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Long T, Li J, Yin T, Liu K, Wang Y, Long J, Wang J, Cheng L. A genetic variant in gene NDUFAF4 confers the risk of non-small cell lung cancer by perturbing hsa-miR-215 binding. Mol Carcinog 2024; 63:145-159. [PMID: 37787384 DOI: 10.1002/mc.23642] [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: 03/20/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
Hsa-microRNA-215 (hsa-miR-215) plays multiple roles in carcinogenesis through regulating its target genes. Genetic variants in hsa-miR-215 target sites thus may affect hsa-miR-215-mRNA interactions, result in altered expression of target genes and even influence cancer susceptibility. This study aimed to investigate the associations of genetic variants which located in the binding sites of hsa-miR-215 with non-small cell lung cancer (NSCLC) susceptibility in the Chinese population and reveal the potential regulatory mechanism of functional variants in NSCLC development. The candidate genetic variants were predicted and screened through bioinformatics analysis based on the degree of complementarity of hsa-miR-215 sequences. The potential effects of genetic variants on the binding ability of hsa-miR-215 and target genes were also predicted. A case-control study with 932 NSCLC patients and 1036 healthy controls was conducted to evaluate the association of candidate genetic variants with NSCLC susceptibility, and an independent case-control study with 552 NSCLC cases and 571 controls were used to further validate the promising associations. Dual luciferase reporter gene assay was applied to explore the regulation of the genetic variants on transcription activity of target gene. Cell phenotyping experiments in vitro and RNA sequencing (RNA-seq) were then carried out to preliminarily explore the potential regulatory mechanisms of the target genes in NSCLC. A total of five candidate genetic variants located in the binding sites of hsa-miR-215 were screened. The two-stage case-control study showed that a variant rs1854268 A > T, which located in the 3' untranslated (3'UTR) region of NDUFAF4 gene, was associated with decreased risk of NSCLC (additive model, odds ratio [OR] = 0.83, 95% confidence interval [CI]: 0.75-0.92, p < 0.001). Functional annotation displayed that rs1854268 A > T might downregulate the expression of NDUFAF4 by enhancing the binding affinity of hsa-miR-215-5p to NDUFAF4 mRNA. Additionally, transient knockdown of the NDUFAF4 could inhibit lung cancer cell migration and promote lung cancer cell apoptosis. Further RNA-seq analysis revealed that the knockdown of NDUFAF4 may affect NSCLC development by downregulating the nuclear factor kappa B (NF-κB) and phosphoinositide 3 kinase-AKT (PI3K-AKT) signaling pathways. Moreover, the overexpression of CCND1 could partially attenuate the effects of NDUFAF4 knock down on lung cancer cell migration and apoptosis, indicating that CCND1 may be involved in the tumor-promoting effects of NDUFAF4 as a downstream molecule of NDUFAF4 gene. In conclusion, the genetic variant rs1854268 (A > T) on NDUFAF4 confers NSCLC susceptibility by altering the binding affinity of hsa-miR-215-5p, thus regulating the expression of NDUFAF4 and subsequently influencing downstream tumor molecules and pathways such as CCND1, NF kappa B, and PI3K-AKT signaling pathways.
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Affiliation(s)
- Tingting Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tongxin Yin
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jieyi Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianing Wang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Bi Y, Hu J, Zeng L, Chen G, Cai H, Cao H, Ma Q, Wu X. Characteristics of HPV integration in cervical adenocarcinoma and squamous carcinoma. J Cancer Res Clin Oncol 2023; 149:17973-17986. [PMID: 37966613 PMCID: PMC10725361 DOI: 10.1007/s00432-023-05494-4] [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: 08/13/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023]
Abstract
PURPOSE HPV integration usually occurs in HPV-related cancer, and is the main cause of cancer. But the carcinogenic mechanism of HPV integration is unclear. The study aims to provide a theoretical basis for understanding the pathogenesis of cervical adenocarcinoma (AC) and cervical squamous carcinoma (SCC). METHODS We used HPV capture sequencing to obtain HPV integration sites in AC and SCC, and analyzed cytobands, distribution of genetic and genomic elements, identified integration hotspot genes, clinicopathological parameters, breakpoints of HPV16 and performed pathway analysis. Then we conducted immunohistochemical (IHC) assay to preliminarily verify the expression of most frequently integrated genes in AC, STARD3 and ERBB2. RESULTS The results revealed that the most frequently observed integrated cytoband was 17q12 in AC and 21p11.2 in SCC, respectively. The breakpoints in both AC and SCC were more tended to occur within gene regions, compared to intergenetic regions. Compared to SCC samples, AC samples had a higher prevalence of genomic elements. In AC, HPV integration has no significantly difference with clinicopathological parameters, but in SCC integration correlated with differentiation (P < 0.05). Breakpoints of HPV in SCC located in LCR more frequently compared to AC, which destroyed the activation of promoter p97. Hotspot genes of HPV integration were STARD3 and ERBB2 in AC, and RNA45S rDNA and MIR3648-1 in SCC, respectively. Meanwhile, we preliminarily proved that the expression of STARD3 and ERBB2, the most frequently integrated genes, would increase after integration. CONCLUSION These results suggested that HPV may utilize the powerful hosts' promoters to express viral oncogenes and overexpression of viral oncogenes plays a significant role in the carcinogenesis of SCC. In AC, HPV integration may affect hosts' oncogenes, and the dysregulation of oncogenes may primarily contribute to progression of AC.
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Affiliation(s)
- Yuxin Bi
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Junbo Hu
- Department of Pathology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Ling Zeng
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Center for Medical Genetics, Wuhan, China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongning Cai
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Huang Cao
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
- Hubei Provincial Center for Medical Genetics, Wuhan, China
| | - Quanfu Ma
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Xufeng Wu
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China.
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Kourie HR, Zouein J, Succar B, Mardirossian A, Ahmadieh N, Chouery E, Mehawej C, Jalkh N, kattan J, Nemr E. Genetic Polymorphisms Involved in Bladder Cancer: A Global Review. Oncol Rev 2023; 17:10603. [PMID: 38025894 PMCID: PMC10657888 DOI: 10.3389/or.2023.10603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Bladder cancer (BC) has been associated with genetic susceptibility. Single peptide polymorphisms (SNPs) can modulate BC susceptibility. A literature search was performed covering the period between January 2000 and October 2020. Overall, 334 articles were selected, reporting 455 SNPs located in 244 genes. The selected 455 SNPs were further investigated. All SNPs that were associated with smoking and environmental exposure were excluded from this study. A total of 197 genes and 343 SNPs were found to be associated with BC, among which 177 genes and 291 SNPs had congruent results across all available studies. These genes and SNPs were classified into eight different categories according to their function.
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Affiliation(s)
- Hampig Raphael Kourie
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Joseph Zouein
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Bahaa Succar
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Avedis Mardirossian
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Nizar Ahmadieh
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Eliane Chouery
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
| | - Cybel Mehawej
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
| | - Nadine Jalkh
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Joseph kattan
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Elie Nemr
- Urology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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Shirvaliloo M. LncRNA H19 promotes tumor angiogenesis in smokers by targeting anti-angiogenic miRNAs. Epigenomics 2023; 15:61-73. [PMID: 36802727 DOI: 10.2217/epi-2022-0145] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
A key concept in drug discovery is the identification of candidate therapeutic targets such as long noncoding RNAs (lncRNAs) because of their extensive involvement in neoplasms, and impressionability by smoking. Induced by exposure to cigarette smoke, lncRNA H19 targets and inactivates miR-29, miR-30a, miR-107, miR-140, miR-148b, miR-199a and miR-200, which control the rate of angiogenesis by inhibiting BiP, DLL4, FGF7, HIF1A, HIF1B, HIF2A, PDGFB, PDGFRA, VEGFA, VEGFB, VEGFC, VEGFR1, VEGFR2 and VEGFR3. Nevertheless, these miRNAs are often dysregulated in bladder cancer, breast cancer, colorectal cancer, glioma, gastric adenocarcinoma, hepatocellular carcinoma, meningioma, non-small-cell lung carcinoma, oral squamous cell carcinoma, ovarian cancer, prostate adenocarcinoma and renal cell carcinoma. As such, the present perspective article seeks to establish an evidence-based hypothetical model of how a smoking-related lncRNA known as H19 might aggravate angiogenesis by interfering with miRNAs that would otherwise regulate angiogenesis in a nonsmoking individual.
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Affiliation(s)
- Milad Shirvaliloo
- Infectious & Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 15731, Iran.,Future Science Group, Unitec House, 2 Albert Place, London, N3 1QB, UK
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High S100A7 expression is associated with early muscle invasion and poor survival in bladder carcinoma. Ann Diagn Pathol 2021; 56:151847. [PMID: 34742033 DOI: 10.1016/j.anndiagpath.2021.151847] [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: 09/11/2021] [Revised: 10/09/2021] [Accepted: 10/23/2021] [Indexed: 11/22/2022]
Abstract
Muscle-invasive bladder carcinoma (MIBC) accounts for 25% of newly diagnosed bladder carcinomas (BCs) and presents a high risk of progression and metastasis. This study aimed to identify reliable biomarkers associated with muscle invasion and prognosis to identify potential therapeutic targets for MIBC. Four gene datasets were downloaded from the Gene Expression Omnibus, and the integrated differentially expressed genes (DEGs) were then subjected to gene ontology (GO) terms and pathway enrichment analyses. Correlation analysis between the expression of the top-ranking DEGs and pathological T stages was performed to identify the genes associated with early muscle invasion. The corresponding prognostic values were evaluated, and co-expressed genes mined in the cBioPortal database were loaded into ClueGo in Cytoscape for pathway enrichment analysis. Using data mining from the STRING and TCGA databases, protein-protein interaction and competitive endogenous RNA networks were constructed. In total, 645 integrated DEGs were identified and these were mainly enriched in 26 pathways, including cell cycle, bladder cancer, DNA replication, and PPAR signaling pathway. S100A7 expression was significantly increased from the T2 stage and showed significantly worse overall survival and disease-specific survival in patients with BC. In total, 144 genes co-expressed with S100A7 in BC were significantly enriched in the IL-17 pathway. S100A7 was predicted to directly interact with LYZ, which potentially shows competitive binding with hsa-mir-140 to affect the expression of six lncRNAs in MIBC. In conclusion, high S100A7 expression was predicted to be associated with early muscle invasion and poor survival in patients with BC.
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Lange M, Begolli R, Giakountis A. Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine. Noncoding RNA 2021; 7:47. [PMID: 34449663 PMCID: PMC8395730 DOI: 10.3390/ncrna7030047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022] Open
Abstract
The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.
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Affiliation(s)
- Marios Lange
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
- Institute for Fundamental Biomedical Research, B.S.R.C “Alexander Fleming”, 34 Fleming Str., 16672 Vari, Greece
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7
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Zhang Q, Long J, Li N, Ma X, Zheng L. Circ_CLASP2 Regulates High Glucose-Induced Dysfunction of Human Endothelial Cells Through Targeting miR-140-5p/FBXW7 Axis. Front Pharmacol 2021; 12:594793. [PMID: 33776760 PMCID: PMC7990784 DOI: 10.3389/fphar.2021.594793] [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: 09/22/2020] [Accepted: 01/18/2021] [Indexed: 01/10/2023] Open
Abstract
Hyperglycemia exposure results in the dysfunction of endothelial cells (ECs) and the development of diabetic complications. Circular RNAs (circRNAs) have been demonstrated to play critical roles in EC dysfunction. The current study aimed to explore the role and mechanism of circRNA CLIP–associating protein 2 (circ_CLASP2, hsa_circ_0064772) on HG-induced dysfunction in human umbilical vein endothelial cells (HUVECs). Quantitative real-time polymerase chain reaction (qRT-PCR) was used to assess the levels of circ_CLASP2, miR-140-5p and F-box, and WD repeat domain-containing 7 (FBXW7). The stability of circ_CLASP2 was identified by the actinomycin D and ribonuclease (RNase) R assays. Cell colony formation, proliferation, and apoptosis were measured by a standard colony formation assay, colorimetric 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl-2H-tetrazolium bromide (MTT) assay, and flow cytometry, respectively. Western blot analysis was performed to determine the expression of related proteins. Targeted correlations among circ_CLASP2, miR-140-5p, and FBXW7 were confirmed by dual-luciferase reporter assay. High glucose (HG) exposure downregulated the expression of circ_CLASP2 in HUVECs. Circ_CLASP2 overexpression or miR-140-5p knockdown promoted proliferation and inhibited apoptosis of HUVECs under HG conditions. Circ_CLASP2 directly interacted with miR-140-5p via pairing to miR-140-5p. The regulation of circ_CLASP2 overexpression on HG-induced HUVEC dysfunction was mediated by miR-140-5p. Moreover, FBXW7 was a direct target of miR-140-5p, and miR-140-5p regulated HG-induced HUVEC dysfunction via FBXW7. Furthermore, circ_CLASP2 mediated FBXW7 expression through sponging miR-140-5p. Our current study suggested that the overexpression of circ_CLASP2 protected HUVEC from HG-induced dysfunction at least partly through the regulation of the miR-140-5p/FBXW7 axis, highlighting a novel therapeutic approach for the treatment of diabetic-associated vascular injury.
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Affiliation(s)
- Qin Zhang
- Department of Cardiovascular, Dongying People's Hospital, Dongying, China
| | - Jing Long
- Department of Critical Care Medicine, Dongying People's Hospital, Dongying, China
| | - Nannan Li
- Department of Cardiovascular, Dongying People's Hospital, Dongying, China
| | - Xuelian Ma
- Department of Clinical Laboratory, Dongying People's Hospital, Dongying, China
| | - Lisheng Zheng
- Department of Cardiovascular, Dongying People's Hospital, Dongying, China
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8
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Wang Y, Chen J, Wang X, Wang K. miR-140-3p inhibits bladder cancer cell proliferation and invasion by targeting FOXQ1. Aging (Albany NY) 2020; 12:20366-20379. [PMID: 33098639 PMCID: PMC7655201 DOI: 10.18632/aging.103828] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Upregulation of the forkhead box protein Q1 (FOXQ1) promotes bladder cancer (BCa) cell growth and metastasis. Factors affecting FOXQ1 expression at the post-transcriptional level have not yet been identified. We performed cell proliferation, cell invasion, and tumorigenesis experiments to characterize the relationship between FOXQ1 and miR-140-3p. We found that FOXQ1 was significantly upregulated and miR-140-3p was significantly downregulated in BCa tissues. We also identified an inverse correlation between miR-140-3p and FOXQ1 expression in BCa tissues. Overexpression of miR-140-3p reduced FOXQ1 expression, suppressing BCa cell proliferation and invasion. A luciferase assay confirmed that miR-140-3p bound to the 3’-UTR of FOXQ1 mRNA and decreased its expression. In addition, we used a mouse xenograft model to demonstrate that miR-140-3p suppressed tumor cell growth in vivo. Our findings suggest that miR-140-3p suppresses BCa cell proliferation and invasion by directly decreasing FOXQ1 expression.
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Affiliation(s)
- Yuan Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Junwen Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
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Liu W, Liu P, Gao H, Wang X, Yan M. Long non-coding RNA PGM5-AS1 promotes epithelial-mesenchymal transition, invasion and metastasis of osteosarcoma cells by impairing miR-140-5p-mediated FBN1 inhibition. Mol Oncol 2020; 14:2660-2677. [PMID: 32412676 PMCID: PMC7530781 DOI: 10.1002/1878-0261.12711] [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: 01/27/2020] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 01/31/2023] Open
Abstract
Osteosarcoma is an uncommon tumor occurring in bone, accompanied by elevated incidence and reduced rate of healing. Epithelial‐to‐mesenchymal transition (EMT) serves as a conceptual paradigm to explain the invasion and metastasis of osteosarcoma and other cancers. Hence, developing effective therapeutic strategy to treat the EMT of osteosarcoma is essential. Here, we identified the molecular mechanism of long noncoding RNA (lncRNA) PGM5‐AS1 in EMT and progression of osteosarcoma. Microarray‐based analysis was employed to screen the osteosarcoma‐related differentially expressed lncRNAs. The levels of PGM5‐AS1 as well as microRNA‐140‐5p (miR‐140‐5p) and fibrillin‐1 (FBN1) in osteosarcoma tissues and cells were determined. Dual‐luciferase reporter gene assay, RNA pull‐down assay, and RNA immunoprecipitation assay were conducted to validate the relationship among PGM5‐AS1, miR‐140‐5p, and FBN1. Expression of PGM5‐AS1, miR‐140‐5p, and FBN1 was altered by overexpression, shRNA, mimic, or inhibitors in order to investigate how they regulated migration, invasion, and EMT of osteosarcoma cells in vitro. Loss‐ and gain‐of‐function approaches were employed in nude mice to detect their roles in tumorigenesis in vivo. Osteosarcoma tissues and cells exhibited low expression of miR‐140‐5p, but high expression of PGM5‐AS1 and FBN1. PGM5‐AS1 competitively bound to miR‐140‐5p to upregulate FBN1. Furthermore, hindering PGM5‐AS1 and FBN1 or overexpressing miR‐140‐5p dampened migration, invasion, and EMT of osteosarcoma cells in vitro. Furthermore, silencing PGM5‐AS1 or FBN1, or overexpressing miR‐140‐5p markedly inhibited tumorigenesis in nude mice in vivo. Taken together, PGM5‐AS1 depletion causes FBN1 reduction to retard osteosarcoma processes by negatively modulating miR‐140‐5p.
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Affiliation(s)
- Wei Liu
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Pengcheng Liu
- Department of Hand and Foot Surgery, The First Hospital of Jilin University, Changchun, China
| | - Hang Gao
- Department of Bone and Joint Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xu Wang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Ming Yan
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
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Huang C, Li J, Zhang X, Xiong T, Ye J, Yu J, Gui Y. The miR-140-5p/KLF9/KCNQ1 axis promotes the progression of renal cell carcinoma. FASEB J 2020; 34:10623-10639. [PMID: 32596959 DOI: 10.1096/fj.202000088rr] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022]
Abstract
Although renal cell carcinoma (RCC) is a common malignant urological cancer, its pathogenesis remains unclear. Previous studies have indicated that miR-140-5p acts as a tumor suppressor in various tumors, including bladder cancer, hepatocellular carcinoma, and gastric cancer, but its biological function in RCC remains unknown. In the present study, we found that miR-140-5p was upregulated in RCC tissues, whereas Krüppel-like factor 9 (KLF9) was downregulated and correlated inversely with miR-140-5p in RCC tissues. miR-140-5p promoted the proliferation, migration, and invasion of RCC cells in vitro, and knockdown of miR-140-5p significantly suppressed tumor growth and lung metastasis in nude mouse model of RCC. We also found that miR-140-5p significantly suppressed the expression of KLF9 by binding to the 3'-UTR of KLF9 mRNA and that KLF9, as a transcription factor, upregulates KCNQ1 (also called Kv 7.1 and Kv LQT1) expression by binding to the site (-841/-827) in the KCNQ1 promoter region in RCC cells. Moreover, forced expression of KCNQ1 decreased the growth and metastasis of RCC cells. These results suggest that the miR-140-5p/KLF9/KCNQ1 axis functions as a key signaling pathway in RCC progression and metastasis and represents a potential target of RCC therapies.
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Affiliation(s)
- Chenchen Huang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Clinical College of Anhui Medical University, Shenzhen, China
- Anhui Medical University, Hefei, China
| | - Jianfa Li
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Clinical College of Anhui Medical University, Shenzhen, China
| | - Xiaoting Zhang
- Shenzhen Bao'an District Songgang People's Hospital, Shenzhen, China
| | - Tiefu Xiong
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Clinical College of Anhui Medical University, Shenzhen, China
| | - Jing Ye
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Clinical College of Anhui Medical University, Shenzhen, China
| | - Jing Yu
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Clinical College of Anhui Medical University, Shenzhen, China
- Anhui Medical University, Hefei, China
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Fehlmann T, Sahay S, Keller A, Backes C. A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites. Brief Bioinform 2020; 20:1011-1020. [PMID: 29186316 DOI: 10.1093/bib/bbx155] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/23/2017] [Indexed: 12/16/2022] Open
Abstract
Modern precision medicine comprises the knowledge and understanding of individual differences in the genomic sequence of patients to provide tailor-made treatments. Regularly, such variants are considered in coding regions only, and their effects are predicted based on their impact on the amino acid sequence of expressed proteins. However, assessing the effects of variants in noncoding elements, in particular microRNAs (miRNAs) and their binding sites, is important as well, as a single miRNA can influence the expression patterns of many genes at the same time. To analyze the effects of variants in miRNAs and their target sites, several databases storing variant impact predictions have been published. In this review, we will compare the core functionalities and features of these databases and discuss the importance of up-to-date data resources in the context of web applications. Finally, we will outline some recommendations for future developments in the field.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Shashwat Sahay
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
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Jacinta-Fernandes A, Xavier JM, Magno R, Lage JG, Maia AT. Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk. NPJ Genom Med 2020; 5:4. [PMID: 32128252 PMCID: PMC7018948 DOI: 10.1038/s41525-019-0112-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Most breast cancer (BC) risk-associated single-nucleotide polymorphisms (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting microRNA (miRNA) genes and/or miRNA binding. To test this, we adapted two miRNA-binding prediction algorithms-TargetScan and miRanda-to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant ( P ≤ 5 × 10 - 8 ) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3'-untranslated regions of putative miRNA target genes were predicted to alter miRNA::mRNA (messenger RNA) pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and reinforce the role of miRNA-mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.
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Affiliation(s)
- Ana Jacinta-Fernandes
- 1Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, 8005-139 Portugal.,2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Joana M Xavier
- 1Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, 8005-139 Portugal.,2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Ramiro Magno
- 2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Joel G Lage
- 1Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, 8005-139 Portugal.,2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Ana-Teresa Maia
- 1Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, 8005-139 Portugal.,2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
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13
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Akkoc Y, Gozuacik D. MicroRNAs as major regulators of the autophagy pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118662. [PMID: 32001304 DOI: 10.1016/j.bbamcr.2020.118662] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/13/2020] [Accepted: 01/23/2020] [Indexed: 01/17/2023]
Abstract
Autophagy is a cellular stress response mechanism activation of which leads to degradation of cellular components, including proteins as well as damaged organelles in lysosomes. Defects in autophagy mechanisms were associated with several pathologies (e.g. cancer, neurodegenerative diseases, and rare genetic diseases). Therefore, autophagy regulation is under strict control. Transcriptional and post-translational mechanisms that control autophagy in cells and organisms studied in detail. Recent studies introduced non-coding small RNAs, and especially microRNAs (miRNAs) in the post-translational orchestration of the autophagic activity. In this review article, we analyzed in detail the current status of autophagy-miRNA connections. Comprehensive documentation of miRNAs that were directly involved in autophagy regulation resulted in the emergence of common themes and concepts governing these complex and intricate interactions. Hence, a better and systematic understanding of these interactions reveals a central role for miRNAs in the regulation of autophagy.
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Affiliation(s)
- Yunus Akkoc
- Sabanci University, Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Orhanli-Tuzla 34956, Istanbul, Turkey
| | - Devrim Gozuacik
- Sabanci University, Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Orhanli-Tuzla 34956, Istanbul, Turkey; Sabanci University Nanotechnology Research and Application Center, Sabanci University, Istanbul 34956, Turkey.
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14
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Cipollini M, Luisi S, Piomboni P, Luddi A, Landi D, Melaiu O, Figlioli G, Garritano S, Cappelli V, Viganò P, Gemignani F, Petraglia F, Landi S. Functional polymorphism within NUP210 encoding for nucleoporin GP210 is associated with the risk of endometriosis. Fertil Steril 2019; 112:343-352.e1. [PMID: 31256999 DOI: 10.1016/j.fertnstert.2019.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To investigate whether nucleoporin 210 (GP210, encoded by NUP210 gene) is involved in endometriosis. DESIGN Immunohistofluorescence analysis for assessing whether GP210 is expressed in endometrial tissues from patients and controls; genotyping and case-control study for assessing the association between rs354476 within NUP210 and risk of endometriosis; in vitro luciferase assay for assessing the functional activity of rs354476. SETTING University. PATIENT(S) Histologically diagnosed cases (n = 175) of endometriosis: minimal or mild (stage I-II) in 48 cases (28%), moderate (stage III) in 69 cases (39%), and severe (stage IV) in 58 cases (33%). Controls (n = 557) were female blood donors collected at Meyer Hospital of Florence. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) GP210 tissue expression; genotype distribution and risk of endometriosis; in vitro gene expression measurements. RESULT(S) GP210 had positive nuclear immunohistofluorescence staining in endometrial glandular epithelium. Carriers of the variant allele were associated with increased risks: C/T, odds ratio (OR) 1.83, 95% confidence interval (CI) 1.04-3.21; T/T, OR 2.55, 95% CI 1.36-4.80. In vitro, luciferase assay showed that rs354476 is a bona fide target for hsa-miR-125b-5p. CONCLUSION(S) Nucleoporin GP210 is involved in endometriosis. Rs354476 polymorphism affects the regulation of NUP210 gene expression by altering the binding with hsa-miR-125b-5p, a microRNA already known as playing an important role for endometriosis. This provides the rationale for the observed increased risk of endometriosis in carriers of the variant allele.
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Affiliation(s)
| | - Stefano Luisi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Paola Piomboni
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Alice Luddi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Debora Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | | | | | - Sonia Garritano
- Centre for Integrated Biology, University of Trento, Trento, Italy
| | - Valentina Cappelli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Paola Viganò
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | | | - Felice Petraglia
- Obstetrics and Gynecology, Department of Biomedical, Experimental and Clinical Sciences "Mario Serio" University of Florence, Florence, Italy
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
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15
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Souza LC, Crozeta BM, Guajardo L, Brasil da Costa FH, Sousa-Neto MD, Letra A, Silva RM. Potential role of TP63 in apical periodontitis development. Int Endod J 2019; 52:1344-1353. [PMID: 31025362 DOI: 10.1111/iej.13133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/23/2019] [Indexed: 12/25/2022]
Abstract
AIM To investigate the expression of TP63 in apical periodontitis (AP) tissues and the association of single nucleotide polymorphisms (SNPs) in the TP63 gene with AP using a case-control dataset. METHODOLOGY Expression of TP63 in human AP lesions (apical abscess, radicular cyst, periapical granuloma) was evaluated using immunohistochemistry. A case-control association study was performed to assess the association of TP63 polymorphisms in individuals having AP with or without associated pain. Cases were defined as subjects with deep caries and AP (n = 151) and subjects with symptomatic apical periodontitis or acute apical abscess (n = 124). Subjects without AP (n = 169) and asymptomatic (n = 196) were used as controls, respectively. Saliva samples were collected as source of genomic DNA. Twelve SNPs in the TP63 gene were selected for genotyping using Taqman chemistry in real-time PCR. Data analysis was performed using PLINK software. The Bonferroni method was applied to correct for multiple testing; α ≤ 0.004 indicates significant differences between groups. RESULTS TP63 expression was evident in apical abscesses and radicular cysts, while weaker expression was observed in periapical granulomas. Positive expression was observed in mononuclear cells in the granulation tissues of all AP lesions. Regarding the presence of AP, a trend for allelic association was observed for rs16864812 and rs9810322 (P = 0.04) and rs9810322 genotypes were also nominally associated with AP under a dominant model (P = 0.04). When considering the presence of periapical pain, a trend for allelic and genotypic association was observed for rs10155037 (P = 0.03). Haplotypes were also associated with AP and periapical pain (P ≤ 0.05). CONCLUSIONS Apical periodontitis is a complex multifactorial condition and it is likely that multiple genes and environmental effects may influence its susceptibility, progression or both. TP63 variants may play a role in AP pathogenesis and susceptibility, individually or interactively with other genes. Additional studies in other populations and functional studies are needed to improve understanding of the role of TP63 in AP.
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Affiliation(s)
- L C Souza
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston.,Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, TX, USA
| | - B M Crozeta
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston.,Department of Endodontics, University of São Paulo, Ribeirão Preto, Brazil
| | - L Guajardo
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston
| | | | - M D Sousa-Neto
- Department of Endodontics, University of São Paulo, Ribeirão Preto, Brazil
| | - A Letra
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston.,Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, TX, USA.,Department of Diagnostic and Biomedical Sciences, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - R M Silva
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston.,Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, TX, USA
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16
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Gu D, Li S, Du M, Tang C, Chu H, Tong N, Zhang Z, Wang M, Chen J. A genetic variant located in the miR-532-5p-binding site of TGFBR1 is associated with the colorectal cancer risk. J Gastroenterol 2019; 54:141-148. [PMID: 29971498 DOI: 10.1007/s00535-018-1490-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/22/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Genome-wide association studies have identified genes in the transforming growth factor-β (TGFβ) signaling pathway that are responsible for regulating carcinogenesis. METHODS We searched for single-nucleotide polymorphisms (SNPs) located within 3'-untranslated regions (3'-UTRs) that might affect the ability of miRNAs to bind genes in the TGFβ pathway for further analysis. We used TaqMan technology to genotype these SNPs in a population-based case-control study of 1147 colorectal cancer patients and 1203 matched controls in a Chinese population. RESULTS The rs1590 variant of TGFBR1 exhibited a significant association with colorectal cancer risk. Compared with individuals carrying the rs1590 TT genotype, individuals carrying the GT/GG genotypes had a decreased risk of colorectal cancer [odd ratio (OR) = 0.82, 95% confidence interval (CI) = 0.68-0.97], which was more evident among older individuals with a family history of cancer. Luciferase assays confirmed that the rs1590 T allele altered the capacity of miR-532-5p to bind TGFBR1. CONCLUSIONS Based on these findings, the rs1590 variant in the 3'-UTR of TGFBR1 may contribute to the susceptibility to colorectal cancer, predominantly by altering miR-532-5p binding.
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Affiliation(s)
- Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, People's Republic of China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, People's Republic of China.,Department of Biostatistics, Nanjing Medical University, Nanjing, 211166, People's Republic of China
| | - Cuiju Tang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, People's Republic of China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Na Tong
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, People's Republic of China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, People's Republic of China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, People's Republic of China. .,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, China.
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17
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Dudek AM, Vermeulen SH, Kolev D, Grotenhuis AJ, Kiemeney LALM, Verhaegh GW. Identification of an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk. Cell Oncol (Dordr) 2018; 41:555-568. [PMID: 29956121 PMCID: PMC6153957 DOI: 10.1007/s13402-018-0393-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2018] [Indexed: 12/24/2022] Open
Abstract
Purpose Genome-wide association studies (GWAS) have led to the identification of a bladder cancer susceptibility variant (rs710521) in a non-coding intergenic region between the TP63 and LEPREL1 genes on chromosome 3q28, suggesting a role in the transcriptional regulation of these genes. In this study, we aimed to functionally characterize the 3q28 bladder cancer risk locus. Methods Fine-mapping was performed by focusing on the region surrounding rs710521, and variants were prioritized for further experiments using ENCODE regulatory data. The enhancer activity of the identified region was evaluated using dual-luciferase assays. CRISPR/Cas9-mediated deletion of the enhancer region was performed and the effect of this deletion on cell proliferation and gene expression levels was evaluated using CellTiter-Glo and RT-qPCR, respectively. Results Fine-mapping of the GWAS signal region led to the identification of twenty SNPs that showed a stronger association with bladder cancer risk than rs710521. Using publicly available data on regulatory elements and sequences, an enhancer region containing the bladder cancer risk variants was identified. Through reporter assays, we found that the presence of the enhancer region significantly increased ΔNTP63 promoter activity in bladder cancer-derived cell lines. CRISPR/Cas9-mediated deletion of the enhancer region reduced the viability of bladder cancer cells by decreasing the expression of ΔNTP63 and p63 target genes. Conclusions Taken together, our data show that bladder cancer risk-associated variants on chromosome 3q28 are located in an active enhancer region. Further characterization of the allele-specific activity of the identified enhancer and its target genes may lead to the identification of novel signaling pathways involved in bladder carcinogenesis. Electronic supplementary material The online version of this article (10.1007/s13402-018-0393-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleksandra M Dudek
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
| | - Sita H Vermeulen
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dimitar Kolev
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne J Grotenhuis
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lambertus A L M Kiemeney
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gerald W Verhaegh
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands.
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18
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Ma M, Zhao J, Wu Q, Xiao K, Li S, Zhu H, Liu C, Xie H, Zuo C. MiRNA-545 negatively regulates the oncogenic activity of EMS1 in gastric cancer. Cancer Med 2018; 7:2452-2462. [PMID: 29733519 PMCID: PMC6010719 DOI: 10.1002/cam4.1520] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/17/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022] Open
Abstract
Gastric cancer (GC) is a common malignant tumor of the digestive system. In addition, GC metastasis is an extremely complicated process. In this article, high expression levels of EMS1 mRNA and protein were found to be positively correlated with an enhanced malignant potential of GC cells and a poor clinical prognosis of GC patients. Interestingly, the expression levels of EMS1 mRNA and protein in GC cells were inhibited by microRNA-545 (miR-545), which was identified by a bioinformatics analysis. The expression level of miR-545 in carcinoma tissues was significantly lower than that in para-carcinoma tissues. The proliferation and epithelial-mesenchymal transition (EMT) of GC cells were suppressed by exogenous oligonucleotides of miR-545 mimics. In addition, the expression levels of EMT-associated markers were altered with the expression of miR-545. Notably, the growth rates of tumors in nude mice were seriously restrained by an intratumoral injection of oligonucleotides of the miR-545 mimics. These results suggest a negative regulatory role of miR-545 on the oncogenic activity of EMS1. In addition, EMS1 and miR-545 may be potential biomarkers for GC diagnosis. Synthesized oligonucleotides of miR-545 mimics may be developed as important gene medicines for GC therapy in the future.
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Affiliation(s)
- Min Ma
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, Hunan, 410013, China
| | - Juanxia Zhao
- Institute of Cancer Research, School of Medicine, University of South China, Hengyang, Hunan, 421001, China
| | - Qunfeng Wu
- Department of Pathology and Laboratory Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, 07103
| | - Ke Xiao
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, Hunan, 410013, China
| | - Shuang Li
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, Hunan, 410013, China
| | - Haizhen Zhu
- Department of Molecular Medicine, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, 410082, China
| | - Chen Liu
- Department of Pathology and Laboratory Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, 07103
| | - Hailong Xie
- Institute of Cancer Research, School of Medicine, University of South China, Hengyang, Hunan, 421001, China
| | - Chaohui Zuo
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, Hunan, 410013, China
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de Maturana EL, Rava M, Anumudu C, Sáez O, Alonso D, Malats N. Bladder Cancer Genetic Susceptibility. A Systematic Review. Bladder Cancer 2018; 4:215-226. [PMID: 29732392 PMCID: PMC5929300 DOI: 10.3233/blc-170159] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Background: The variant/gene candidate approach to explore bladder cancer (BC) genetic susceptibility has been applied in many studies with significant findings reported. However, results are not always conclusive due to the lack of replication by subsequent studies. Objectives: To identify all epidemiological investigations on the genetic associations with BC risk, to quantify the likely magnitude of the associations by applying metaanalysis methodology and to assess whether there is a potential for publication/reporting bias. Methods: To address our aims, we have catalogued all genetic association studies published in the field of BC risk since 2000. Furthermore, we metaanalysed all polymorphisms with data available from at least three independent case-control studies with subjects of Caucasian origin analyzed under the same mode of inheritance. Results: The characterization of the genetic susceptibility of BC is composed of 28 variants, GWAS contributing most of them. Most of the significant variants associated with BC risk are located in genes belonging to chemical carcinogenesis, DNA repair, and cell cycle pathways. Causal relationship was also provided by functional analysis for GSTM1-null, NAT2-slow, APOBEC-rs1014971, CCNE1-rs8102137, SLC14A1-rs10775480, PSCA-rs2294008, UGT1A-rs1189203, and TP63-rs35592567. Conclusions: Genetic susceptibility of BC is still poorly defined, with GWAS contributing most of the strongest evidence. The systematic review did not provide evidence of further genetic associations. The potential public health translation of the existing knowledge on genetic susceptibility on BC is still limited.
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Affiliation(s)
| | - Marta Rava
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and CIBERONC, Spain
| | - Chiaka Anumudu
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and CIBERONC, Spain
| | - Olga Sáez
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and CIBERONC, Spain
| | - Dolores Alonso
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and CIBERONC, Spain
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and CIBERONC, Spain
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20
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Dysregulation of miRNAs in bladder cancer: altered expression with aberrant biogenesis procedure. Oncotarget 2018; 8:27547-27568. [PMID: 28187437 PMCID: PMC5432357 DOI: 10.18632/oncotarget.15173] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/24/2017] [Indexed: 12/31/2022] Open
Abstract
Aberrant expression profiles of miRNAs are widely observed in the clinical tissue specimens and urine samples as well as the blood samples of bladder cancer patients. These profiles are closely related to the pathological features of bladder cancer, such as the tumour stage/grade, metastasis, recurrence and chemo-sensitivity. MiRNA biogenesis forms the basis of miRNA expression and function, and its dysregulation has been shown to be essential for variations in miRNA expression profiles as well as tumourigenesis and cancer progression. In this review, we summarize the up-to-date and widely reported miRNAs in bladder cancer that display significantly altered expression. We then compare the miRNA expression profiles among three different sample types (tissue, urine and blood) from patients with bladder cancer. Moreover, for the first time, we outline the dysregulated miRNA biogenesis network in bladder cancer from different levels and analyse its possible relationship with aberrant miRNA expression and the pathological characteristics of the disease.
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21
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Ingelmo-Torres M, Lozano JJ, Izquierdo L, Carrion A, Costa M, Gómez L, Ribal MJ, Alcaraz A, Mengual L. Urinary cell microRNA-based prognostic classifier for non-muscle invasive bladder cancer. Oncotarget 2017; 8:18238-18247. [PMID: 28212556 PMCID: PMC5392323 DOI: 10.18632/oncotarget.15315] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/30/2016] [Indexed: 01/06/2023] Open
Abstract
Current prognostic tools for non-muscle invasive bladder cancer (NMIBC) do not have enough discriminative capacity to predict the risk of tumour progression. This study aimed to identify urinary cell microRNAs that may be useful as non-invasive predictive biomarkers of tumour progression in NMIBC patients. To this end, 210 urine samples from NMIBC patients were included in the study. RNA was extracted from urinary cells and expression of 8 microRNAs, previously described by our group, was analysed by quantitative PCR. A tumour progression predicting model was developed by Cox regression analysis and validated by bootstrapping. Regression analysis identified miR-140-5p and miR-92a-3p as independent predictors of tumour progression. The risk score derived from the model containing these two microRNAs was able to discriminate between two groups with a highly significant different probability of tumour progression (HR, 5.204; p<0.001) which was maintained when patients were stratified according to tumour risk. The algorithm was also able to identify two groups with different cancer-specific survival (HR, 3.879; p=0.021). Although the data needs to be externally validated, miRNA analysis in urine appears to be a valuable prognostic tool in NMIBC patients.
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Affiliation(s)
- Mercedes Ingelmo-Torres
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Juan José Lozano
- CIBERehd, Plataforma de Bioinformática, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Laura Izquierdo
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Albert Carrion
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Meritxell Costa
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Lidia Gómez
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - María José Ribal
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Antonio Alcaraz
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Lourdes Mengual
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
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Dai F, Mei L, Meng S, Ma Z, Guo W, Zhou J, Zhang J. The global expression profiling in esophageal squamous cell carcinoma. Genomics 2017; 109:241-250. [PMID: 28442363 DOI: 10.1016/j.ygeno.2017.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/30/2017] [Accepted: 04/21/2017] [Indexed: 02/07/2023]
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Moszyńska A, Gebert M, Collawn JF, Bartoszewski R. SNPs in microRNA target sites and their potential role in human disease. Open Biol 2017; 7:170019. [PMID: 28381629 PMCID: PMC5413909 DOI: 10.1098/rsob.170019] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 03/08/2017] [Indexed: 12/14/2022] Open
Abstract
In the post-genomic era, the goal of personalized medicine is to determine the correlation between genotype and phenotype. Developing high-throughput genotyping technologies such as genome-wide association studies (GWAS) and the 1000 Genomes Project (http://www.internationalgenome.org/about/#1000G_PROJECT) has dramatically enhanced our ability to map where changes in the genome occur on a population level by identifying millions of single nucleotide polymorphisms (SNPs). Polymorphisms, particularly those within the coding regions of proteins and at splice junctions, have received the most attention, but it is also now clear that polymorphisms in the non-coding regions are important. In these non-coding regions, the enhancer and promoter regions have received the most attention, whereas the 3'-UTR regions have until recently been overlooked. In this review, we examine how SNPs affect microRNA-binding sites in these regions, and how mRNA stability changes can lead to disease pathogenesis.
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Affiliation(s)
- Adrianna Moszyńska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gebert
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
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