed and/or phosphorylated proteins showed that they were enriched in pathways involving ribosome biogenesis, PI3K−Akt signaling, MAPK signaling, nucleic acid binding as well as other pathways. Protein–protein interactions were explored using the STRING database, and we identified nine protein modules and 15 hub proteins. Finally, we identified 57 motifs using motif analysis of phosphosites and found 16 motifs were experimentally verified for known protein kinases, while 41 appear to be novel. These findings may help clarify how triptolide works against CRC and may guide the development of novel treatments.
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Affiliation(s)
- Xinqiang Song
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China.,College of Medicine, Xinyang Normal University, Xinyang 464000, China
| | - Huanhuan He
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Yu Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Jinke Fan
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Lei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
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15
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Peerapen P, Sueksakit K, Boonmark W, Yoodee S, Thongboonkerd V. ARID1A knockdown enhances carcinogenesis features and aggressiveness of Caco-2 colon cancer cells: An in vitro cellular mechanism study. J Cancer 2022; 13:373-384. [PMID: 35069887 PMCID: PMC8771531 DOI: 10.7150/jca.65511] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/30/2021] [Indexed: 01/05/2023] Open
Abstract
Loss of ARID1A, a tumor suppressor gene, is associated with the higher grade of colorectal cancer (CRC). However, molecular and cellular mechanisms underlying the progression and aggressiveness of CRC induced by the loss of ARID1A remain poorly understood. Herein, we evaluated cellular mechanisms underlying the effects of ARID1A knockdown on the carcinogenesis features and aggressiveness of CRC cells. A human CRC cell line (Caco-2) was transfected with small interfering RNA (siRNA) specific to ARID1A (siARID1A) or scrambled (non-specific) siRNA (siControl). Cell death, proliferation, senescence, chemoresistance and invasion were then evaluated. In addition, formation of polyploid giant cancer cells (PGCCs), self-aggregation (multicellular spheroid) and secretion of an angiogenic factor, vascular endothelial growth factor (VEGF), were examined. The results showed that ARID1A knockdown led to significant decreases in cell death and senescence. On the other hand, ARID1A knockdown enhanced cell proliferation, chemoresistance and invasion. The siARID1A-transfected cells also had greater number of PGCCs and larger spheroid size and secreted greater level of VEGF compared with the siControl-transfected cells. These data, at least in part, explain the cellular mechanisms of ARID1A deficiency in carcinogenesis and aggressiveness features of CRC.
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Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Kanyarat Sueksakit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanida Boonmark
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sunisa Yoodee
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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16
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AU-Rich Element RNA Binding Proteins: At the Crossroads of Post-Transcriptional Regulation and Genome Integrity. Int J Mol Sci 2021; 23:ijms23010096. [PMID: 35008519 PMCID: PMC8744917 DOI: 10.3390/ijms23010096] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 12/14/2022] Open
Abstract
Genome integrity must be tightly preserved to ensure cellular survival and to deter the genesis of disease. Endogenous and exogenous stressors that impose threats to genomic stability through DNA damage are counteracted by a tightly regulated DNA damage response (DDR). RNA binding proteins (RBPs) are emerging as regulators and mediators of diverse biological processes. Specifically, RBPs that bind to adenine uridine (AU)-rich elements (AREs) in the 3' untranslated region (UTR) of mRNAs (AU-RBPs) have emerged as key players in regulating the DDR and preserving genome integrity. Here we review eight established AU-RBPs (AUF1, HuR, KHSRP, TIA-1, TIAR, ZFP36, ZFP36L1, ZFP36L2) and their ability to maintain genome integrity through various interactions. We have reviewed canonical roles of AU-RBPs in regulating the fate of mRNA transcripts encoding DDR genes at multiple post-transcriptional levels. We have also attempted to shed light on non-canonical roles of AU-RBPs exploring their post-translational modifications (PTMs) and sub-cellular localization in response to genotoxic stresses by various factors involved in DDR and genome maintenance. Dysfunctional AU-RBPs have been increasingly found to be associated with many human cancers. Further understanding of the roles of AU-RBPS in maintaining genomic integrity may uncover novel therapeutic strategies for cancer.
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17
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Wyżewski Z, Gradowski M, Krysińska M, Dudkiewicz M, Pawłowski K. A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution. PeerJ 2021; 9:e11051. [PMID: 33854844 PMCID: PMC7955679 DOI: 10.7717/peerj.11051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/11/2021] [Indexed: 01/12/2023] Open
Abstract
The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers full understanding of the functioning of the living cells. ADP-ribosylation is a common post-translational modification of proteins; also nucleic acids and small molecules can be modified by the covalent attachment of ADP-ribose. This modification, important in cellular signalling and infection processes, is usually executed by enzymes from the large superfamily of ADP-ribosyltransferases (ARTs). Here, using bioinformatics approaches, we identify a novel putative ADP-ribosyltransferase family, conserved in eukaryotic evolution, with a divergent active site. The hallmark of these proteins is the ART domain nestled between flanking leucine-rich repeat (LRR) domains. LRRs are typically involved in innate immune surveillance. The novel family appears as putative novel ADP-ribosylation-related actors, most likely pseudoenzymes. Sequence divergence and lack of clearly detectable “classical” ART active site suggests the novel domains are pseudoARTs, yet atypical ART activity, or alternative enzymatic activity cannot be excluded. We propose that this family, including its human member LRRC9, may be involved in an ancient defense mechanism, with analogies to the innate immune system, and coupling pathogen detection to ADP-ribosyltransfer or other signalling mechanisms.
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Affiliation(s)
- Zbigniew Wyżewski
- Institute of Biological Sciences, Cardinal Stefan Wyszynski University in Warsaw, Warszawa, Poland
| | - Marcin Gradowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Marianna Krysińska
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Translational Medicine, Lund University, Lund, Sweden
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18
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Che Mat MF, Mohamad Hanif EA, Abdul Murad NA, Ibrahim K, Harun R, Jamal R. Silencing of ZFP36L2 increases sensitivity to temozolomide through G2/M cell cycle arrest and BAX mediated apoptosis in GBM cells. Mol Biol Rep 2021; 48:1493-1503. [PMID: 33590411 DOI: 10.1007/s11033-021-06144-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Despite the advancements in primary brain tumour diagnoses and treatments, the mortality rate remains high, particularly in glioblastoma (GBM). Chemoresistance, predominantly in recurrent cases, results in decreased mean survival of patients with GBM. We aimed to determine the chemosensitisation and oncogenic characteristics of zinc finger protein 36-like 2 (ZFP36L2) in LN18 GBM cells via RNA interference (RNAi) delivery. We conducted a meta-analysis of microarray datasets and RNAi screening using pooled small interference RNA (siRNA) to identify the druggable genes responsive to GBM chemosensitivity. Temozolomide-resistant LN18 cells were used to evaluate the effects of gene silencing on chemosensitisation to the sub-lethal dose (1/10 of the median inhibitory concentration [IC50]) of temozolomide. ZFP36L2 protein expression was detected by western blotting. Cell viability, proliferation, cell cycle and apoptosis assays were carried out using commercial kits. A human apoptosis array kit was used to determine the apoptosis pathway underlying chemosensitisation by siRNA against ZFP36L2 (siZFP36L2). Statistical analyses were performed using one-way analysis of variance; p > 0.05 was considered significant. The meta-analysis and RNAi screening identified ZFP36L2 as a potential marker of GBM. ZFP36L2 knockdown significantly induced apoptosis (p < 0.05). Moreover, ZFP36L2 inhibition led to increased cell cycle arrest and decreased cell proliferation. Downstream analysis showed that the sub-lethal dose of temozolomide and siZFP26L2 caused major upregulation of BCL2-associated X, apoptosis regulator (BAX). ZFP36L2 has oncogenic and chemosensitive characteristics and may play an important role in gliomagenesis through cell proliferation, cell cycle arrest and apoptosis. This suggests that RNAi combined with chemotherapy treatment such as temozolomide may be a potential GBM therapeutic intervention in the future.
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Affiliation(s)
- Mohd Firdaus Che Mat
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Ezanee Azlina Mohamad Hanif
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Nor Azian Abdul Murad
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Kamariah Ibrahim
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Roslan Harun
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia.
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia.
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19
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Xing Q, Liu S, Jiang S, Li T, Wang Z, Wang Y. Prognostic model of 10 immune-related genes and identification of small molecule drugs in bladder urothelial carcinoma (BLCA). Transl Androl Urol 2020; 9:2054-2070. [PMID: 33209669 PMCID: PMC7658175 DOI: 10.21037/tau-20-696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background We aimed to establish an immune-related gene (IRG) based signature that could provide guidance for clinical bladder cancer (BC) prognostic surveillance. Methods Differentially expressed IRGs and transcription factors (TFs) between BCs and normal tissues were extracted from transcriptome data downloaded from the TCGA database. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out to identify related pathways based on differently expressed IRGs. Then, univariate Cox regression analysis was performed to investigate IRGs with prognostic values and LASSO penalized Cox regression analysis was utilized to develop the prognostic index (PI) model. Results A total of 411 BC tissue samples and 19 normal bladder tissues in the TCGA database were enrolled in this study and 259 differentially expressed IRGs were identified. Networks between TFs and IRGs were also provided to seek the upstream regulators of differentially expressed IRGs. By means of univariate Cox regression analysis, 57 IRGs were analyzed with prognostic values and 10 IRGs were finally identified by LASSO penalized Cox regression analysis to construct the PI model. This model could significantly classified BC patients into high-risk group and low-risk group in terms of OS (P=9.923e-07) and its AUC reached 0.711. By means of univariate and multivariate COX regression analysis, this PI was proven to be a valuable independent prognostic factor (HR =1.119, 95% CI =1.066-1.175, P<0.001). CMap database analysis was also utilized to screen out 10 small molecules drugs with the potential for the treatment of BC. Conclusions Our study successfully provided a novel PI based on IRGs with the potential to predict the prognosis of BC and screened out 10 small molecules drugs with the potential to treat BC. Besides, networks between TFs and IRGs were also displayed to seek its upstream regulators for future researches.
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Affiliation(s)
- Qianwei Xing
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shouyong Liu
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Silin Jiang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tao Li
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Zengjun Wang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi Wang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, China
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20
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Zhao Q, Liu Y, Wang T, Yang Y, Ni H, Liu H, Guo Q, Xi T, Zheng L. MiR-375 inhibits the stemness of breast cancer cells by blocking the JAK2/STAT3 signaling. Eur J Pharmacol 2020; 884:173359. [PMID: 32738343 DOI: 10.1016/j.ejphar.2020.173359] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/04/2020] [Accepted: 07/08/2020] [Indexed: 12/17/2022]
Abstract
The relapse of breast cancer could be due to the existence of breast cancer stem cells (BCSCs). Other and our researches have indicated the suppressive roles of miR-375 in various tumors, however, its roles in breast cancer stemness remain confusing. Here, we constructed breast cancer cells with miR-375 stable overexpression via lentivirus infection. Flow cytometry, Western blot, mammosphere formation, cell colony formation and CCK8 as well as in vivo assays were performed to identify the role of miR-375 in the stemness of breast cancer cells. Luciferase reporter, RNA-Fluorescence in situ hybridization (RNA-FISH) and RNA-binding protein immunoprecipitation (RIP) assays were utilized to elucidate the mechanism whereby miR-375 exerts its effects. It was found that miR-375 not only reduced the stemness, but also decreased adriamycin resistance of breast cancer cells. These results were characterized by the decrease of BCSC rate, mammosphere-forming and tumor-initiating ability, and IC50 value of adriamycin, and weakened by JAK2 re-expression. This work indicates that miR-375 suppresses the stemness of breast cancer cells through targeting JAK2.
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Affiliation(s)
- Qiong Zhao
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Longmian Road 639, Nanjing, 211198, PR China
| | - Yichen Liu
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Longmian Road 639, Nanjing, 211198, PR China
| | - Ting Wang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Longmian Road 639, Nanjing, 211198, PR China
| | - Yue Yang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Longmian Road 639, Nanjing, 211198, PR China
| | - Haiwei Ni
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Longmian Road 639, Nanjing, 211198, PR China
| | - Hai Liu
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Longmian Road 639, Nanjing, 211198, PR China
| | - Qianqian Guo
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450003, PR China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Longmian Road 639, Nanjing, 211198, PR China.
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Longmian Road 639, Nanjing, 211198, PR China.
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21
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The Tristetraprolin Family of RNA-Binding Proteins in Cancer: Progress and Future Prospects. Cancers (Basel) 2020; 12:cancers12061539. [PMID: 32545247 PMCID: PMC7352335 DOI: 10.3390/cancers12061539] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays a key role in cellular proliferation, differentiation, migration, and apoptosis. Increasing evidence suggests dysregulated post-transcriptional gene expression as an important mechanism in the pathogenesis of cancer. The tristetraprolin family of RNA-binding proteins (RBPs), which include Zinc Finger Protein 36 (ZFP36; commonly referred to as tristetraprolin (TTP)), Zinc Finger Protein 36 like 1 (ZFP36L1), and Zinc Finger Protein 36 like 2 (ZFP36L2), play key roles in the post-transcriptional regulation of gene expression. Mechanistically, these proteins function by binding to the AU-rich elements within the 3′-untranslated regions of their target mRNAs and, in turn, increasing mRNA turnover. The TTP family RBPs are emerging as key regulators of multiple biological processes relevant to cancer and are aberrantly expressed in numerous human cancers. The TTP family RBPs have tumor-suppressive properties and are also associated with cancer prognosis, metastasis, and resistance to chemotherapy. Herein, we summarize the various hallmark molecular traits of cancers that are reported to be regulated by the TTP family RBPs. We emphasize the role of the TTP family RBPs in the regulation of trait-associated mRNA targets in relevant cancer types/cell lines. Finally, we highlight the potential of the TTP family RBPs as prognostic indicators and discuss the possibility of targeting these TTP family RBPs for therapeutic benefits.
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22
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Chen R, Sugiyama A, Kataoka N, Sugimoto M, Yokoyama S, Fukuda A, Takaishi S, Seno H. Promoter-Level Transcriptome Identifies Stemness Associated With Relatively High Proliferation in Pancreatic Cancer Cells. Front Oncol 2020; 10:316. [PMID: 32266133 PMCID: PMC7099289 DOI: 10.3389/fonc.2020.00316] [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: 11/02/2019] [Accepted: 02/21/2020] [Indexed: 11/13/2022] Open
Abstract
Both pancreatic intraepithelial neoplasia (PanIN), a frequent precursor of pancreatic cancer, and intraductal papillary mucinous neoplasm (IPMN), a less common precursor, undergo several phases of molecular conversions and finally develop into highly malignant solid tumors with negative effects on the quality of life. We approached this long-standing issue by examining the following PanIN/IPMN cell lines derived from mouse models of pancreatic cancer: Ptf1a-Cre; KrasG12D; p53f/+ and Ptf1a-Cre; KrasG12D; and Brg1f/f pancreatic ductal adenocarcinomas (PDAs). The mRNA from these cells was subjected to a cap analysis of gene expression (CAGE) to map the transcription starting sites and quantify the expression of promoters across the genome. Two RNA samples extracted from three individual subcutaneous tumors generated by the transplantation of PanIN or IPMN cancer cell lines were used to generate libraries and Illumina Seq, with four RNA samples in total, to depict discrete transcriptional network between IPMN and PanIN. Moreover, in IPMN cells, the transcriptome tended to be enriched for suppressive and inhibitory biological processes. In contrast, the transcriptome of PanIN cells exhibited properties of stemness. Notably, the proliferation capacity of the latter cells in culture was only minimally constrained by well-known chemotherapy drugs such as GSK690693 and gemcitabine. The various transcriptional factor network systems detected in PanIN and IPMN cells reflect the distinct molecular profiles of these cell types. Further, we hope that these findings will enhance our mechanistic understanding of the characteristic molecular alterations underlying pancreatic cancer precursors. These data may provide a promising direction for therapeutic research.
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Affiliation(s)
- Ru Chen
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aiko Sugiyama
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoyuki Kataoka
- Laboratory of Cell Regulation, Department of Applied Animal Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies Health Promotion and Preemptive Medicine, Tokyo Medical University, Tokyo, Japan
| | - Shoko Yokoyama
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihisa Fukuda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigeo Takaishi
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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23
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Gong R, Jiang Y. Non-coding RNAs in Pancreatic Ductal Adenocarcinoma. Front Oncol 2020; 10:309. [PMID: 32257946 PMCID: PMC7089935 DOI: 10.3389/fonc.2020.00309] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/20/2020] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are reported to be expressed in human cancers, including pancreatic ductal adenocarcinoma (PDAC). These ncRNAs affect the growth, migration and invasion of tumor cells by regulating cell cycle and apoptosis, as well as playing important roles in epigenetic processes, transcription and post-transcriptional regulation. It is still unclear whether alterations in ncRNAs influence PDAC development and progression. Because of this, analysis based on existing data on ncRNAs, which are crucial for modulating pancreatic tumorigenesis, will be important for future research on PDAC. Here, we summarize ncRNAs with tumor-promoting functions: HOTAIR, HOTTIP, MALAT1, lncRNA H19, lncRNA PVT1, circ-RNA ciRS-7, circ-0030235, circ-RNA_100782, circ-LDLRAD3, circ-0007534, circRHOT1, circZMYM2, circ-IARS, circ-RNA PDE8A, miR-21, miR-155, miR-221/222, miR-196b, miR-10a. While others including GAS5, MEG3, and lncRNA ENST00000480739, has_circ_0001649, miR-34a, miR-100, miR-217, miR-143 inhibit the proliferation and invasion of PDAC. Hence, we summarize the functions of ncRNAs in the occurrence, development and metastasis of PDAC, with the goal to provide guidance in the clinical diagnosis and treatment of PDAC.
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Affiliation(s)
- Ruining Gong
- Department of Gastroenterology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yueping Jiang
- Department of Gastroenterology, Affiliated Hospital of Qingdao University, Qingdao, China
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24
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Sahin K, Orhan C, Ozercan IH, Tuzcu M, Elibol B, Sahin TK, Kilic U, Qazi S, Uckun FM. Chemopreventive efficacy of stampidine in a murine breast cancer model. Expert Opin Ther Targets 2020; 24:155-162. [PMID: 32005098 DOI: 10.1080/14728222.2020.1724961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background: The purpose of the present study was to examine the chemopreventive effect of stampidine, an aryl phosphate derivative of stavudine, in side by side comparison with the standard anti-breast cancer drug paclitaxel in the well-established 7,12-dimethylbenz(a)anthracene (DMBA)-induced murine breast cancer model.Methods: Groups of 20 female mice were challenged with the DMBA. DMBA-challenged mice were assigned to various chemoprevention treatments, including stampidine, paclitaxel, and stampidine plus paclitaxel according to the same treatment schedules for 25 weeks.Results: Stampidine resulted in substantially reduced numbers of tumors, tumor weight as well as tumor size in DMBA-treated mice. Stampidine was as effective as paclitaxel in the model and their combination exhibited greater chemopreventive activity, as measured by reduced tumor incidence and improved tumor-free survival as well as overall survival of DMBA-treated mice. The length of time for the initial tumor to appear in DMBA-challenged mice treated with stampidine was longer than that of mice treated DMBA-challenged control mice. Tumors from mice treated with stampidine or stampidine plus paclitaxel displayed unique changes of a signature protein cassette comprised BRCA1, p21, Bax, and Bcl-2.Conclusion: Stampidine has potent chemopreventive activity and is as effective as the standard chemotherapy drug paclitaxel in the chemical carcinogenesis.
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Affiliation(s)
- Kazim Sahin
- Department of Animal Nutrition, Faculty of Veterinary Medicine, Firat University, Elazig, Turkey
| | - Cemal Orhan
- Department of Animal Nutrition, Faculty of Veterinary Medicine, Firat University, Elazig, Turkey
| | | | - Mehmet Tuzcu
- Department of Molecular Biology, Faculty of Science, Firat University, Elazig, Turkey
| | - Birsen Elibol
- Department of Medical Biology, University of Bezmialem, School of Medicine, Istanbul, Turkey
| | - Taha Koray Sahin
- Department of Internal Medicine, University of Hacettepe School of Medicine, Ankara, Turkey
| | - Ulkan Kilic
- Department of Medical Biology, University of Health Sciences, School of Medicine, Istanbul, Turkey
| | - Sanjive Qazi
- Division of Hematology-Oncology, Department of Pediatrics, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine (USC KSOM), Los Angeles, CA, USA.,Department of Immuno-Oncology, Ares Pharmaceuticals, St. Paul, MN, USA.,Gustavus Adolphus College, St. Peter, MN, USA
| | - Fatih Mehmet Uckun
- Division of Hematology-Oncology, Department of Pediatrics, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine (USC KSOM), Los Angeles, CA, USA.,Department of Immuno-Oncology, Ares Pharmaceuticals, St. Paul, MN, USA
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25
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Reale E, Taverna D, Cantini L, Martignetti L, Osella M, De Pittà C, Virga F, Orso F, Caselle M. Investigating the epi-miRNome: identification of epi-miRNAs using transfection experiments. Epigenomics 2019; 11:1581-1599. [PMID: 31693439 DOI: 10.2217/epi-2019-0050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: Growing evidence shows a strong interplay between post-transcriptional regulation, mediated by miRNAs (miRs) and epigenetic regulation. Nevertheless, the number of experimentally validated miRs (called epi-miRs) involved in these regulatory circuitries is still very small. Material & methods: We propose a pipeline to prioritize candidate epi-miRs and to identify potential epigenetic interactors of any given miR starting from miR transfection experiment datasets. Results & conclusion: We identified 34 candidate epi-miRs: 19 of them are known epi-miRs, while 15 are new. Moreover, using an in-house generated gene expression dataset, we experimentally proved that a component of the polycomb-repressive complex 2, the histone methyltransferase enhancer of zeste homolog 2 (EZH2), interacts with miR-214, a well-known prometastatic miR in melanoma and breast cancer, highlighting a miR-214-EZH2 regulatory axis potentially relevant in tumor progression.
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Affiliation(s)
- Elisa Reale
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
| | - Daniela Taverna
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy.,Center for Complex Systems in Molecular Biology & Medicine, University of Torino, 10123, Torino, Italy
| | - Laura Cantini
- Institut Curie, PSL Research University, INSERM U900, Paris, France.,Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, 75005 Paris, France
| | | | - Matteo Osella
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
| | | | - Federico Virga
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy
| | - Francesca Orso
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy.,Center for Complex Systems in Molecular Biology & Medicine, University of Torino, 10123, Torino, Italy
| | - Michele Caselle
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
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26
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Tuerxun X, Abudumijiti H, Fen GC, Hasimu A. The functional role of RNF113A in cervical carcinogenesis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:3570-3582. [PMID: 31934207 PMCID: PMC6949850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
RNF113A is thought to function as an E3 ligase, engaged in the regulation of the turnover and activity of many target proteins. However, the fuctional role of RNF113A in cervical cancer remains unclear. In this study, by performing an immunohistochemistry (IHC) assay, we found that the RNF113A protein was significantly up-regulated in cervical cancer cells, and a high RNF113A expression was associated with malignant phenotypes. To determine the role of RNF113A in cervical cancer aggressiveness, we performed a gain and loss of functional experiments in cervical cancer cells with cell transfection, wound healing, transwell migration, and flow cytometry analysis. The results showed that RNF113A promotes the proliferation and survival ability of cervical cancer cells, enhances migration and invasion, and inhibits the apoptosis of cervical cancer cells. By silencing RNF113A in CSCC cell lines, we observed an up-regulation of the P53 protein level, indicating that P53 may function as a target of the RNF113A E3 ligase, and RNF113A may inhibit tumor cell apoptosis by degrading the TP53 protein.
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Affiliation(s)
- Xiayida Tuerxun
- Department of Pathology, College of Basic Medical Sciences, Xinjiang Medical UniversityUrumqi, Xinjiang Uyghur Autonomous Region, China
| | - Huerxidan Abudumijiti
- Department of Pathology, College of Basic Medical Sciences, Xinjiang Medical UniversityUrumqi, Xinjiang Uyghur Autonomous Region, China
| | - Guo Chun Fen
- Department of Gynecology in The First Affiliated Hospital, Medical University of XinjiangUrumqi, China
| | - Axiangu Hasimu
- Department of Pathology, College of Basic Medical Sciences, Xinjiang Medical UniversityUrumqi, Xinjiang Uyghur Autonomous Region, China
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27
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Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. Nat Commun 2019; 10:3107. [PMID: 31308362 PMCID: PMC6629701 DOI: 10.1038/s41467-019-10808-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/04/2019] [Indexed: 12/16/2022] Open
Abstract
Here we train cis-regulatory models of prostate tissue gene expression and impute expression transcriptome-wide for 233,955 European ancestry men (14,616 prostate cancer (PrCa) cases, 219,339 controls) from two large cohorts. Among 12,014 genes evaluated in the UK Biobank, we identify 38 associated with PrCa, many replicating in the Kaiser Permanente RPGEH. We report the association of elevated TMPRSS2 expression with increased PrCa risk (independent of a previously-reported risk variant) and with increased tumoral expression of the TMPRSS2:ERG fusion-oncogene in The Cancer Genome Atlas, suggesting a novel germline-somatic interaction mechanism. Three novel genes, HOXA4, KLK1, and TIMM23, additionally replicate in the RPGEH cohort. Furthermore, 4 genes, MSMB, NCOA4, PCAT1, and PPP1R14A, are associated with PrCa in a trans-ethnic meta-analysis (N = 9117). Many genes exhibit evidence for allele-specific transcriptional activation by PrCa master-regulators (including androgen receptor) in Position Weight Matrix, Chip-Seq, and Hi-C experimental data, suggesting common regulatory mechanisms for the associated genes.
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28
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Xing R, Zhou Y, Yu J, Yu Y, Nie Y, Luo W, Yang C, Xiong T, Wu WKK, Li Z, Bing Y, Lin S, Zhang Y, Hu Y, Li L, Han L, Yang C, Huang S, Huang S, Zhou R, Li J, Wu K, Fan D, Tang G, Dou J, Zhu Z, Ji J, Fang X, Lu Y. Whole-genome sequencing reveals novel tandem-duplication hotspots and a prognostic mutational signature in gastric cancer. Nat Commun 2019; 10:2037. [PMID: 31048690 PMCID: PMC6497673 DOI: 10.1038/s41467-019-09644-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/22/2019] [Indexed: 01/22/2023] Open
Abstract
Genome-wide analysis of genomic signatures might reveal novel mechanisms for gastric cancer (GC) tumorigenesis. Here, we analysis structural variations (SVs) and mutational signatures via whole-genome sequencing of 168 GCs. Our data demonstrates diverse models of complex SVs operative in GC, which lead to high-level amplification of oncogenes. We find varying proportion of tandem-duplications (TDs) among individuals and identify 24 TD hotspots involving well-established cancer genes such as CCND1, ERBB2 and MYC. Specifically, we nominate a novel hotspot involving the super-enhancer of ZFP36L2 presents in approximately 10% GCs from different cohorts, the oncogenic role of which is further confirmed by experimental data. In addition, our data reveal a mutational signature, specifically occurring in noncoding region, significantly enriched in tumors with cadherin 1 mutations, and associated with poor prognoses. Collectively, our data suggest that TDs might serve as an important mechanism for cancer gene activation and provide a novel signature for stratification. Structural variations in gastric cancer impact progression. Here, the authors perform whole-genome sequencing on 168 gastric cancer patients and identified tandem-duplications of super-enhancer ZFP36L2 in 10% of gastric cancer, and mutational signatures in tumors with cadherin 1 mutations that associated with poor prognoses.
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Affiliation(s)
- Rui Xing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China.
| | - Yong Zhou
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Shenzhen, 518000, China
| | - Yingyan Yu
- Department of Surgery, Rui-jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Wen Luo
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Chao Yang
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Teng Xiong
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - William K K Wu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Shenzhen, 518000, China
| | - Zhongwu Li
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yang Bing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Shuye Lin
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yaping Zhang
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yingqi Hu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Lin Li
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumours, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, 200025, Shanghai, China
| | - Lijuan Han
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Chen Yang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Shaogang Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Suiping Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Rui Zhou
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jing Li
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Guangbo Tang
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Jianhua Dou
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Zhenggang Zhu
- Department of Surgery, Rui-jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jiafu Ji
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China.
| | - Xiaodong Fang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China.
| | - Youyong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China. .,Department of Medical Oncology, Beijing Hospital, 100730, Beijing, China.
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29
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Fukuhisa H, Seki N, Idichi T, Kurahara H, Yamada Y, Toda H, Kita Y, Kawasaki Y, Tanoue K, Mataki Y, Maemura K, Natsugoe S. Gene regulation by antitumor miR-130b-5p in pancreatic ductal adenocarcinoma: the clinical significance of oncogenic EPS8. J Hum Genet 2019; 64:521-534. [DOI: 10.1038/s10038-019-0584-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 12/15/2022]
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30
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Khalid M, Idichi T, Seki N, Wada M, Yamada Y, Fukuhisa H, Toda H, Kita Y, Kawasaki Y, Tanoue K, Kurahara H, Mataki Y, Maemura K, Natsugoe S. Gene Regulation by Antitumor miR-204-5p in Pancreatic Ductal Adenocarcinoma: The Clinical Significance of Direct RACGAP1 Regulation. Cancers (Basel) 2019; 11:cancers11030327. [PMID: 30866526 PMCID: PMC6468488 DOI: 10.3390/cancers11030327] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 12/13/2022] Open
Abstract
Previously, we established a microRNA (miRNA) expression signature in pancreatic ductal adenocarcinoma (PDAC) tissues using RNA sequencing and found significantly reduced expression of miR-204-5p. Here, we aimed to investigate the functional significance of miR-204-5p and to identify miR-204-5p target genes involved in PDAC pathogenesis. Cancer cell migration and invasion were significantly inhibited by ectopic expression of miR-204-5p in PDAC cells. Comprehensive gene expression analyses and in silico database searches revealed 25 putative targets regulated by miR-204-5p in PDAC cells. Among these target genes, high expression levels of RACGAP1, DHRS9, AP1S3, FOXC1, PRP11, RHBDL2 and MUC4 were significant predictors of a poor prognosis of patients with PDAC. In this study, we focused on RACGAP1 (Rac guanosine triphosphatase-activating protein 1) because its expression was most significantly predictive of PDAC pathogenesis (overall survival rate: p = 0.0000548; disease-free survival rate: p = 0.0014). Overexpression of RACGAP1 was detected in PDAC clinical specimens, and its expression enhanced the migration and invasion of PDAC cells. Moreover, downstream genes affected by RACGAP1 (e.g., MMP28, CEP55, CDK1, ANLN and S100A14) are involved in PDAC pathogenesis. Our strategy to identify antitumor miRNAs and their target genes will help elucidate the molecular pathogenesis of PDAC.
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Affiliation(s)
- Muhammad Khalid
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan.
| | - Masumi Wada
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Yasutaka Yamada
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan.
| | - Haruhi Fukuhisa
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Hiroko Toda
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Yoshiaki Kita
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Yota Kawasaki
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Kiyonori Tanoue
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Yuko Mataki
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Kosei Maemura
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
| | - Shoji Natsugoe
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890-8580, Japan.
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Shimonosono M, Idichi T, Seki N, Yamada Y, Arai T, Arigami T, Sasaki K, Omoto I, Uchikado Y, Kita Y, Kurahara H, Maemura K, Natsugoe S. Molecular pathogenesis of esophageal squamous cell carcinoma: Identification of the antitumor effects of miR‑145‑3p on gene regulation. Int J Oncol 2018; 54:673-688. [PMID: 30535463 DOI: 10.3892/ijo.2018.4657] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/19/2018] [Indexed: 11/06/2022] Open
Abstract
Although miR‑145‑5p (the guide strand of the miR‑145 duplex) is established as a tumor suppressive microRNA (miRNA or miR), the functional significance of miR‑145‑3p (the passenger strand of the miR‑145 duplex) in cancer cells and its targets remains obscure. In our continuing analysis of esophageal squamous cell carcinoma (ESCC) pathogenesis, the aim of the present study was to identify important oncogenes and proteins that are controlled by miR‑145‑3p. Overexpression of miR‑145‑3p significantly reduced cancer cell proliferation, migration and invasive abilities, and further increased apoptotic abilities. In ESCC cells, 30 possible oncogenic targets were identified that might be regulated by miR‑145‑3p. Among these targets, dehydrogenase/reductase member 2 (DHRS2) and myosin IB (MYO1B) were focused on to investigate their functional roles in ESCC cells. DHRS2 and MYO1B were directly regulated by miR‑145‑3p in ESCC cells by dual luciferase reporter assays. Aberrantly expressed DHRS2 and MYOIB were detected in ESCC clinical specimens, and their overexpression enhanced cancer cell aggressiveness. Genes regulated by antitumor miR‑145‑3p were closely associated with the molecular pathogenesis of ESCC. The approach based on antitumor miRNAs may contribute to the understanding of ESCC molecular pathogenesis.
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Affiliation(s)
- Masataka Shimonosono
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260‑8670, Japan
| | - Yasutaka Yamada
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260‑8670, Japan
| | - Takayuki Arai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260‑8670, Japan
| | - Takaaki Arigami
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Ken Sasaki
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Itaru Omoto
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Yasuto Uchikado
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Yoshiaki Kita
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Kosei Maemura
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
| | - Shoji Natsugoe
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima 890‑8520, Japan
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Park SB, Chung CK, Gonzalez E, Yoo C. Causal Inference Network of Genes Related with Bone Metastasis of Breast Cancer and Osteoblasts Using Causal Bayesian Networks. J Bone Metab 2018; 25:251-266. [PMID: 30574470 PMCID: PMC6288606 DOI: 10.11005/jbm.2018.25.4.251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
Background The causal networks among genes that are commonly expressed in osteoblasts and during bone metastasis (BM) of breast cancer (BC) are not well understood. Here, we developed a machine learning method to obtain a plausible causal network of genes that are commonly expressed during BM and in osteoblasts in BC. Methods We selected BC genes that are commonly expressed during BM and in osteoblasts from the Gene Expression Omnibus database. Bayesian Network Inference with Java Objects (Banjo) was used to obtain the Bayesian network. Genes registered as BC related genes were included as candidate genes in the implementation of Banjo. Next, we obtained the Bayesian structure and assessed the prediction rate for BM, conditional independence among nodes, and causality among nodes. Furthermore, we reported the maximum relative risks (RRs) of combined gene expression of the genes in the model. Results We mechanistically identified 33 significantly related and plausibly involved genes in the development of BC BM. Further model evaluations showed that 16 genes were enough for a model to be statistically significant in terms of maximum likelihood of the causal Bayesian networks (CBNs) and for correct prediction of BM of BC. Maximum RRs of combined gene expression patterns showed that the expression levels of UBIAD1, HEBP1, BTNL8, TSPO, PSAT1, and ZFP36L2 significantly affected development of BM from BC. Conclusions The CBN structure can be used as a reasonable inference network for accurately predicting BM in BC.
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Affiliation(s)
- Sung Bae Park
- Department of Neurosurgery, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Chun Kee Chung
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Clinical Research Institute, Seoul, Korea
| | - Efrain Gonzalez
- Department of Biostatistics, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Changwon Yoo
- Department of Biostatistics, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
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Zeng JH, Liang XZ, Lan HH, Zhu X, Liang XY. The biological functions of target genes in pan-cancers and cell lines were predicted by miR-375 microarray data from GEO database and bioinformatics. PLoS One 2018; 13:e0206689. [PMID: 30379973 PMCID: PMC6209324 DOI: 10.1371/journal.pone.0206689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/17/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND MicroRNA is endogenous non-coding small RNA that negative regulate and control gene expression, and increasing evidence links microRNA to oncogenesis and the pathogenesis of cancer. The goal of this study was to explore the potential molecular mechanism of miR-375 in various cancers. METHODS MiR-375 overexpression in different tumor cell lines was probed with microarray data from Gene Expression Omnibus (GEO). The common target genes of miR-375 were obtained by Robust Rank Aggregation (RRA), and identified by miRWalk2.0 software for target gene prediction. Additionally, we directed in silico analysis including Protein-Protein Interactions (PPI) analysis, gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways annotations to provide a summary of the function of miR-375 in various carcinomas. Eventually, data was obtained from The Cancer Genome Atlas (TCGA) were utilized for a validation in 7 cancers. RESULTS The nine miR-375 related chips were acquired by the GEO data. The 5 down regulated genes came from 9 available microarray datasets, which overlapped with the potential target genes predicted by miRWalk2.0 software. The target genes were intensely enriched in amino acid biosynthetic and metabolic process from biological process (GO) and Cysteine and methionine metabolism (KEGG analysis). In view of these approaches, VASN, MAT2B, HERPUD1, TPAPPC6B and TAT are probably the most important miR-375 targets. In addition, miR-375 was negatively correlated with MAT2B, which was verified in 5 tumors of TCGA. CONCLUSION In summary, this study based on common target genes provides an innovative perspective for exploring the molecular mechanism of miR-375 in human tumors.
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Affiliation(s)
- Jiang-Hui Zeng
- Department of ClinicaHl Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People’s Hospital, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Xu-Zhi Liang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Hui-Hua Lan
- Department of Clinical Laboratory, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Xu Zhu
- Department of ClinicaHl Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People’s Hospital, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Xiu-Yun Liang
- Department of ClinicaHl Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People’s Hospital, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
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Lin DC, Dinh HQ, Xie JJ, Mayakonda A, Silva TC, Jiang YY, Ding LW, He JZ, Xu XE, Hao JJ, Wang MR, Li C, Xu LY, Li EM, Berman BP, Phillip Koeffler H. Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas. Gut 2018; 67:1769-1779. [PMID: 28860350 PMCID: PMC5980794 DOI: 10.1136/gutjnl-2017-314607] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Oesophageal squamous cell carcinoma (OSCC) and adenocarcinoma (OAC) are distinct cancers in terms of a number of clinical and epidemiological characteristics, complicating the design of clinical trials and biomarker developments. We analysed 1048 oesophageal tumour-germline pairs from both subtypes, to characterise their genomic features, and biological and clinical significance. DESIGN Previously exome-sequenced samples were re-analysed to identify significantly mutated genes (SMGs) and mutational signatures. The biological functions of novel SMGs were investigated using cell line and xenograft models. We further performed whole-genome bisulfite sequencing and chromatin immunoprecipitation (ChIP)-seq to characterise epigenetic alterations. RESULTS OSCC and OAC displayed nearly mutually exclusive sets of driver genes, indicating that they follow independent developmental paths. The combined sample size allowed the statistical identification of a number of novel subtype-specific SMGs, mutational signatures and prognostic biomarkers. Particularly, we identified a novel mutational signature similar to Catalogue Of Somatic Mutations In Cancer (COSMIC)signature 16, which has prognostic value in OSCC. Two newly discovered SMGs, CUL3 and ZFP36L2, were validated as important tumour-suppressors specific to the OSCC subtype. We further identified their additional loss-of-function mechanisms. CUL3 was homozygously deleted specifically in OSCC and other squamous cell cancers (SCCs). Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; DNA hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancer-associated SCC suppressor. CONCLUSIONS These data comprehensively contrast differences between OSCC and OAC at both genomic and epigenomic levels, and reveal novel molecular features for further delineating the pathophysiological mechanisms and treatment strategies for these cancers.
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Affiliation(s)
- De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Huy Q Dinh
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jian-Jun Xie
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tiago Chedraoui Silva
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jian-Zhong He
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Xiu-E Xu
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Jia-Jie Hao
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunquan Li
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Li-Yan Xu
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- National University Cancer Institute, National University Hospital Singapore, Singapore
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Involvement of anti-tumor miR-124-3p and its targets in the pathogenesis of pancreatic ductal adenocarcinoma: direct regulation of ITGA3 and ITGB1 by miR-124-3p. Oncotarget 2018; 9:28849-28865. [PMID: 29988949 PMCID: PMC6034741 DOI: 10.18632/oncotarget.25599] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 05/24/2018] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs (miRNAs) are unique in that a single miRNA molecule regulates a vast number of RNA transcripts. Thus, aberrantly expressed miRNAs disrupt tightly controlled RNA networks in cancer cells. Our functional screening showed that expression of miR-124-3p was downregulated in pancreatic ductal adenocarcinoma (PDAC) tissues. Here, we aimed to investigate the anti-tumor roles of miR-124-3p in PDAC cells and to identify miR-124-3p-mediated oncogenic signaling in this disease. Ectopic expression of miR-124-3p inhibited cancer cell migration and invasion in PDAC cells. Moreover, restoration of miR-124-3p suppressed oncogenic signaling, as demonstrated by reduced phosphorylation of focal adhesion kinase, AKT, and extracellular signal-regulated kinase, in PDAC cells. Our in silico database analyses and luciferase reporter assays showed that two cell-surface matrix receptors, integrin α3 (ITGA3) and integrin β1 (ITGB1), were directly regulated by miR-124-3p in PDAC cells. Overexpression of ITGA3 and ITGB1 was confirmed in PDAC clinical specimens. Interestingly, a large number of cohort analyses from TCGA database showed that high expressions of ITGA3 and ITGB1 were significantly associated with poor prognosis of patients with PDAC. Knockdown of ITGA3 and ITGB1 by siRNAs markedly suppressed the migration and invasion abilities of PDAC cells. Moreover, downstream oncogenic signaling was inhibited by ectopic expression of miR-124-3p or knockdown of the two integrins. The discovery of anti-tumor miRNAs and miRNA-mediated oncogenic signaling may provide novel therapeutic targets for the treatment of PDAC.
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Chen Z, Ma Y, Pan Y, Zhu H, Yu C, Sun C. MiR-1297 suppresses pancreatic cancer cell proliferation and metastasis by targeting MTDH. Mol Cell Probes 2018; 40:19-26. [PMID: 29908229 DOI: 10.1016/j.mcp.2018.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/25/2018] [Accepted: 06/11/2018] [Indexed: 12/17/2022]
Abstract
Dysregulation of miR-1297 has been detected in various human cancers, and miR-1297 can function as either an oncogene or tumor suppressor. However, the role of miR-1297 in pancreatic adenocarcinoma has not been previously reported. Here, we investigated miR-1297 expression in pancreatic cancer and the role it plays in the development and metastasis of pancreatic adenocarcinoma. In the present study, MiR-1297 and metadherin (MTDH) expression in pancreatic cancer tissue was detected using quantitative real-time PCR (qRT-PCR) and western blot methods. The CCK-8 assay and EdU incorporation assay were used to analyze the impact of miR-1297 and MTDH on cell proliferation. Flow cytometric and Hoechst 33342 staining methods were used to explore how miR-1297 and MTDH affect cell apoptosis. The Transwell assay and scratch wound healing assay were used to analyze cell migration and invasion capabilities. The dual-luciferase assay was used to confirm that miR-1297 targets MTDH. Here, we found that miR-1297 expression was decreased in pancreatic adenocarcinoma tissues, while MTDH expression was increased in those tissues. Furthermore, western blot and dual-luciferase assay results confirmed that MTDH was a direct target of miR-1297. Additionally, overexpression of miR-1297 or knockdown of MTDH suppressed BxPC-3 and PANC-1 cell proliferation, and upregulation of miR-1297 or suppression of MTDH promoted BxPC-3 and PANC-1 cell apoptosis. Finally, BxPC-3 and PANC-1 cell migration and invasion abilities were suppressed by either overexpression of miR-1297 or downregulation of MTHD. In conclusion, our results suggest that miR-1297 inhibits the growth and metastasis of pancreatic adenocarcinoma by downregulating MTDH expression, and the miR-1297/MTDH pathway is a potential target for treating pancreatic adenocarcinoma.
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Affiliation(s)
- Zili Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, 28 Guiyi Street, Yunyan District, Guiyang, 550004, Guizhou, China
| | - Yifei Ma
- Department of Otorhinolaryngology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi Street, Yunyan District, Guiyang, 550004, Guizhou, China
| | - Yaozhen Pan
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, 28 Guiyi Street, Yunyan District, Guiyang, 550004, Guizhou, China
| | - Haitao Zhu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, 28 Guiyi Street, Yunyan District, Guiyang, 550004, Guizhou, China
| | - Chao Yu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, 28 Guiyi Street, Yunyan District, Guiyang, 550004, Guizhou, China.
| | - Chengyi Sun
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, 28 Guiyi Street, Yunyan District, Guiyang, 550004, Guizhou, China.
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Idichi T, Seki N, Kurahara H, Fukuhisa H, Toda H, Shimonosono M, Okato A, Arai T, Kita Y, Mataki Y, Kijima Y, Maemura K, Natsugoe S. Molecular pathogenesis of pancreatic ductal adenocarcinoma: Impact of passenger strand of pre-miR-148a on gene regulation. Cancer Sci 2018; 109:2013-2026. [PMID: 29660218 PMCID: PMC5989856 DOI: 10.1111/cas.13610] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 01/05/2023] Open
Abstract
We previously used RNA sequencing to establish the microRNA (miRNA) expression signature of pancreatic ductal adenocarcinoma (PDAC). We found that both strands of pre-miR-148a (miR-148a-5p: the passenger strand and miR-148a-3p: the guide strand) were downregulated in cancer tissues. Ectopic expression of miR-148a-5p and miR-148a-3p significantly inhibited cancer cell migration and invasion, indicating that both strands of pre-miR-148a had tumor-suppressive roles in PDAC cells. In silico database and genome-wide gene expression analyses identified a total of 15 genes that were putative targets regulated by these miRNAs. High expression of miR-148a-5p targets (PHLDA2, LPCAT2 and AP1S3) and miR-148a-3p targets (SMA, ENDOD1 and UHMK1) was associated with poor prognosis of patients with PDAC. Moreover, knockdown of PHLDA2 expression inhibited cancer cell aggressiveness, suggesting PHLDA2 acted as an oncogene in PDAC cells. Involvement of the passenger strand of pre-miR-148a (miR-148-5p) is a new concept in cancer research. Novel approaches that identify tumor-suppressive miRNA regulatory networks in lethal PDAC might provide new prognostic markers and therapeutic targets for this disease.
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Affiliation(s)
- Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Haruhi Fukuhisa
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Hiroko Toda
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Masataka Shimonosono
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Atsushi Okato
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Takayuki Arai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yoshiaki Kita
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Yuko Mataki
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Yuko Kijima
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Kosei Maemura
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Shoji Natsugoe
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
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Wang L, Hou Z, Hasim A, Abuduerheman A, Zhang H, Niyaz M, Awut I, Upur H, Sheyhidin I. RNF113A promotes the proliferation, migration and invasion, and is associated with a poor prognosis of esophageal squamous cell carcinoma. Int J Oncol 2018; 52:861-871. [PMID: 29393393 DOI: 10.3892/ijo.2018.4253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/04/2017] [Indexed: 11/06/2022] Open
Abstract
Ring finger protein 113A (RNF113A) possesses a C3HC4 zinc finger domain and this domain is found in E3 ubiquitin ligase and is involved in tumorigenesis. To date, and at least to the best of our knowledge, there are no studies available which have investigated RNF113A in cancer. Thus, this study aimed to explore the role of RNF113A in the development of esophageal squamous cell carcinoma (ESCC). For this purpose, paraffin-embedded samples from 117 patients with ESCC were selected, as well as 41 pairs of fresh-frozen ESCC and adjacent normal tissue samples. RNF113A expression was examined by immunohistochemistry and reverse transcription-quantitative PCR (RT-qPCR). RNF113A was overexpressed or silenced in the EC9706 and Eca109 cells. The cells were examined for cell cycle progression, apoptosis, invasiveness and migration. Xenograft tumors were also created in mice using the Eca109 cells. Tumor differentiation (P=0.008) and T classification (P<0.001) were found to be significantly associated with RNF113A expression. No statistically significant association was observed between RNF113A expression and sex, age, histological type, tumor location and lymph node metastasis (N classification). Kaplan-Meier analysis revealed that the patients with ESCC with ahigh expression of RNF113A had a lower survival rate than those with a low expression (P=0.002). Multivariate analysis revealed that RNF113A expression (HR=2.406; 95% CI, 1.301-4.449, P=0.005) was independently associated with overall survival in patients with ESCC. The overexpression of RNF113A promoted proliferation, migration, and invasiveness of ESCC cell lines in vitro, and RNF113A silencing reversed these malignant behaviors. RNF113A knockdown inhibited tumor growth in vivo. Thus, these results indicate that RNF113A promotes the proliferation, migration and invasiveness of ESCC cell lines. RNF113A expression in ESCC is this associated with a poor prognosis of affected patients.
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Affiliation(s)
- Lei Wang
- Department of Thoracic Surgery, Τhe First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Zhichao Hou
- Department of Thoracic Surgery, Τhe First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Ayshamgul Hasim
- Department of Pathology, Medical University of Xinjiang, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Abulajiang Abuduerheman
- Department of Thoracic Surgery, Τhe First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Haiping Zhang
- Department of Thoracic Surgery, Τhe First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Madiniyat Niyaz
- Clinical Medical Research Institute, Τhe First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Idiris Awut
- Department of Thoracic Surgery, Τhe First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Halmurat Upur
- Department of Uyghur Medicine, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Ilyar Sheyhidin
- Department of Thoracic Surgery, Τhe First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
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Wever CM, Geoffrion D, Grande BM, Yu S, Alcaide M, Lemaire M, Riazalhosseini Y, Hébert J, Gavino C, Vinh DC, Petrogiannis-Haliotis T, Dmitrienko S, Mann KK, Morin RD, Johnson NA. The genomic landscape of two Burkitt lymphoma cases and derived cell lines: comparison between primary and relapse samples. Leuk Lymphoma 2018; 59:2159-2174. [PMID: 29295643 DOI: 10.1080/10428194.2017.1413186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Relapse occurs in 10-40% of Burkitt lymphoma (BL) patients that have completed intensive chemotherapy regimens and is typically fatal. While treatment-naive BL has been characterized, the genomic landscape of BL at the time of relapse (rBL) has never been reported. Here, we present a genomic characterization of two rBL patients. The diagnostic samples had mutations common in BL, including MYC and CCND3. Additional mutations were detected at relapse, affecting important pathways such as NFκB (IKBKB) and MEK/ERK (NRAS) signaling, glutamine metabolism (SIRT4), and RNA processing (ZFP36L2). Genes implicated in drug resistance were also mutated at relapse (TP53, BAX, ALDH3A1, APAF1, FANCI). This concurrent genomic profiling of samples obtained at diagnosis and relapse has revealed mutations not previously reported in this disease. The patient-derived cell lines will be made available and, along with their detailed genetics, will be a valuable resource to examine the role of specific mutations in therapeutic resistance.
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Affiliation(s)
- Claudia M Wever
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | | | - Bruno M Grande
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada.,d Genome Sciences Centre, BC Cancer Agency , Vancouver , Canada
| | - Stephen Yu
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada
| | - Miguel Alcaide
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada
| | - Maryse Lemaire
- b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | - Yasser Riazalhosseini
- e Department of Human Genetics , McGill University , Montreal , Canada.,f McGill University and Genome Quebec Innovation Centre , Montreal , Canada
| | - Josée Hébert
- g Department of Medicine, Faculty of Medicine , Université de Montréal , Montreal , Canada.,h Research Centre and Division of Hematology-Oncology Maisonneuve-Rosemont Hospital , The Québec Leukemia Cell Bank , Montreal , Canada
| | - Christina Gavino
- i Infectious Disease Susceptibility Program (Research Institute-McGill University Health Centre) , Montreal , Canada.,j Department of Medicine , Medical Microbiology and Human Genetics (McGill University Health Centre) , Montreal , Canada
| | - Donald C Vinh
- i Infectious Disease Susceptibility Program (Research Institute-McGill University Health Centre) , Montreal , Canada.,j Department of Medicine , Medical Microbiology and Human Genetics (McGill University Health Centre) , Montreal , Canada
| | | | | | - Koren K Mann
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | - Ryan D Morin
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada.,d Genome Sciences Centre, BC Cancer Agency , Vancouver , Canada
| | - Nathalie A Johnson
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
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40
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Shi L, Zhao SM, Luo Y, Zhang AW, Wei LH, Xie ZY, Li YY, Ma W. MiR-375: A prospective regulator in medullary thyroid cancer based on microarray data and bioinformatics analyses. Pathol Res Pract 2017; 213:1344-1354. [PMID: 29033189 DOI: 10.1016/j.prp.2017.09.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/17/2017] [Accepted: 09/20/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND This research aims to investigate the prospective molecular mechanism of miR-375 in Medullary Thyroid Cancer (MTC). MATERIAL AND METHODS The expression level of miR-375 in MTC was explored with microarray data from Gene Expression Omnibus (GEO). To gather the putative target genes of miR-375, we selected eligible datasets in GEO, in which antagomir-375 and premir-375 were transfected to provide the miR-375-related genes. Subsequently, we attained the intersection of the results of GEO microarray data and 12 online target genes prediction database as the prospective target genes. Furthermore, we conducted in silico analysis including gene ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways annotations and Protein-Protein Interactions (PPI) analysis to provide an overview of the function of miR-375 in MTC. Finally, data from The Cancer Genome Atlas (TCGA) and The Human Protein Atlas (THPA) were used for a validation. RESULTS Up-regulation could be confirmed with the data from GSE40807. GEO dataset GSE67742 provided 10,596 miR-375-related genes, while 12 online prediction databases showed that 3352 target genes appeared no less than four times. Finally, the intersection of the two groups of genes included 1132 prospective targets. In aspect of functional annotation, negative regulation of transcription from RNA polymerase II promoter (P=9.83E-06), golgi membrane (P=9.98E-05) and pathway of protein binding (P=3.63E-07) were highlighted as the most enriched terms with GO analysis. With regards to PPI network, 162 hub genes that interacted with no less than 10 other different genes was visualized, among which PI3K/Akt signaling pathway was the most enriched pathway as assessed by KEGG. Furthermore, two genes (JAK2 and NGFR) in PI3K/Akt signaling pathway showed down-regulated patterns in both mRNA and protein levels. CONCLUSION The higher expression level of miR-375 might play a pivotal role in the tumorigenesis of MTC via targeting multiple key pathways, especially PI3K/Akt pathway. However, the exact molecular mechanism of miR-375 needs to be verified with in-depth investigation in the future.
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Affiliation(s)
- Lin Shi
- Department of Pathology, Medical College, The Guangxi University of Science and Technology, China.
| | - Shi-Mei Zhao
- Department of Pathology, Medical College, The Guangxi University of Science and Technology, China
| | - Yu Luo
- Department of Pathology, Medical College, The Guangxi University of Science and Technology, China
| | - An-Wen Zhang
- Department of Pathology, Medical College, The Guangxi University of Science and Technology, China
| | - Li-Hua Wei
- Department of Pathology, Medical College, The Guangxi University of Science and Technology, China
| | - Zheng-Yi Xie
- Department of Pathology, Medical College, The Guangxi University of Science and Technology, China
| | - Yuan-Yuan Li
- Department of Pathology, Medical College, The Guangxi University of Science and Technology, China
| | - Wei Ma
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, China
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41
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Yonemori K, Seki N, Idichi T, Kurahara H, Osako Y, Koshizuka K, Arai T, Okato A, Kita Y, Arigami T, Mataki Y, Kijima Y, Maemura K, Natsugoe S. The microRNA expression signature of pancreatic ductal adenocarcinoma by RNA sequencing: anti-tumour functions of the microRNA-216 cluster. Oncotarget 2017; 8:70097-70115. [PMID: 29050264 PMCID: PMC5642539 DOI: 10.18632/oncotarget.19591] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/26/2017] [Indexed: 12/20/2022] Open
Abstract
We analysed the RNA sequence-based microRNA (miRNA) signature of pancreatic ductal adenocarcinoma (PDAC). Aberrantly expressed miRNAs were successfully identified in this signature. Using the PDAC signature, we focused on 4 clustered miRNAs, miR-216a-5p, miR-216a-3p, miR-216b-5p and miR-216b-3p on human chromosome 2p16.1. All members of the miR-216 cluster were significantly reduced in PDAC specimens. Ectopic expression of these miRNAs suppressed cancer cell aggressiveness, suggesting miR-216 cluster as anti-tumour miRNAs in PDAC cells. The impact of miR-216b-3p (passenger strand of pre-miR-216b) on cancer cells is still ambiguous. Forkhead box Q1 (FOXQ1) was directly regulated by miR-216b-3p and overexpression of FOXQ1 was confirmed in clinical specimens. High expression of FOXQ1 predicted a shorter survival of patients with PDAC by Kaplan–Meier analysis. Loss-of-function assays showed that cancer cell migration and invasion activities were significantly reduced by siFOXQ1 transfectants. We investigated pathways downstream from FOXQ1 by using genome-wide gene expression analysis. Identification of the miR-216-3p/FOXQ1-mediated network in PDAC should enhance understanding of PDAC aggressiveness at the molecular level.
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Affiliation(s)
- Keiichi Yonemori
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chuo-ku, Chiba 260-8670, Japan
| | - Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Yusaku Osako
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Keiichi Koshizuka
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chuo-ku, Chiba 260-8670, Japan
| | - Takayuki Arai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chuo-ku, Chiba 260-8670, Japan
| | - Atsushi Okato
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chuo-ku, Chiba 260-8670, Japan
| | - Yoshiaki Kita
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Takaaki Arigami
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Yuko Mataki
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Yuko Kijima
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Kosei Maemura
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
| | - Shoji Natsugoe
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Sakuragaoka, Kagoshima 890-8520, Japan
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42
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Idichi T, Seki N, Kurahara H, Yonemori K, Osako Y, Arai T, Okato A, Kita Y, Arigami T, Mataki Y, Kijima Y, Maemura K, Natsugoe S. Regulation of actin-binding protein ANLN by antitumor miR-217 inhibits cancer cell aggressiveness in pancreatic ductal adenocarcinoma. Oncotarget 2017; 8:53180-53193. [PMID: 28881803 PMCID: PMC5581102 DOI: 10.18632/oncotarget.18261] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/08/2017] [Indexed: 01/05/2023] Open
Abstract
Analysis of our microRNA (miRNA) expression signature of pancreatic ductal adenocarcinoma (PDAC) revealed that microRNA-217 (miR-217) was significantly reduced in cancer tissues. The aim of this study was to investigate the antitumor roles of miR-217 in PDAC cells and to identify miR-217-mediated molecular pathways involved in PDAC aggressiveness. The expression levels of miR-217 were significantly reduced in PDAC clinical specimens. Ectopic expression of miR-217 significantly suppressed cancer cell migration and invasion. Transcription of actin-binding protein Anillin (coded by ANLN) was detected by our in silico and gene expression analyses. Moreover, luciferase reporter assays showed that ANLN was a direct target of miR-217 in PDAC cells. Overexpression of ANLN was detected in PDAC clinical specimens by real-time PCR methods and immunohistochemistry. Interestingly, Kaplan-Meier survival curves showed that high expression of ANLN predicted shorter survival in patients with PDAC by TCGA database analysis. Silencing ANLN expression markedly inhibited cancer cell migration and invasion capabilities of PDAC cell lines. We further investigated ANLN-mediated downstream pathways in PDAC cells. "Focal adhesion" and "Regulation of actin binding protein" were identified as ANLN-modulated downstream pathways in PDAC cells. Identification of antitumor miR-217/ANLN-mediated PDAC pathways will provide new insights into the potential mechanisms underlying the aggressive course of PDAC.
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Affiliation(s)
- Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Keiichi Yonemori
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Yusaku Osako
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Takayuki Arai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Atsushi Okato
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yoshiaki Kita
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Takaaki Arigami
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Yuko Mataki
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Yuko Kijima
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Kosei Maemura
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Shoji Natsugoe
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
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43
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Yonemori K, Seki N, Kurahara H, Osako Y, Idichi T, Arai T, Koshizuka K, Kita Y, Maemura K, Natsugoe S. ZFP36L2 promotes cancer cell aggressiveness and is regulated by antitumor microRNA-375 in pancreatic ductal adenocarcinoma. Cancer Sci 2017; 108:124-135. [PMID: 27862697 PMCID: PMC5276842 DOI: 10.1111/cas.13119] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/04/2016] [Accepted: 11/09/2016] [Indexed: 12/31/2022] Open
Abstract
Due to its aggressive nature, pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal and hard-to-treat malignancies. Recently developed targeted molecular strategies have contributed to remarkable improvements in the treatment of several cancers. However, such therapies have not been applied to PDAC. Therefore, new treatment options are needed for PDAC based on current genomic approaches. Expression of microRNA-375 (miR-375) was significantly reduced in miRNA expression signatures of several types of cancers, including PDAC. The aim of the present study was to investigate the functional roles of miR-375 in PDAC cells and to identify miR-375-regulated molecular networks involved in PDAC aggressiveness. The expression levels of miR-375 were markedly downregulated in PDAC clinical specimens and cell lines (PANC-1 and SW1990). Ectopic expression of miR-375 significantly suppressed cancer cell proliferation, migration and invasion. Our in silico and gene expression analyses and luciferase reporter assay showed that zinc finger protein 36 ring finger protein-like 2 (ZFP36L2) was a direct target of miR-375 in PDAC cells. Silencing ZFP36L2 inhibited cancer cell aggressiveness in PDAC cell lines, and overexpression of ZFP36L2 was confirmed in PDAC clinical specimens. Interestingly, Kaplan-Meier survival curves showed that high expression of ZFP36L2 predicted shorter survival in patients with PDAC. Moreover, we investigated the downstream molecular networks of the miR-375/ZFP36L2 axis in PDAC cells. Elucidation of tumor-suppressive miR-375-mediated PDAC molecular networks may provide new insights into the potential mechanisms of PDAC pathogenesis.
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Affiliation(s)
- Keiichi Yonemori
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Naohiko Seki
- Department of Functional GenomicsChiba University Graduate School of MedicineChibaJapan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Yusaku Osako
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Takayuki Arai
- Department of Functional GenomicsChiba University Graduate School of MedicineChibaJapan
| | - Keiichi Koshizuka
- Department of Functional GenomicsChiba University Graduate School of MedicineChibaJapan
| | - Yoshiaki Kita
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Kosei Maemura
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Shoji Natsugoe
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
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