1
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Yu X, Du Z, Zhu P, Liao B. Diagnostic, prognostic, and therapeutic potential of exosomal microRNAs in renal cancer. Pharmacol Rep 2024; 76:273-286. [PMID: 38388810 DOI: 10.1007/s43440-024-00568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Renal cell carcinoma (RCC) arises from the tubular epithelial cells of the nephron. It has the highest mortality rate among urological cancers. There are no effective therapeutic approaches and no non-invasive biomarkers for diagnosis and follow-up. Thus, suitable novel biomarkers and therapeutic targets are essential for improving RCC diagnosis/prognosis and treatment. Circulating exosomes such as exosomal microRNAs (Exo-miRs) provide non-invasive prognostic/diagnostic biomarkers and valuable therapeutic targets, as they can be easily isolated and quantified and show high sensitivity and specificity. Exosomes secreted by an RCC can exhibit alterations in the miRs' profile that may reflect the cellular origin and (patho)physiological state, as a ''signature'' or ''fingerprint'' of the donor cell. It has been shown that the transportation of renal-specific miRs in exosomes can be rapidly detected and measured, holding great potential as biomarkers in RCC. The present review highlights the studies reporting tumor microenvironment-derived Exo-miRs with therapeutic potential as well as circulating Exo-miRs as potential diagnostic/prognostic biomarkers in patients with RCC.
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Affiliation(s)
- Xiaodong Yu
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Zhongbo Du
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Pingyu Zhu
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Bo Liao
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
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2
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Rehman A, Fatima I, Wang Y, Tong J, Noor F, Qasim M, Peng Y, Liao M. Unveiling the multi-target compounds of Rhazya stricta: Discovery and inhibition of novel target genes for the treatment of clear cell renal cell carcinoma. Comput Biol Med 2023; 165:107424. [PMID: 37717527 DOI: 10.1016/j.compbiomed.2023.107424] [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: 06/02/2023] [Revised: 07/24/2023] [Accepted: 08/28/2023] [Indexed: 09/19/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a prevalent kidney malignancy with a pressing need for innovative therapeutic strategies. In this context, emerging research has focused on exploring the medicinal potential of plants such as Rhazya stricta. Nevertheless, the complex molecular mechanisms underlying its potential therapeutic efficacy remain largely elusive. Our study employed an integrative approach comprising data mining,network pharmacology,tissue cell type analysis, and molecular modelling approaches to identify potent phytochemicals from R. stricta, with potential relevance for ccRCC treatments. Initially, we collected data on R. stricta's phytochemical from public databases. Subsequently, we integrated this information with differentially expressed genes (DEGs) in ccRCC, which were derived from microarray datasets(GSE16441,GSE66270, and GSE76351). We identified potential intersections between R. stricta and ccRCC targets, which enabled us to construct a compound-genes-pathway network using Cytoscape software. This helped illuminate R. stricta's multi-target pharmacological effects on ccRCC. Moreover, tissue cell type analysis added another layer of insight into the cellular specificity of potential therapeutic targets in the kidney. Through further Kaplan-Meier survival analysis, we pinpointed MMP9,ACE,ERBB2, and HSP90AA1 as prospective diagnostic and prognostic biomarkers for ccRCC. Notably, our study underscores the potential of R. stricta derived compounds-namely quebrachamine,corynan-17-ol, stemmadenine,strictanol,rhazinilam, and rhazimolare-to impede ccRCC progression by modulating the activity of MMP9,ACE,ERBB2, and HSP90AA1 genes. Further, molecular docking and dynamic simulations confirmed the plausible binding affinities of these compounds. Despite these promising findings, we recognize the need for comprehensive in vivo and in vitro studies to further investigate the pharmacokinetics and biosafety profiles of these compounds.
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Affiliation(s)
- Abdur Rehman
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Israr Fatima
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yinuo Wang
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiapei Tong
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, 38000, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, 38000, Pakistan
| | - Yuzhong Peng
- Key Lab of Scientific Computing and Intelligent Information Processing in Universities of Guangxi, Nanning Normal University, Nanning, 530001, China.
| | - Mingzhi Liao
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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3
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Pordel S, Khorrami M, Saadatpour F, Rezaee D, Cho WC, Jahani S, Aghaei-Zarch SM, Hashemi E, Najafi S. The role of microRNA-185 in the pathogenesis of human diseases: A focus on cancer. Pathol Res Pract 2023; 249:154729. [PMID: 37639952 DOI: 10.1016/j.prp.2023.154729] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/29/2023] [Indexed: 08/31/2023]
Abstract
MicroRNAs (miRNAs) are a widely-studied class of non-coding RNAs characterized by their short length (18-25 nucleotides). The precise functions of miRNAs are not well-elucidated; however, an increasing number of studies suggest their involvement in various physiologic processes and deregulation in pathologic conditions. miRNA-185 (miR-185) is among the mostly-studied miRNAs in human diseases, which is found to play putative roles in conditions like metabolic disorders, asthma, frailty, schizophrenia, and hepatitis. Notably, many cancer studies report the downregulation of miR-185 in cell lines, tumor tissues, and plasma specimens of patients, while it demonstrates a suppressing role on the malignant properties of cancer cells in vitro and in vivo. Accordingly, miR-185 can be considered a tumor suppressor miRNA in human malignancies, while a few studies also report inconsistent findings. Being suggested as a prognostic/diagnostic biomarker, mi-185 is also found to offer clinical potentials, particularly for early diagnosis and prediction of the prognosis of cancer patients. In this review, we have outlined the studies that have evaluated the functions and clinical significance of miR-185 in different human diseases with a particular focus on cancer.
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Affiliation(s)
- Safoora Pordel
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Immunology and Allergy, The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Saadatpour
- Pharmaceutical Biotechnology Lab, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong, China
| | | | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elham Hashemi
- Department of Anatomical Sciences, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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4
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Choi S, Kim K, Yeo H, Lee G, Kim I, Oh J, An HJ, Lee S. miR-4284 Functions as a Tumor Suppressor in Renal Cell Carcinoma Cells by Targeting Glutamate Decarboxylase 1. Cancers (Basel) 2023; 15:3888. [PMID: 37568704 PMCID: PMC10417762 DOI: 10.3390/cancers15153888] [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: 06/12/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
MicroRNAs (miRNAs) play a crucial role as oncogenic or tumor suppressors in the pathogenesis and progression of tumors. However, few studies have investigated the exact role of miR-4284 in renal cell carcinoma (RCC). We aimed to investigate the role of miR-4284 as a tumor suppressor in renal cancer cell lines. A498 and Caki-1 were transfected with miR-4284. The Cell Counting Kit-8, colony formation, apoptosis assays, and quantitative reverse transcription-polymerase chain reaction were used to evaluate tumor growth-inhibiting functions. The wound-healing, transwell, and sphere-formation assays were conducted to investigate tumorigenic characteristics. The potential target genes of miR-4284 were predicted and experimentally verified. A xenograft experiment was performed to estimate the tumor-growth-suppressive function of miR-4284. miR-4284 overexpression suppressed proliferation, induced apoptosis, and suppressed tumorigenic features of renal cancer cells. Glutamate decarboxylase 1 (GAD1) was directly targeted by miR-4284. A xenograft mouse model injected with Caki-1 cells transfected with miR-4284 showed significantly decreased tumor growth rate and volume. miR-4284 affected tumor growth, metastasis, and apoptosis of renal cancer cells in vitro and in vivo. These findings highlight the potential of miR-4284 as a target for anticancer miRNA therapeutics in RCC.
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Affiliation(s)
- Sujin Choi
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University School of Medicine, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (S.C.); (H.Y.); (G.L.)
| | - Kyeongmi Kim
- Department of Laboratory Medicine, CHA Ilsan Medical Center, CHA University School of Medicine, 1205, Jungang-ro, Ilsandong-gu, Goyang-si 10414, Gyeonggi-do, Republic of Korea;
| | - Hyunjeong Yeo
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University School of Medicine, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (S.C.); (H.Y.); (G.L.)
| | - Gyurim Lee
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University School of Medicine, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (S.C.); (H.Y.); (G.L.)
| | - Isaac Kim
- Department of General Surgery, CHA Bundang Medical Center, CHA University School of Medicine, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea;
| | - Jisu Oh
- Division of Hemato-Oncology, Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, 363 Dongbaekjukjeon-daero, Giheung-gu, Seoul 16995, Gyeonggi-do, Republic of Korea;
| | - Hyun-Ju An
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University School of Medicine, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (S.C.); (H.Y.); (G.L.)
- SL Bio, Inc., 120 Haeryong-ro, Pocheon-si 11160, Gyeonggi-do, Republic of Korea
| | - Soonchul Lee
- Department of Orthopaedic Surgery, CHA Bundang Medical Center, CHA University School of Medicine, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (S.C.); (H.Y.); (G.L.)
- SL Bio, Inc., 120 Haeryong-ro, Pocheon-si 11160, Gyeonggi-do, Republic of Korea
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5
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Guo L, An T, Wan Z, Huang Z, Chong T. SERPINE1 and its co-expressed genes are associated with the progression of clear cell renal cell carcinoma. BMC Urol 2023; 23:43. [PMID: 36959648 PMCID: PMC10037920 DOI: 10.1186/s12894-023-01217-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 03/17/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma(ccRCC) is a frequently occurring malignant tumor of the urinary system. Despite extensive research, the regulatory mechanisms underlying the pathogenesis and progression of ccRCC remain largely unknown. METHODS We downloaded 5 ccRCC expression profiles from the Gene Expression Omnibus (GEO) database and obtained the list of differentially expressed genes (DEGs). Using String and Cytoscape tools, we determined the hub genes of ccRCC, and then analyzed their relationship with ccRCC patient survival. Ultimately, we identified SERPINE1 as a prognostic factor in ccRCC. Meanwhile, we confirmed the role of SERPINE1 in 786-O cells by cell transfection and in vitro experiments. RESULTS Our analysis yielded a total of 258 differentially expressed genes, comprising 105 down-regulated genes and 153 up-regulated genes. Survival analysis of SERPINE1 expression in The Cancer Genome Atlas (TCGA) confirmed its association with the increase of tumor grade, lymph node metastasis, and tumor stage, as well as with shorter survival. Furthermore, we found that SERPINE1 expression levels were associated with CD8 + T cells, CD4 + T cells, B cells, macrophages, neutrophils, and dendritic cells. Cell experiments showed that knockdown SERPINE1 expression could inhibit the proliferation, migration and invasion of ccRCC cells. Among the co-expressed genes with the highest correlation, ITGA5, SLC2A3, SLC2A14, SHC1, CEBPB, and ADA were overexpressed and associated with shorter overall survival (OS) in ccRCC. CONCLUSIONS In this study, we identified hub genes that are strongly related to ccRCC, and highlights the potential utility of overexpressed SERPINE1 and its co-expressed genes could be used as prognostic and diagnostic biomarkers in ccRCC.
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Affiliation(s)
- Lingyu Guo
- Department of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Tian An
- Department of Dermatology and Plastic Surgery, The Second Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, China
| | - Ziyan Wan
- Department of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Zhixin Huang
- Department of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Tie Chong
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 West Fifth Road, Xi'an, 710000, China.
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The Effects of circ_000558/miR-1225-5p/ARL4C on Regulating the Proliferation of Renal Cell Carcinoma Cells. JOURNAL OF ONCOLOGY 2023; 2023:1303748. [PMID: 36778920 PMCID: PMC9911241 DOI: 10.1155/2023/1303748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 02/05/2023]
Abstract
Renal cell carcinoma (RCC) is one of the top ten tumors over the world. RCC is not sensitive to radiotherapy and chemotherapy. Therefore, it is necessary to find new targets for the treatment. CircRNAs are a special type of noncoding RNAs, which play important roles in many types of cancer. In this study, we found circ_000558 was upregulated in RCC cells, and it elevated the proliferation ability of RCC cells. The relationship between miR-1225-5p and circ_000558 or ARL4C was predicted via circBank and circular RNA interactome and confirmed by dual-luciferase reporter assay. Then, the effects of circ_000558/miR-1225-5p/ARL4C on RCC cell proliferation and apoptosis were assessed by CCK-8 assay. The results revealed that the knockdown of ARL4C significantly reduced RCC cell proliferation and overexpression of circ_000558 could significantly induce RCC cell proliferation after miR-1225-5p treatment further promoted the inhibitory ability of ARL4C knockdown. Overall, our study suggested that circ_000558/miR-1225-5p/ARL4C network was related to the RCC cell proliferation. This finding could provide new targets for the treatment and prognosis of RCC.
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Fakhrezare F, Ebrahimi SO, Reiisi S. The association between genetic variation rs2292832 and the processing efficiency of pre-mir-149 affects the risk of breast cancer. Mol Biol Rep 2023; 50:679-685. [PMID: 36371555 DOI: 10.1007/s11033-022-08027-3] [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: 05/07/2022] [Accepted: 10/12/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND microRNAs (miRNAs) play key roles in regulating cancer development, including breast cancer. Variation in miRNA genes can associate with the risk of cancer by alterations in the miRNA's processing and maturation. Therefore, human blood samples and breast cancer cell line (MCF7) were analyzed to study any possible association between the genetic variant (rs2292832) in the miR-149 precursor and breast cancer susceptibility. METHODS To study the role of rs2292832 polymorphism in breast cancer, the miR-149 gene variant was genotyped using PCR-RFLP. For evaluating the effect of SNP on function and expression levels of mature miR-149, we inserted pre-miR-149 and flanking region with CC or TT genotype into a pEGFPN1 expression vector, and qPCR was accomplished. Cell survival, proliferation, and migration properties investigated by MTT and wound healing assay. Statistical analysis was carried out for data analysis. RESULTS T allele in variant rs2292832 is associated with an increased risk of breast cancer. Such association was also obtained in co-dominant (OR = 2.5) and dominant (OR = 2.016) models. The variant allele led to reduced production of mature miR-149 and resulted in increased cell proliferation and migration of MCF7 cells. CONCLUSION These findings suggest that miR-149 suppresses tumor cell proliferation, and the pre-mir-149 polymorphism affects the processing of miR-149, causing an alteration in the abundance of the miRNA mature form, which can regulate tumor progression and metastasis.
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Affiliation(s)
- Farzaneh Fakhrezare
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Seyed Omar Ebrahimi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Somayeh Reiisi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran.
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Peng L, Cao Z, Wang Q, Fang L, Yan S, Xia D, Wang J, Bi L. Screening of possible biomarkers and therapeutic targets in kidney renal clear cell carcinoma: Evidence from bioinformatic analysis. Front Oncol 2022; 12:963483. [PMID: 36313709 PMCID: PMC9606658 DOI: 10.3389/fonc.2022.963483] [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: 06/11/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Renal cell carcinoma (RCC), as one of the most common urological malignancies, has many histologic and molecular subtypes, among which clear cell renal cell carcinoma (ccRCC) is one of the most common causes of tumor-related deaths. However, the molecular mechanism of ccRCC remains unclear. In order to identify the candidate genes that may exist in the occurrence and development of ccRCC, microarray datasets GSE6344, GSE16441, GSE36895, GSE53757 and GSE76351 had been downloaded from Gene Expression Omnibus (GEO) database. Apart from that, the differentially expressed genes (DEGs) were screened through Bioinformatics & Evolutionary Genomics. In addition, the protein-protein interaction network (PPI) was constructed, and the module analysis was performed using STRING and Cytoscape. By virtue of DAVID online database, GO/KEGG enrichment analysis of DEGs was performed. Consequently, a total of 118 DEGs were screened, including 24 up-regulated genes and 94 down-regulated genes. The plug-in MCODE of Cytoscape was adopted to analyze the most significant modules of DEGs. What’s more, the genes with degree greater than 10 in DEGs were selected as the hub genes. The overall survival (OS) and disease progression free survival (DFS) of 9 hub genes were analyzed through GEPIA2 online platform. As shown by the survival analysis, SLC34A1, SLC12A3, SLC12A1, PLG, and ENO2 were closely related to the OS of ccRCC, whereas SLC34A1 and LOX were closely related to DFS. Among 11 SLC members, 6 SLC members were highly expressed in non-cancerous tissues (SLC5A2, SLC12A1, SLC12A3, SLC34A1, SLC34A2, SLC34A3). Besides, SLC12A5 and SLC12A7 were highly expressed in ccRCC. Furthermore, SLC12A1-A7, SLC34A1 and SLC34A3 were closely related to OS, whereas SLC12A2/A4/A6/A7 and SLC34A1/A3 were closely related to DFS. In addition, 5 algorithms were used to analyze hub genes, the overlapping genes were AQP2 and KCNJ1. To sum up, hub gene can help us understand the molecular mechanism of the occurrence and development of ccRCC, thereby providing a theoretical basis for the diagnosis and targeted therapy of ccRCC.
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9
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Histone deacetylase 3 promotes alveolar epithelial-mesenchymal transition and fibroblast migration under hypoxic conditions. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:922-931. [PMID: 35804191 PMCID: PMC9355949 DOI: 10.1038/s12276-022-00796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 11/12/2022]
Abstract
Epithelial–mesenchymal transition (EMT), a process by which epithelial cells undergo a phenotypic conversion that leads to myofibroblast formation, plays a crucial role in the progression of idiopathic pulmonary fibrosis (IPF). Recently, it was revealed that hypoxia promotes alveolar EMT and that histone deacetylases (HDACs) are abnormally overexpressed in the lung tissues of IPF patients. In this study, we showed that HDAC3 regulated alveolar EMT markers via the AKT pathway during hypoxia and that inhibition of HDAC3 expression by small interfering RNA (siRNA) decreased the migration ability and invasiveness of diseased human lung fibroblasts. Furthermore, we found that HDAC3 enhanced the migratory and invasive properties of fibroblasts by positively affecting the EMT process, which in turn was affected by the increased and decreased levels of microRNA (miR)-224 and Forkhead Box A1 (FOXA1), respectively. Lastly, we found this mechanism to be valid in an in vivo system; HDAC3 siRNA administration inhibited bleomycin-induced pulmonary fibrosis in mice. Thus, it is reasonable to suggest that HDAC3 may accelerate pulmonary fibrosis progression under hypoxic conditions by enhancing EMT in alveolar cells through the regulation of miR-224 and FOXA1. This entire process, we believe, offers a novel therapeutic approach for pulmonary fibrosis. Inhibiting an enzyme that boosts the invasiveness of fibrosis-related cells could prove to be a novel therapeutic strategy for treating idiopathic lung fibrosis. Lung fibrosis progresses via the transition of epithelial cells into myofibroblasts, which are migratory invasive cell types that secrete collagen and deposit excessive extracellular material. Low oxygen conditions (hypoxia) accelerate this transition process. Scientists recently identified a group of histone deacetylases (HDACs) that are significantly overexpressed in the lung tissues of patients with fibrosis. In experiments on mice and human cell lines, Jeong-Woong Park and Se-Hee Kim at Gachon University Gil Medical Center, Incheon, South Korea, and co-workers demonstrated that under hypoxic conditions, HDAC3 increases the cellular transition to myofibroblasts by regulating the expression of a key microRNA and its target gene. Inhibiting HDAC3 suppresses the migration and invasiveness of lung myofibroblasts.
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10
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Tzeng HE, Lin SL, Thadevoos LA, Lien MY, Yang WH, Ko CY, Lin CY, Huang YW, Liu JF, Fong YC, Chen HT, Tang CH. Nerve growth factor promotes lysyl oxidase-dependent chondrosarcoma cell metastasis by suppressing miR-149-5p synthesis. Cell Death Dis 2021; 12:1101. [PMID: 34815382 PMCID: PMC8611026 DOI: 10.1038/s41419-021-04392-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022]
Abstract
Chondrosarcoma is a malignancy of soft tissue and bone that has a high propensity to metastasize to distant organs. Nerve growth factor (NGF) is critical for neuronal cell growth, apoptosis, and differentiation, and also appears to promote the progression and metastasis of several different types of tumors, although the effects of NGF upon chondrosarcoma mechanisms are not very clear. We report that NGF facilitates lysyl oxidase (LOX)-dependent cellular migration and invasion in human chondrosarcoma cells, and that NGF overexpression enhances lung metastasis in a mouse model of chondrosarcoma. NGF-induced stimulation of LOX production and cell motility occurs through the inhibition of miR-149-5p expression, which was reversed by PI3K, Akt, and mTOR inhibitors and their respective short interfering RNAs. Notably, levels of NGF and LOX expression correlated with tumor stage in human chondrosarcoma samples. Thus, NGF appears to be a worthwhile therapeutic target for metastatic chondrosarcoma.
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Affiliation(s)
- Huey-En Tzeng
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Division of Hematology/Oncology, Department of Medicine, Taipei Medical University Hospital, Taipei, Taiwan.,School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Syuan-Ling Lin
- Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Louis Anoop Thadevoos
- International Master Program of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Ming-Yu Lien
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan.,School and Medicine, China Medical University, Taichung, Taiwan
| | - Wei-Hung Yang
- School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Department of Nursing, National Taichung University of Science and Technology, Taichung, Taiwan.,Department of Orthopedic Surgery, Taichung Hospital, Ministry of Health and Welfare, Taichung, Taiwan
| | - Chih-Yuan Ko
- Department of Orthopedic Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Chih-Yang Lin
- Department of Pharmacology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Yu-Wen Huang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Ju-Fang Liu
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Chin Fong
- Department of Sports Medicine, College of Health Care, China Medical University, Taichung, Taiwan.,Department of Orthopedic Surgery, China Medical University Beigang Hospital, Yunlin, Taiwan
| | - Hsien-Te Chen
- Department of Orthopedic Surgery, China Medical University Hospital, Taichung, Taiwan. .,Department of Sports Medicine, College of Health Care, China Medical University, Taichung, Taiwan.
| | - Chih-Hsin Tang
- Department of Pharmacology, School of Medicine, China Medical University, Taichung, Taiwan. .,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan. .,Department of Biotechnology, College of Health Science, Asia University, Taichung, Taiwan. .,Chinese Medicine Research Center, China Medical University, Taichung, Taiwan.
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11
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The emerging role of miR-200 family in metastasis: focus on EMT, CSCs, angiogenesis, and anoikis. Mol Biol Rep 2021; 48:6935-6947. [PMID: 34510322 DOI: 10.1007/s11033-021-06666-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Cancer is the second major threat to human society and one of the main challenges facing healthcare systems. One of the main problems of cancer care is the metastases of cancer cells that cause 90% of deaths due to cancer. Multiple molecular mechanisms are involved in cancer cell metastasis. Therefore, a better understanding of these molecular mechanisms is necessary for designing restrictive strategies against cancer cell metastasis. Accumulating data suggests that MicroRNAs (miRNAs) are involved in metastasis and invasion of human tumors through regulating multiple genes expression levels that are involved in molecular mechanisms of metastasis. The goal of this review is to present the molecular pathways by which the miR 200 family manifests its effects on EMT, cancer stem cells, angiogenesis, anoikis, and the effects of tumor cell metastases. METHODS A detailed literature search was conducted to find information about the role of the miR-200 family in the processes involved in metastasis in various databases. RESULTS Numerous lines of evidence revealed an association between the mir-200 family and metastasis of human tumors by impressing processes such as cancer stem cells, EMT, angiogenesis, and anoikis. CONCLUSIONS Understanding the molecular mechanisms associated with metastasis in which the miR-200 family is involved can be effective in treating metastatic cancers.
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12
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Zhang S, Hu X, Luo Z, Jiang Y, Sun Y, Ma S. Biomarker-guided heterogeneity analysis of genetic regulations via multivariate sparse fusion. Stat Med 2021; 40:3915-3936. [PMID: 33906263 PMCID: PMC8277716 DOI: 10.1002/sim.9006] [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: 04/20/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 11/06/2022]
Abstract
Heterogeneity is a hallmark of many complex diseases. There are multiple ways of defining heterogeneity, among which the heterogeneity in genetic regulations, for example, gene expressions (GEs) by copy number variations (CNVs), and methylation, has been suggested but little investigated. Heterogeneity in genetic regulations can be linked with disease severity, progression, and other traits and is biologically important. However, the analysis can be very challenging with the high dimensionality of both sides of regulation as well as sparse and weak signals. In this article, we consider the scenario where subjects form unknown subgroups, and each subgroup has unique genetic regulation relationships. Further, such heterogeneity is "guided" by a known biomarker. We develop a multivariate sparse fusion (MSF) approach, which innovatively applies the penalized fusion technique to simultaneously determine the number and structure of subgroups and regulation relationships within each subgroup. An effective computational algorithm is developed, and extensive simulations are conducted. The analysis of heterogeneity in the GE-CNV regulations in melanoma and GE-methylation regulations in stomach cancer using the TCGA data leads to interesting findings.
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Affiliation(s)
- Sanguo Zhang
- School of Mathematical Sciences, and Key Laboratory of Big Data Mining and Knowledge Management, Chinese Academy of Science, Beijing, China
| | - Xiaonan Hu
- School of Mathematical Sciences, and Key Laboratory of Big Data Mining and Knowledge Management, Chinese Academy of Science, Beijing, China
| | - Ziye Luo
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Yu Jiang
- School of Public Health, University of Memphis, Tennessee, USA
| | - Yifan Sun
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Shuangge Ma
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
- Department of Biostatistics, Yale University, Connecticut, USA
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Jin C, Shi L, Li K, Liu W, Qiu Y, Zhao Y, Zhao B, Li Z, Li Y, Zhu Q. Mechanism of tumor‑derived extracellular vesicles in regulating renal cell carcinoma progression by the delivery of MALAT1. Oncol Rep 2021; 46:187. [PMID: 34278501 PMCID: PMC8298989 DOI: 10.3892/or.2021.8138] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Renal cell carcinoma (RCC) is a major healthcare burden globally. Tumor-derived extracellular vesicles (EVs) contribute to the formation of a pro-metastatic microenvironment. In the present study, we explored the role and mechanism of RCC cell 786-O-derived EVs (786-O-EVs) in RCC. First, 786-O-EVs were extracted and identified, and EV internalization of RCC cells was observed. RCC cell malignant behaviors and long noncoding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) expression patterns were detected before and after 786-O-EV treatment. MALAT1 was intervened to evaluate RCC cell behaviors. The downstream mechanism involving MALAT1 was predicted. In addition, the relationship among MALAT1, transcription factor CP2 like 1 (TFCP2L1) and ETS proto-oncogene 1, transcription factor (ETS1) was analyzed. TFCP2L1 expression patterns were measured after 786-O-EV exposure. Tumor xenograft formation assay and lung metastasis model were adopted to verify the role of 786-O-EVs in vivo in RCC. It was found that 786-O-EVs could be internalized by RCC cells. 786-O-EVs promoted RCC cell malignant behaviors, accompanied by elevated MALAT1 expression levels. The 786-O-EVs with MALAT1 knockdown attenuated the promotive effect of sole 786-O-EVs on RCC cells. MALAT1 located ETS1 in the TFCP2L1 promoter and negatively regulated TFCP2L1, and ETS1 protein could specifically bind to MALAT1. 786-O-EVs enhanced the binding of ETS1 and the TFCP2L1 promoter and decreased TFCP2L1 expression. In vivo, 786-O-EVs promoted tumor growth and RCC lung metastasis, which was suppressed following inhibition of MALAT1. Our findings indicated that 786-O-EVs promoted RCC invasion and metastasis by transporting MALAT1 to promote the binding of transcription factor ETS1 and TFCP2L1 promoter.
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Affiliation(s)
- Chengluo Jin
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Linmei Shi
- School of Health Management, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Kunlun Li
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Wei Liu
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Yu Qiu
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Yakun Zhao
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Bai Zhao
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Zhexun Li
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Yifei Li
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
| | - Qingguo Zhu
- Department of Urology, The Second Affiliated Hospital, Harbin Medical University, Nangang, Harbin, Heilongjiang 150086, P.R. China
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Xiong L, Feng Y, Hu W, Tan J, Li S, Wang H. Expression of AOX1 Predicts Prognosis of Clear Cell Renal Cell Carcinoma. Front Genet 2021; 12:683173. [PMID: 34290740 PMCID: PMC8287305 DOI: 10.3389/fgene.2021.683173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/08/2021] [Indexed: 01/16/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent kidney cancer worldwide, and appropriate cancer biomarkers facilitate early diagnosis, treatment, and prognosis prediction in cancer management. However, an accurate biomarker for ccRCC is lacking. This study identified 356 differentially expressed genes in ccRCC tissues compared with normal kidney tissues by integrative analysis of eight ccRCC datasets. Enrichment analysis of the differentially expressed genes unveiled improved adaptation to hypoxia and metabolic reprogramming of the tumor cells. Aldehyde oxidase 1 (AOX1) gene was identified as a biomarker for ccRCC among all the differentially expressed genes. ccRCC tissues expressed significantly lower AOX1 than normal kidney tissues, which was further validated by immunohistochemistry at the protein level and The Cancer Genome Atlas (TCGA) data mining at the mRNA level. Higher AOX1 expression predicted better overall survival in ccRCC patients. Furthermore, AOX1 DNA copy number deletion and hypermethylation were negatively correlated with AOX1 expression, which might be the potential mechanism for its dysregulation in ccRCC. Finally, we illustrated that the effect of AOX1 as a tumor suppressor gene is not restricted to ccRCC but universally exists in many other cancer types. Hence, AOX1 may act as a potential prognostic biomarker and therapeutic target for ccRCC.
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Affiliation(s)
- Luyang Xiong
- Department of Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuchen Feng
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Hu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiahong Tan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shusheng Li
- Department of Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongjie Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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Novel Epigenetic Eight-Gene Signature Predictive of Poor Prognosis and MSI-Like Phenotype in Human Metastatic Colorectal Carcinomas. Cancers (Basel) 2021; 13:cancers13010158. [PMID: 33466447 PMCID: PMC7796477 DOI: 10.3390/cancers13010158] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The global methylation profile of two human metastatic colorectal carcinoma subgroups with significantly different outcomes (primary-resistant versus drug-sensitive tumors) was analyzed and compared with the gene expression and methylation data from The Cancer Genome Atlas COlon ADenocarcinoma (TCGA COAD) metastatic colorectal carcinoma dataset with the aim to identify a prognostic signature of functionally methylated genes. A novel epigenetic eight-gene signature, with hypermethylation of the promoter regions, was identified and validated for its capacity to predict poor outcome, which had a CpG-island methylator phenotype (CIMP)-high status and microsatellite instability (MSI)-like phenotype. Abstract Epigenetics is involved in tumor progression and drug resistance in human colorectal carcinoma (CRC). This study addressed the hypothesis that the DNA methylation profiling may predict the clinical behavior of metastatic CRCs (mCRCs). The global methylation profile of two human mCRC subgroups with significantly different outcome was analyzed and compared with gene expression and methylation data from The Cancer Genome Atlas COlon ADenocarcinoma (TCGA COAD) and the NCBI GENE expression Omnibus repository (GEO) GSE48684 mCRCs datasets to identify a prognostic signature of functionally methylated genes. A novel epigenetic signature of eight hypermethylated genes was characterized that was able to identify mCRCs with poor prognosis, which had a CpG-island methylator phenotype (CIMP)-high and microsatellite instability (MSI)-like phenotype. Interestingly, methylation events were enriched in genes located on the q-arm of chromosomes 13 and 20, two chromosomal regions with gain/loss alterations associated with adenoma-to-carcinoma progression. Finally, the expression of the eight-genes signature and MSI-enriching genes was confirmed in oxaliplatin- and irinotecan-resistant CRC cell lines. These data reveal that the hypermethylation of specific genes may provide prognostic information that is able to identify a subgroup of mCRCs with poor prognosis.
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Dual Role of the PTPN13 Tyrosine Phosphatase in Cancer. Biomolecules 2020; 10:biom10121659. [PMID: 33322542 PMCID: PMC7763032 DOI: 10.3390/biom10121659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023] Open
Abstract
In this review article, we present the current knowledge on PTPN13, a class I non-receptor protein tyrosine phosphatase identified in 1994. We focus particularly on its role in cancer, where PTPN13 acts as an oncogenic protein and also a tumor suppressor. To try to understand these apparent contradictory functions, we discuss PTPN13 implication in the FAS and oncogenic tyrosine kinase signaling pathways and in the associated biological activities, as well as its post-transcriptional and epigenetic regulation. Then, we describe PTPN13 clinical significance as a prognostic marker in different cancer types and its impact on anti-cancer treatment sensitivity. Finally, we present future research axes following recent findings on its role in cell junction regulation that implicate PTPN13 in cell death and cell migration, two major hallmarks of tumor formation and progression.
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18
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Zhao Y, Tao Z, Chen X. Identification of the miRNA-mRNA regulatory pathways and a miR-21-5p based nomogram model in clear cell renal cell carcinoma. PeerJ 2020; 8:e10292. [PMID: 33194441 PMCID: PMC7648458 DOI: 10.7717/peerj.10292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background The purpose of this study was to determine the key microRNAs (miRNAs) and their regulatory networks in clear cell renal cell carcinoma (ccRCC). Methods Five mRNA and three microRNA microarray datasets were downloaded from the Gene Expression Omnibus database and used to screen the differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs). Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed with Metascape. A miRNA-mRNA network was mapped with the Cytoscape tool. The results were validated with data from The Cancer Genome Atlas (TCGA) and qRT-PCR. A nomogram model based on independent prognostic key DEMs, stage and grade was constructed for further investigation. Results A total of 26 key DEMs and 307 DEGs were identified. Dysregulation of four key DEMs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) was identified to correlate with overall survival. The results were validated with TCGA data and qRT-PCR. The nomogram model showed high accuracy in predicting the prognosis of patients with ccRCC. Conclusion We identified 26 DEMs that may play vital roles in the regulatory networks of ccRCC. Four miRNAs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) were considered as potential biomarkers in the prognosis of ccRCC, among which only miR-21-5p was found to be an independent prognostic factor. A nomogram model was then created on the basis of independent factors for better prediction of prognosis for patients with ccRCC. Our results suggest a need for further experimental validation studies.
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Affiliation(s)
- Yiqiao Zhao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zijia Tao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Long Q, Sun J, Lv J, Liang Y, Li H, Li X. PTPN13 acts as a tumor suppressor in clear cell renal cell carcinoma by inactivating Akt signaling. Exp Cell Res 2020; 396:112286. [PMID: 32919955 DOI: 10.1016/j.yexcr.2020.112286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 01/24/2023]
Abstract
Protein tyrosine phosphatase, nonreceptor type 13 (PTPN13), has emerged as a critical cancer-related gene that is implicated in a wide range of cancer types. However, the role of PTPN13 in clear cell renal cell carcinoma (ccRCC) is poorly understood. In the present study, we aimed to evaluate whether PTPN13 participates in the progression of ccRCC. Decreased expression of PTPN13 was found in ccRCC tissues, which predicted a shorter survival rate in ccRCC patients. PTPN13 expression was also lower in ccRCC cell lines, and the upregulation of PTPN13 repressed the proliferation, colony formation and invasion, but enhanced the apoptosis of ccRCC cells. In contrast, the silencing of PTPN13 produced the opposite effects. Further data showed that PTPN13 overexpression decreased the phosphorylation of Akt, while PTPN13 silencing increased the phosphorylation of Akt. Treatment with Akt inhibitor markedly abrogated the PTPN13 silencing-evoked oncogenic effect in ccRCC cells. Xenograft tumor experiments revealed that overexpression of PTPN13 remarkably restricted the tumor formation and growth of ccRCC cells in vivo associated with inactivation of Akt. In conclusion, our data demonstrated that overexpression of PTPN13 restricts the proliferation and invasion of ccRCC cells through inactivation of Akt. Our study suggests a tumor suppressive function of PTPN13 in ccRCC and highlights the potential role of PTPN13 in the progression of ccRCC.
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Affiliation(s)
- Qingzhi Long
- Department of Urology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiping Sun
- Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jia Lv
- Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yu Liang
- Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Huixian Li
- Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xudong Li
- Department of Urology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, China.
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Lei H, Tao K. Somatic mutations in colorectal cancer are associated with the epigenetic modifications. J Cell Mol Med 2020; 24:11828-11836. [PMID: 32865336 PMCID: PMC7579689 DOI: 10.1111/jcmm.15799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/22/2020] [Accepted: 08/09/2020] [Indexed: 01/13/2023] Open
Abstract
Colorectal cancer (CRC) mostly arises from progressive accumulation of somatic mutations within cells. Most commonly mutated genes like TP53, APC and KRAS can promote survival and proliferation of cancer cells. Although the molecular alterations and landscape of some specific mutations in CRC are well known, the presence of a somatic mutation signature related to genomic regions and epigenetic markers remain unclear. To find the signatures from a random distribution of somatic mutations in CRCs, we carried out enrichment analysis in different genomic regions and identified peaks of epigenetic markers. We validated that the mutation frequency in miRNA is dramatically higher than in flanking genomic regions. Moreover, we observed that somatic mutations in CRC and colon cancer cell lines are significantly enriched in CTCF binding sites. We also found these mutations are enriched for H3K27me3 in both normal sigmoid colon and colon cancer cell lines. Taken together, our findings suggest that there are some common somatic mutations signatures which provide new directions to study CRC.
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Affiliation(s)
- Hongwei Lei
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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21
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Moynihan MJ, Sullivan TB, Burks E, Schober J, Calabrese M, Fredrick A, Kalantzakos T, Warrick J, Canes D, Raman JD, Rieger-Christ K. MicroRNA profile in stage I clear cell renal cell carcinoma predicts progression to metastatic disease. Urol Oncol 2020; 38:799.e11-799.e22. [PMID: 32534961 DOI: 10.1016/j.urolonc.2020.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/29/2020] [Accepted: 05/09/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE This study sought to identify microRNA (miRNA) profiles of small, pathologically confirmed stage 1 clear cell renal cell carcinoma (ccRCC) tumors that are associated with progression to metachronous metastatic disease. MATERIALS AND METHODS Fifty-five pathologic stage 1 ccRCC tumors ≤5cm, from 2 institutions, were examined in a miRNA screening, followed by a validation study. For the screening phase 752 miRNA were evaluated on each sample to identify those with differential expression between tumors that subsequently did (n = 10) or did not (n = 10) progress to metastatic disease. For the validation, 35 additional samples (20 nonprogressors and 15 with distant progression) were utilized to investigate 20 miRNA to determine if a miRNA panel could differentiate aggressive tumors: associations of miRNA expression with cancer specific survival was also investigated. RESULTS In the screening analysis, 35 miRNA were differentially expressed (P < 0.05, FDR < 0.1) between the groups. In the validation, 11 miRNA were confirmed to have differential expression. The miRNA -10a-5p, -23b-3p, and -26a-5p differentiated nonprogressive and distant progressive disease with a sensitivity of 73.3% and a specificity of 85% (AUC=0.893). In addition, levels of miR-30a-3p and -145-5p were identified as independent prognostic factors of cancer specific survival. CONCLUSIONS This investigation identified miRNA biomarkers that may differentiate between non-progressive ccRCC tumors and those that progress to metastatic disease in this group of stage I tumors. The miRNA profiles determined in this study have the potential to identify patients with small renal masses who are likely to have progressive ccRCC. Such information may be valuable to incorporate into predictive models.
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Affiliation(s)
| | - Travis B Sullivan
- Department of Translational Research, Lahey Hospital & Medical Center, Burlington, MA
| | - Eric Burks
- Department of Pathology, Lahey Hospital & Medical Center, Burlington, MA
| | - Jared Schober
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA
| | - Marc Calabrese
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA
| | - Ariel Fredrick
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA
| | - Thomas Kalantzakos
- Department of Translational Research, Lahey Hospital & Medical Center, Burlington, MA
| | - Joshua Warrick
- Department of Pathology, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - David Canes
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA
| | - Jay D Raman
- Department of Urology, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Kimberly Rieger-Christ
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA; Department of Translational Research, Lahey Hospital & Medical Center, Burlington, MA.
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Cui H, Xu L, Li Z, Hou KZ, Che XF, Liu BF, Liu YP, Qu XJ. Integrated bioinformatics analysis for the identification of potential key genes affecting the pathogenesis of clear cell renal cell carcinoma. Oncol Lett 2020; 20:1573-1584. [PMID: 32724399 PMCID: PMC7377202 DOI: 10.3892/ol.2020.11703] [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] [Received: 09/13/2019] [Accepted: 04/15/2020] [Indexed: 12/17/2022] Open
Abstract
Clear cell renal cell carcinoma (CCRCC) is a typical type of RCC with the worst prognosis among the common epithelial neoplasms of the kidney. However, its molecular pathogenesis remains unknown. Therefore, the aim of the present study was to screen for effective and potential pathogenic biomarkers of CCRCC. The gene expression profile of the GSE16441, GSE36895, GSE40435, GSE46699, GSE66270 and GSE71963 datasets were downloaded from the Gene Expression Omnibus database. First, the limma package in R language was used to identify differentially expressed genes (DEGs) in each dataset. The robust and strong DEGs were explored using the robust rank aggregation method. A total of 980 markedly robust DEGs were identified (429 upregulated and 551 downregulated). According to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, these DEGs exhibited an obvious enrichment in various cancer-related biological pathways and functions. The Search Tool for the Retrieval of Interacting Genes/Proteins database was used for the construction of a protein-protein interaction (PPI) network, the Cytoscape MCODE plug-in for module analysis and the cytoHubba plug-in to identify hub genes from the aforementioned DEGs. A total of four key modules were identified in the PPI network. A total of six hub genes, including C-X-C motif chemokine ligand 12, bradykinin receptor B2, adenylate cyclase 7, calcium sensing receptor (CASR), kininogen 1 and lysophosphatidic acid receptor 5, were identified. The DEG results of the hub genes were verified using The Cancer Genome Atlas database, and CASR was found to be significantly associated with the prognosis of patients with CCRCC. In conclusion, the present study provided new insight and potential biomarkers for the diagnosis and prognosis of CCRCC.
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Affiliation(s)
- Hao Cui
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Lei Xu
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Zhi Li
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Ke-Zuo Hou
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Xiao-Fang Che
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Bo-Fang Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yun-Peng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Xiu-Juan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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Klimentova EA, Gilyazova IR, Bermisheva MA, Blinnikova AM, Safiullin RI, Izmailov AA, Yang B, Pavlov VN, Khusnutdinova EK. Investigation of the Role of microRNA Associated with the VHL-HIFα-Dependent Pathway in Patients with Clear Cell Renal Cell Carcinoma. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420030096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chen J, Zhong Y, Li L. miR-124 and miR-203 synergistically inactivate EMT pathway via coregulation of ZEB2 in clear cell renal cell carcinoma (ccRCC). J Transl Med 2020; 18:69. [PMID: 32046742 PMCID: PMC7014595 DOI: 10.1186/s12967-020-02242-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is one of the most aggressive urological malignancies. MicroRNAs (miRNAs) are post-transcriptional gene regulators in tumor pathophysiology. As miRNAs exert cooperative repressive effects on target genes, studying the miRNA synergism is important to elucidate the regulation mechanism of miRNAs. METHODS We first created a miRNA-mRNA association network based on sequence complementarity and co-expression patterns of miRNA-targets. The synergism between miRNAs was then defined based on their expressional coherence and the concordance between target genes. The miRNA and mRNA expression were detected in RCC cell lines (786-O) using quantitative RT-PCR. Potential miRNA-target interaction was identified by Dual-Luciferase Reporter assay. Cell proliferation and migration were assessed by CCK-8 and transwell assay. RESULTS A synergistic miRNA-miRNA interaction network of 28 miRNAs (52 miRNA pairs) with high coexpression level were constructed, among which miR-124 and miR-203 were identified as most tightly connected. ZEB2 expression is inversely correlated with miR-124 and miR-203 and verified as direct miRNA target. Cotransfection of miR-124 and miR-203 into 786-O cell lines effectively attenuated ZEB2 level and normalized renal cancer cell proliferation and migration. The inhibitory effects were abolished by ZEB2 knockdown. Furthermore, pathway analysis suggested that miR-124 and miR-203 participated in activation of epithelial-to-mesenchymal transition (EMT) pathway via regulation of ZEB2. CONCLUSIONS Our findings provided insights into the role of miRNA-miRNA collaboration as well as a novel therapeutic approach in ccRCC.
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Affiliation(s)
- Jiajia Chen
- School of Chemistry, Biology and Materials Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou, 215011, China.
| | - Yuqing Zhong
- School of Chemistry, Biology and Materials Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou, 215011, China
| | - Liangzhi Li
- School of Chemistry, Biology and Materials Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou, 215011, China
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25
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Abstract
Extracellular vesicles (EVs) have an essential functional role in local tumour progression, metastatic spread and the emergence of drug resistance in bladder, kidney and prostate cancer. Thus, EVs could be diagnostic, prognostic and predictive biomarkers for these malignancies. Virtually all biomolecules (including DNA, mRNA, microRNA, long non-coding RNA, proteins and lipids) packaged into EVs have been tested as biomarkers in blood and urine samples. The results are very heterogeneous, but promising biomarker candidates have been identified. Differing methods of EV isolation, characterization and analysis of their content have been used owing to a lack of international consensus; hence, comparing study results is challenging. Furthermore, validation of potential biomarkers in independent cohorts or prospective trials has rarely been performed. Future efforts to establish EV-derived biomarkers need to adequately address these points. In addition, emerging technologies such as mass spectroscopy and chip-based approaches can identify surface markers specific for cancer-associated EVs and will enable specific separation from blood and urine EVs, which probably will improve their performance as biomarkers. Moreover, EVs could be harnessed as therapeutic drug delivery vehicles for precise and effective anticancer therapy.
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Marin DE, Braicu C, Dumitrescu G, Pistol GC, Cojocneanu R, Neagoe IB, Taranu I. MicroRNA profiling in kidney in pigs fed ochratoxin A contaminated diet. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109637. [PMID: 31499447 DOI: 10.1016/j.ecoenv.2019.109637] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
OTA is a toxic metabolite produced by fungus belonging to Aspergillus and Penicillium genera. Kidney is the main target of this toxin; OTA is considered as one of the etiological factors at the origin of the human Balkan endemic nephropathy. microRNA are short non-coding transcrips (18-22 nucleotides in length) regulating key cellular processes. Various miRNAs have been established to play important roles in development of renal carcinoma and urothelial cancer. The objective of this study is to analyse the miRNA profiling in the kidney of piglets experimentally intoxicated with feed contaminated with OTA. Fifteen piglets (five pigs/group) were randomly distributed into 3 groups, fed normal diet (Group 1: control), or diets contaminated with OTA in two concentrations: 50 μg OTA/kg feed (Group 2: 50 μg OTA/kg feed) or 200 μg OTA/kg feed (Group 3: 200 μg OTA/kg feed) for 28 days. At the end of the experiment blood samples were taken for serological analyses. Animals from control group and 200 μg OTA/kg feed were sacrificed and kidney samples were taken for histological and molecular analyses. As resulted from molecular profiling study there are 8 miRNA differentially expressed in OTA kidney vs control kidney, in which five miRNA were overexpressed in the kidney of OTA intoxicated animals: miR-497 (FC = 6.34), miR-133a-3p (FC = 5.75), miR-423-3p (FC = 5.48), miR-34a (FC = 1.68), miR-542-3p (1.65) while three miRNA were downregulated: miR-421-3p (FC = -3.96); miR-490 (FC = -3.87); miR-9840-3p (FC = -2.13). The altered miRNAs as effect of OTA are strongly connected to the engine of cancer, disturbing nodal points in different pathways, as TP53 signalling. This proof-of-concept study proves the actual utility of miRNAs as biomarkers of mycotoxin exposure, including OTA.
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Affiliation(s)
- Daniela Eliza Marin
- Laboratory of Animal Biology, National Institute for Research and Development for Biology and Animal Nutrition, Calea Bucuresti No. 1, Balotesti, Ilfov, 077015, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Marinescu 23 Street, No. 23, 400012, Cluj-Napoca, Romania
| | - Gabi Dumitrescu
- University of Agricultural Sciences and Veterinary Medicine of Banat, King Mihai I of Romania, Calea Aradului nr. 119, Timisoara, Romania
| | - Gina C Pistol
- Laboratory of Animal Biology, National Institute for Research and Development for Biology and Animal Nutrition, Calea Bucuresti No. 1, Balotesti, Ilfov, 077015, Romania
| | - Roxana Cojocneanu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Marinescu 23 Street, No. 23, 400012, Cluj-Napoca, Romania
| | - Ioana Berindan Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Marinescu 23 Street, No. 23, 400012, Cluj-Napoca, Romania; MedFuture Research Center for Advanced Medicine, "Iuliu Hatieganu" Universty of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Functional Genomics and Experimental Pathology, "Prof. Dr. Ion Chiricuta" Oncology Institute, Republicii 34 Street, Cluj Napoca, Romania
| | - Ionelia Taranu
- Laboratory of Animal Biology, National Institute for Research and Development for Biology and Animal Nutrition, Calea Bucuresti No. 1, Balotesti, Ilfov, 077015, Romania
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Li S, Feng Z, Zhang X, Lan D, Wu Y. Up-regulation of microRNA-200c-3p inhibits invasion and migration of renal cell carcinoma cells via the SOX2-dependent Wnt/β-catenin signaling pathway. Cancer Cell Int 2019; 19:231. [PMID: 31516388 PMCID: PMC6731573 DOI: 10.1186/s12935-019-0944-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/18/2019] [Indexed: 01/01/2023] Open
Abstract
Background MicroRNA-200c-3p (miR-200c-3p) has been revealed to be related to renal cell carcinoma (RCC) progression, while the inner mechanisms remain unknown. In our study, we intend to unearth the capability of miR-200c-3p in RCC development via the Wnt/β-catenin signaling pathway through binding to SOX2. Methods miR-200c-3p, SOX2, β-catenin and GSK3β expression in both tissues and cells of RCC were detected by RT-qPCR or western blot analysis. miR-200c-3p was restored or silenced to determine their biological functions of RCC cells. Expression of SOX2 and related proteins in the Wnt/β-catenin signaling pathway were evaluated by RT-qPCR and western blot analysis. The effect of the combination of downregulated miR-200c-3p and downregulated SOX2 on cell biological behavior change was also determined. Results Initially, we found that miR-200c-3p was declined while SOX2, β-catenin and GSK3β was elevated in RCC tissues and cells. A498 cells with the largest difference in miR-200c-3p expression and OS-RC-2 cells with the smallest difference were selected for subsequent experiments. Additionally, upregulated miR-200c-3p and downregulated SOX2 was determined to suppress proliferation, migration, invasion and induce apoptosis of RCC cells. Furthermore, miR-200c-3p inhibited SOX2 to inactivate the Wnt/β-catenin signaling pathway. Conclusion Collectively, this study highlights that upregulated miR-200c-3p inhibits expression of SOX2, thereby inhibiting development of RCC cells via modulating the Wnt/β-catenin signaling pathway activation.
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Affiliation(s)
- Shuai Li
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, No. 1 Longhu Central Ring Road, Zhengzhou, 450052 People's Republic of China
| | - Ziyu Feng
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, No. 1 Longhu Central Ring Road, Zhengzhou, 450052 People's Republic of China
| | - Xuechong Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, No. 1 Longhu Central Ring Road, Zhengzhou, 450052 People's Republic of China
| | - Dongyang Lan
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, No. 1 Longhu Central Ring Road, Zhengzhou, 450052 People's Republic of China
| | - Yudong Wu
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, No. 1 Longhu Central Ring Road, Zhengzhou, 450052 People's Republic of China
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Le TD, Hoang T, Li J, Liu L, Liu H, Hu S. A Fast PC Algorithm for High Dimensional Causal Discovery with Multi-Core PCs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1483-1495. [PMID: 27429444 DOI: 10.1109/tcbb.2016.2591526] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC algorithm, in the worst-case, is exponential to the number of nodes (variables), and thus it is inefficient when being applied to high dimensional data, e.g., gene expression datasets. On another note, the advancement of computer hardware in the last decade has resulted in the widespread availability of multi-core personal computers. There is a significant motivation for designing a parallelized PC algorithm that is suitable for personal computers and does not require end users' parallel computing knowledge beyond their competency in using the PC algorithm. In this paper, we develop parallel-PC, a fast and memory efficient PC algorithm using the parallel computing technique. We apply our method to a range of synthetic and real-world high dimensional datasets. Experimental results on a dataset from the DREAM 5 challenge show that the original PC algorithm could not produce any results after running more than 24 hours; meanwhile, our parallel-PC algorithm managed to finish within around 12 hours with a 4-core CPU computer, and less than six hours with a 8-core CPU computer. Furthermore, we integrate parallel-PC into a causal inference method for inferring miRNA-mRNA regulatory relationships. The experimental results show that parallel-PC helps improve both the efficiency and accuracy of the causal inference algorithm.
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Song S, Long M, Yu G, Cheng Y, Yang Q, Liu J, Wang Y, Sheng J, Wang L, Wang Z, Xu B. Urinary exosome miR-30c-5p as a biomarker of clear cell renal cell carcinoma that inhibits progression by targeting HSPA5. J Cell Mol Med 2019; 23:6755-6765. [PMID: 31342628 PMCID: PMC6787446 DOI: 10.1111/jcmm.14553] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 06/14/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022] Open
Abstract
Exosome-derived miRNAs are regarded as biomarkers for the diagnosis and prognosis of many human cancers. However, its function in clear cell renal cell carcinoma (ccRCC) remains unclear. In this study, differentially expressed miRNAs from urinal exosomes were identified using next-generation sequencing (NGS) and verified using urine samples of ccRCC patients and healthy donors. Then, the exosomes were analysed in early-stage ccRCC patients, healthy individuals and patients suffering from other urinary system cancers. Thereafter, the target gene of the miRNA was detected. Its biological function was investigated in vitro and in vivo. The results showed that miR-30c-5p could be amplified in a stable manner. Its expression pattern was significantly different only between ccRCC patients and healthy control individuals, but not compared with that of other urinary system cancers, which indicated its specificity for ccRCC. Additionally, the overexpression of miR-30c-5p inhibited ccRCC progression in vitro and in vivo. Heat-shock protein 5 (HSPA5) was found to be a direct target gene of miR-30c-5p. The depletion of HSPA5 caused by miR-30c-5p inhibition reversed the promoting effect of ccRCC growth. In conclusion, urinary exosomal miR-30c-5p acts as a potential diagnostic biomarker of early-stage ccRCC and may be able to modulate the expression of HSPA5, which is correlated with the progression of ccRCC.
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Affiliation(s)
- Shangqing Song
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Manmei Long
- Department of Pathology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guopeng Yu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yajun Cheng
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qing Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jiayi Liu
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yiwei Wang
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jiayan Sheng
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Linhui Wang
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhong Wang
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Bin Xu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Abstract
Clear cell renal cell carcinoma (ccRCC) represents a prevalent urological malignancy among men worldwide. MicroRNAs (miRNAs) are involved in the progression of diverse human cancers. The aim of this study was to explore the expression profile and prognostic value of microRNA-3133 (miR-3133) in ccRCC.The expression of miR-3133 in ccRCC tissues and non-cancerous tissues was measured by quantitative real-time polymerase chain reaction (qRT-PCR). Chi-square test was applied to evaluate the relationship between miR-3133 expression and clinical characteristics. Overall survival curve was constructed by Kaplan-Meier with log-rank test. The prognostic value of miR-3133 in ccRCC was estimated by Cox regression analysis.MiR-3133 was downregulated in ccRCC samples compared to the matched noncancerous samples (P <.01). Moreover, its expression level was correlated with T stage, vascular invasion and lymph node metastasis (all P <.05). Survival curves demonstrated that patients with low level of miR-3133 underwent lower overall survival than those with high level (log rank test, P = .002). MiR-3133 might be an independent prognostic biomarker in ccRCC patients (HR = 2.802, 95% CI = 1.391-5.646, P = .004).MiR-3133 is downregulated, and plays inhibitory roles in aggressive progression of ccRCC. MiR-3133 may be an independent prognostic biomarker for ccRCC.
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Yan H, Xin S, Ma J, Wang H, Zhang H, Liu J. A three microRNA-based prognostic signature for small cell lung cancer overall survival. J Cell Biochem 2019; 120:8723-8730. [PMID: 30536412 DOI: 10.1002/jcb.28159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 11/08/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Small-cell lung cancer (SCLC) is one of the most aggressive cancers with mechanisms far from understood. OBJECTIVE We proposed to identify valuable prognostic signature for SCLC prognosis prediction. METHODS microRNA (miRNA) expression profiles of 42 SCLC patients were acquired from the Gene Expression Omnibus. miRNAs that significantly associated with SCLC overall survival (OS-relevant) were identified through univariate Cox regression analysis followed by random survival forest analysis for identification of more reliable miRNA signature. RESULTS Eleven OS-relevant miRNAs were obtained, and hsa-miR-194, hsa-miR-608, and hsa-miR-9 were further refined through RFS. A formula composed of the three miRNAs' expression values weighted by their multivariate Cox regression coefficients was constructed, and based on which, SCLC patients with longer OS could be well distinguished from those with shorter OS. CONCLUSIONS This study should provide a valuable clue for SCLC prognosis evaluation.
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Affiliation(s)
- Hao Yan
- Department of Oncology, Institute of Integrative Oncology, Tianjin Union Medicine Center, Tianjin, China
| | - Shaobin Xin
- Intensive Care Unit, Tianjin Union Medicine Center, Tianjin, China
| | - Jing Ma
- Department of Integrated Chinese and Western Medicine, Tianjin Anding Hospital, Tianjin, China
| | - Hui Wang
- Department of Oncology, Institute of Integrative Oncology, Tianjin Union Medicine Center, Tianjin, China
| | - Heng Zhang
- Department of Oncology, Institute of Integrative Oncology, Tianjin Union Medicine Center, Tianjin, China
| | - Jindong Liu
- Department of Oncology, Institute of Integrative Oncology, Tianjin Union Medicine Center, Tianjin, China
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Pham VV, Zhang J, Liu L, Truong B, Xu T, Nguyen TT, Li J, Le TD. Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction. BMC Bioinformatics 2019; 20:143. [PMID: 30876399 PMCID: PMC6419852 DOI: 10.1186/s12859-019-2668-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/05/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and they play an important role in various biological processes in the human body. Therefore, identifying their regulation mechanisms is essential for the diagnostics and therapeutics for a wide range of diseases. There have been a large number of researches which use gene expression profiles to resolve this problem. However, the current methods have their own limitations. Some of them only identify the correlation of miRNA and mRNA expression levels instead of the causal or regulatory relationships while others infer the causality but with a high computational complexity. To overcome these issues, in this study, we propose a method to identify miRNA-mRNA regulatory relationships in breast cancer using the invariant causal prediction. The key idea of invariant causal prediction is that the cause miRNAs of their target mRNAs are the ones which have persistent causal relationships with the target mRNAs across different environments. RESULTS In this research, we aim to find miRNA targets which are consistent across different breast cancer subtypes. Thus, first of all, we apply the Pam50 method to categorize BRCA samples into different "environment" groups based on different cancer subtypes. Then we use the invariant causal prediction method to find miRNA-mRNA regulatory relationships across subtypes. We validate the results with the miRNA-transfected experimental data and the results show that our method outperforms the state-of-the-art methods. In addition, we also integrate this new method with the Pearson correlation analysis method and Lasso in an ensemble method to take the advantages of these methods. We then validate the results of the ensemble method with the experimentally confirmed data and the ensemble method shows the best performance, even comparing to the proposed causal method. CONCLUSIONS This research found miRNA targets which are consistent across different breast cancer subtypes. Further functional enrichment analysis shows that miRNAs involved in the regulatory relationships predicated by the proposed methods tend to synergistically regulate target genes, indicating the usefulness of these methods, and the identified miRNA targets could be used in the design of wet-lab experiments to discover the causes of breast cancer.
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Affiliation(s)
- Vu Vh Pham
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia
| | - Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan, China
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia
| | - Buu Truong
- Pham Ngoc Thach University of Medicine, Ho Chi Minh, Vietnam
| | - Taosheng Xu
- Institute of Intelligent Machines, Heifei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Trung T Nguyen
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia
| | - Thuc D Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia.
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Association of miR-34a Expression with Quality of Life of Glioblastoma Patients: A Prospective Study. Cancers (Basel) 2019; 11:cancers11030300. [PMID: 30836600 PMCID: PMC6468714 DOI: 10.3390/cancers11030300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/20/2019] [Accepted: 02/26/2019] [Indexed: 12/28/2022] Open
Abstract
MiR-34a acts as tumor-suppressor by targeting many oncogenes related to proliferation, apoptosis, and invasion of gliomas. We studied the relationships between health-related quality of life (HRQOL), depression, and miR-34a expression status in patients with newly diagnosed glioblastoma (GBM). A comprehensive HRQOL assessment was completed by 38 patients with glioblastoma prior to surgical resection and included the European Organization for Research and Treatment of Cancer (EORTC) questionnaire for cancer patients (QLQ-C30) and the Brain Cancer-Specific Quality of Life Questionnaire (QLQ-BN20), the Patient Health Questionnaire-9 (PHQ-9), the Karnofsky performance index (KPS), and The Glasgow Outcome Scale (GOS). The miR-34a expression in glioblastoma tissue was measured using quantitative reverse transcription PCR. Our findings show that lower miR-34a expression is significantly associated with higher tumor volume, worse physical functioning, lower KPS, and greater depressive symptom severity of GBM patients. Moreover, analysis reveals that miR-34a effects might be gender specific, as stronger relationships between miR-34a and patient functioning measures were observed in males when compared to females. Despite the fact that, due to small sample size, our results should be considered as preliminary, our study suggests that miR-34a is associated with tumor burden and can be important for health-related quality of life, functional status, and mood symptoms of glioblastoma patients.
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MicroRNA-34 family: a potential tumor suppressor and therapeutic candidate in cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:53. [PMID: 30717802 PMCID: PMC6360685 DOI: 10.1186/s13046-019-1059-5] [Citation(s) in RCA: 294] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/27/2019] [Indexed: 12/20/2022]
Abstract
MicroRNA-34 (miR-34) has been reported to be dysregulated in various human cancers and regarded as a tumor suppressive microRNA because of its synergistic effect with the well-known tumor suppressor p53. Along with the application of MRX34, the first tumor-targeted microRNA drug which based on miR-34a mimics, on phase I clinical trial (NCT01829971), the significance of miR-34 is increasingly recognized. miR-34 plays a crucial role on repressing tumor progression by involving in epithelial-mesenchymal transition (EMT) via EMT- transcription factors, p53 and some important signal pathways. Not only that, numerous preclinical researches revealed the giant potential of miR-34a on cancer therapy through diversiform nano-scaled delivery systems. Here, we provide an overview about the function of miR-34 in various cancers and the mechanism of miR-34 in tumor-associated EMT. Furthermore, its potential role as a microRNA therapeutic candidate is also discussed. Notwithstanding some obstacles existed, the extensive application prospect of miR-34 on oncotherapy cannot be neglected.
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Li J, Shen H, Xie H, Ying Y, Jin K, Yan H, Wang S, Xu M, Wang X, Xu X, Xie L. Dysregulation of ncRNAs located at the DLK1‑DIO3 imprinted domain: involvement in urological cancers. Cancer Manag Res 2019; 11:777-787. [PMID: 30697070 PMCID: PMC6339654 DOI: 10.2147/cmar.s190764] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genomic imprinting has been found to be involved in human physical development and several diseases. The DLK1-DIO3 imprinted domain is located on human chromosome 14 and contains paternally expressed protein-coding genes (DLK1, RTL1, DIO3) and numerous maternally expressed ncRNA genes (MEG3, MEG8, antisense RTL1, miRNAs, piRNAs, and snoRNAs). Emerging evidence has implicated that dysregulation of the DLK1-DIO3 imprinted domain especially the imprinted ncRNAs is critical for tumor progressions. Multiple miRNAs and lncRNAs have been investigated in urological cancers, of which several are transcribed from this domain. In this review, we present current data about the associated miRNAs, lncRNAs, and piRNAs and the regulation of differentially methylated regions methylation status in the progression of urological cancers and preliminarily propose certain concepts about the potential regulatory networks involved in DLK1-DIO3 imprinted domain.
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Affiliation(s)
- Jiangfeng Li
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Haixiang Shen
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Haiyun Xie
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Yufan Ying
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Ke Jin
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Huaqing Yan
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Song Wang
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Mingjie Xu
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Xiao Wang
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Xin Xu
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Liping Xie
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
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Ghosh A, Ekka MK, Tawani A, Kumar A, Chakraborty D, Maiti S. Restoration of miRNA-149 Expression by TmPyP4 Induced Unfolding of Quadruplex within Its Precursor. Biochemistry 2019; 58:514-525. [PMID: 30585723 DOI: 10.1021/acs.biochem.8b00880] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Noncoding RNAs are functional RNA molecules that get transcribed from DNA but are not translated into proteins; yet, they can regulate gene expression at transcriptional and post-transcriptional levels. Secondary structures present within these RNAs play a major role in determining their nature of function. In the case of miRNAs, the precursor miRNA have a hairpin stem loop structure which is required for Dicer recognition and further maturation. Alternately, it might assume a G-quadruplex structure. The transition from hairpin to G-quadruplex depends upon the nucleotide sequence as well as the cellular microenvironment, and this might affect the miRNA maturation and other downstream activity. Formation of the G-quadruplex within precursor miRNA-149 has been shown to inhibit Dicer processing activity followed by suppression of miRNA-149 maturation in cancer cells. In this report, we show that suppression of cell proliferation by the upregulated miRNA-149 could be rescued by unfolding the G-quadruplex present in pre-miRNA-149 by TmPyP4 (Porphyrin) treatment. Using UV-visible spectroscopy, circular dichroism, and isothermal titration calorimetry, we observed that TmPyP4 binds strongly to G-quadruplex and unfolds it, which was further verified by NMR spectroscopy. In cellulo, qRT-PCR measurements of miRNA-149 in MCF-7 breast cancer cells showed concentration dependent enhancement of mature miRNA-149 upon treatment of TmPyP4. As a consequence of enhanced miRNA-149 activity, we also observe the reduction in miRNA-149 target protein ZBTB2 that eventually leads to reduced cell proliferation.
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Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology , Mathura Road , Delhi 110025 , India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics & Integrative Biology , Mathura Road , Delhi 110025 , India
| | - Arpita Tawani
- Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Indore , Madhya Pradesh , India
| | - Amit Kumar
- Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Indore , Madhya Pradesh , India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology , Mathura Road , Delhi 110025 , India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology , Mathura Road , Delhi 110025 , India.,Academy of Scientific & Innovative Research , CSIR- Human Resource Development Centre (CSIR-HRDC) Campus , Sector 19 , Kamla Nehru Nagar, Ghaziabad , Uttar Pradesh 201 002 , India
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Barbagallo C, Passanisi R, Mirabella F, Cirnigliaro M, Costanzo A, Lauretta G, Barbagallo D, Bianchi C, Pagni F, Castorina S, Granata A, Di Pietro C, Ragusa M, Malatino LS, Purrello M. Upregulated microRNAs in membranous glomerulonephropathy are associated with significant downregulation of IL6 and MYC mRNAs. J Cell Physiol 2018; 234:12625-12636. [PMID: 30515781 DOI: 10.1002/jcp.27851] [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: 10/02/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022]
Abstract
Membranous glomerulonephropathy (MGN) is a glomerulopathy characterized by subepithelial deposits of immune complexes on the extracapillary side of the glomerular basement membrane. Insertion of C5b-9 (complement membrane-attack complex) into the membrane leads to functional impairment of the glomerular capillary wall. Knowledge of the molecular pathogenesis of MGN is actually scanty. MicroRNA (miRNA) profiling in MGN and unaffected tissues was performed by TaqMan Low-Density Arrays. Expression of miRNAs and miRNA targets was evaluated in Real-Time polymerase chain reaction (PCR). In vitro transient silencing of miRNAs was achieved through transfection with miRNA inhibitors. Ten miRNAs (let-7a-5p, let-7b-5p, let-7c-5p, let-7d-5p, miR-107, miR-129-3p, miR-423-5p, miR-516-3p, miR-532-3p, and miR-1275) were differentially expressed (DE) in MGN biopsies compared to unaffected controls. Interleukin 6 (IL6) and MYC messenger RNAs (mRNAs; targets of DE miRNAs) were significantly downregulated in biopsies from MGN patients, and upregulated in A498 cells following let-7a-5p or let-7c-5p transient silencing. Gene ontology analysis showed that DE miRNAs regulate pathways associated with MGN pathogenesis, including cell cycle, proliferation, and apoptosis. A significant correlation between DE miRNAs and mRNAs and clinical parameters (i.e., antiphospholipid antibodies, serum creatinine, estimated glomerular filtration, proteinuria, and serum cholesterol) has been detected. Based on our data, we propose that DE miRNAs and their downstream network may be involved in MGN pathogenesis and could be considered as potential diagnostic biomarkers of MGN.
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Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Roberta Passanisi
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Department of Thoracic Surgery, Centro Clinico e Diagnostico Morgagni, Catania, Italy
| | - Federica Mirabella
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Matilde Cirnigliaro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Arianna Costanzo
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giovanni Lauretta
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Cristina Bianchi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Section of Pathology, University of Milano-Bicocca, Monza, Italy
| | - Sergio Castorina
- Department of Thoracic Surgery, Centro Clinico e Diagnostico Morgagni, Catania, Italy.,Department of Medical and Surgical Sciences and Advanced Technologies, University of Catania, Catania, Italy
| | - Antonio Granata
- Unit of Nephrology, Ospedale S. Giovanni di Dio, Agrigento, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Oasi Research Institute - IRCCS, Troina, Italy
| | - Lorenzo S Malatino
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Michele Purrello
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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38
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Liu F, Li N, Yang W, Wang R, Yu J, Wang X. The expression analysis of NGAL and NGALR in clear cell renal cell carcinoma. Gene 2018; 676:269-278. [DOI: 10.1016/j.gene.2018.08.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 01/12/2023]
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39
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Tsiakanikas P, Giaginis C, Kontos CK, Scorilas A. Clinical utility of microRNAs in renal cell carcinoma: current evidence and future perspectives. Expert Rev Mol Diagn 2018; 18:981-991. [DOI: 10.1080/14737159.2018.1539668] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Panagiotis Tsiakanikas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Constantinos Giaginis
- Department of Food Science and Nustrition, School of Environment, University of the Aegean, Lemnos, Greece
| | - Christos K. Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
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40
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Toraih EA, Alghamdi SA, El-Wazir A, Hosny MM, Hussein MH, Khashana MS, Fawzy MS. Dual biomarkers long non-coding RNA GAS5 and microRNA-34a co-expression signature in common solid tumors. PLoS One 2018; 13:e0198231. [PMID: 30289954 PMCID: PMC6173395 DOI: 10.1371/journal.pone.0198231] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/16/2018] [Indexed: 12/20/2022] Open
Abstract
Accumulating evidence indicates that non-coding RNAs including microRNAs (miRs) and long non-coding RNAs (lncRNAs) are aberrantly expressed in cancer, providing promising biomarkers for diagnosis, prognosis and/or therapeutic targets. We aimed in the current work to quantify the expression profile of miR-34a and one of its bioinformatically selected partner lncRNA growth arrest-specific 5 (GAS5) in a sample of Egyptian cancer patients, including three prevalent types of cancer in our region; renal cell carcinoma (RCC), glioblastoma (GB), and hepatocellular carcinoma (HCC) as well as to correlate these expression profiles with the available clinicopathological data in an attempt to clarify their roles in cancer. Quantitative real-time polymerase chain reaction analysis was applied. Different bioinformatics databases were searched to confirm the potential miRNAs-lncRNA interactions of the selected ncRNAs in cancer pathogenesis. The tumor suppressor lncRNA GAS5 was significantly under-expressed in the three types of cancer [0.08 (0.006-0.38) in RCC, p <0.001; 0.10 (0.003-0.89) in GB, p < 0.001; and 0.12 (0.015-0.74) in HCC, p < 0.001]. However, levels of miR-34a greatly varied according to the tumor type; it displayed an increased expression in RCC [4.05 (1.003-22.69), p <0.001] and a decreased expression in GB [0.35 (0.04-0.95), p <0.001]. Consistent to the computationally predicted miRNA-lncRNA interaction, negative correlations were observed between levels of GAS5 and miR-34a in RCC samples (r = -0.949, p < 0.001), GB (r = -0.518, p < 0.001) and HCC (r = -0.455, p = 0.013). Kaplan-Meier curve analysis revealed that RCC patients with down-regulated miR-34a levels had significantly poor overall survival than their corresponding (p < 0.05). Hierarchical clustering analysis showed RCC patients could be clustered by GAS5 and miR-34a co-expression profile. Our results suggest potential applicability of GAS5 and miR-34a with other conventional markers for various types of cancer. Further functional validation studies are warranted to confirm miR-34a/GAS5 interplay in cancer.
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Affiliation(s)
- Eman A. Toraih
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence of Molecular and Cellular Medicine, Suez Canal University, Ismailia, Egypt
- * E-mail: (MSF); (EAT)
| | - Saleh Ali Alghamdi
- Medical Genetics, Clinical Laboratory Department, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Aya El-Wazir
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence of Molecular and Cellular Medicine, Suez Canal University, Ismailia, Egypt
| | - Marwa M. Hosny
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | | | | | - Manal S. Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
- * E-mail: (MSF); (EAT)
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41
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Yang S, Zhang W, Cai M, Zhang Y, Jin F, Yan S, Baloch Z, Fang Z, Xue S, Tang R, Xiao J, Huang Q, Sun Y, Wang X. Suppression of Bone Resorption by miR-141 in Aged Rhesus Monkeys. J Bone Miner Res 2018; 33:1799-1812. [PMID: 29852535 DOI: 10.1002/jbmr.3479] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 05/01/2018] [Accepted: 05/04/2018] [Indexed: 12/19/2022]
Abstract
Aging-related osteoporosis (OP) is considered a serious public health concern. Approximately 30% of postmenopausal women suffer from OP; more than 40% of them risk fragility fractures. Multiple drugs have been prescribed to treat OP, but they are not ideal because of low cure rates and adverse side effects. miRNA-based gene therapy is a rapidly developing strategy in disease treatment that presents certain advantages, such as large-scale production capability, genetic safety, and rapid effects. miRNA drugs have been used primarily in cancer treatments; they have not yet been reported as candidates for osteoclast-targeted-OP treatment in primates. Their therapeutic efficacy has been limited by several shortcomings, such as low efficiency of selective delivery, insufficient expression levels in targeting cells, and unexpected side effects. Here, we identify miR-141 as a critical suppressor of osteoclastogenesis and bone resorption. The expression levels of miR-141 are positively correlated with BMD and negatively correlated with the aging of bones in both aged rhesus monkeys (Macaca mulatta) and osteoporotic patients. Selective delivery of miR-141 into the osteoclasts of aged rhesus monkeys via a nucleic acid delivery system allowed for a gradual increase in bone mass without significant effects on the health and function of primary organs. Furthermore, we found that the functional mechanism of miR-141 resides in its targeting of two osteoclast differentiation players, Calcr (calcitonin receptors) and EphA2 (ephrin type-A receptor 2 precursor). Our study suggests that miRNAs, such as miR-141, could play a crucial role in suppressing bone resorption in primates and provide reliable experimental evidence for the clinical application of miRNA in OP treatment. © 2018 American Society for Bone and Mineral Research.
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Affiliation(s)
- Shihua Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Wenhui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Mingxiang Cai
- School & Hospital of Stomatology, Tongji University, Shanghai, China
| | - Yuanxu Zhang
- Department of Cell Biology & Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Fujun Jin
- Department of Cell Biology & Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Sen Yan
- Department of Cell Biology & Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zulqurain Baloch
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Zhihao Fang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Senren Xue
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Rongping Tang
- WinconTheraCells Biotechnologies Co. Ltd, Nanning, China
| | - Jia Xiao
- Department of Cell Biology & Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qunshan Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Yao Sun
- School & Hospital of Stomatology, Tongji University, Shanghai, China
| | - Xiaogang Wang
- Department of Cell Biology & Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100083, China
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42
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Li Y, Ju K, Wang W, Liu Z, Xie H, Jiang Y, Jiang G, Lu J, Dong Z, Tang F. Dinitrosopiperazine-decreased PKP3 through upregulating miR-149 participates in nasopharyngeal carcinoma metastasis. Mol Carcinog 2018; 57:1763-1779. [PMID: 30144176 PMCID: PMC6282612 DOI: 10.1002/mc.22895] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/18/2022]
Abstract
Nasopharyngeal carcinoma (NPC) has a high metastatic clinicopathological feature. As a carcinogen factor, N,N'-dinitrosopiperazine (DNP) is involved in NPC metastasis, but its precise mechanism has not been fully elucidated. Herein, we showed that DNP promotes NPC metastasis through upregulating miR-149. DNP was found to decrease Plakophilin3 (PKP3) expression, further DNP-decreased PKP3 was verified to be through upregulating miR-149. We also found that DNP induced proliferation, adhesion, migration and invasion of NPC cell, which was inhibited by miR-149-inhibitor. DNP may promote NPC metastasis through miR-149-decreased PKP3 expression. Therefore, DNP-increased miR-149 expression may be an important factor of NPC high metastasis, and miR-149 may serve as a molecular target for anti-metastasis therapy of NPC.
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Affiliation(s)
- Yuejin Li
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Zhuhai Hospital of Jinan University, Zhuhai, China
| | - Kunyu Ju
- Metallurgical Science and Engineering, Central South University, Changsha, China
| | - Weiwei Wang
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Zheliang Liu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Haitao Xie
- The First Affiliated Hospital of University of South China, Hengyang, China
| | - Yuan Jiang
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Guanmin Jiang
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jinping Lu
- Zhuhai Hospital of Jinan University, Zhuhai, China
| | - Zigang Dong
- Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Faqing Tang
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Zhuhai Hospital of Jinan University, Zhuhai, China
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43
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Zhu J, Zhu D, Zhang Y, Liu Q, Wang P, Li H, Ma X, Zhang X. MicroRNA‐363 inhibits angiogenesis, proliferation, invasion, and migration of renal cell carcinoma via inactivation of the Janus tyrosine kinases 2–signal transducers and activators of transcription 3 axis by suppressing growth hormone receptor gene. J Cell Physiol 2018; 234:2581-2592. [DOI: 10.1002/jcp.27020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 06/25/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Jie Zhu
- Department of UrologyChinese PLA General HospitalBeijing China
| | - Da‐Qing Zhu
- Department of UrologyHainan Branch of Chinese PLA General HospitalSanya China
| | - Yu Zhang
- Department of UrologyChinese PLA General HospitalBeijing China
| | - Qi‐Ming Liu
- Department of UrologyHainan Branch of Chinese PLA General HospitalSanya China
| | - Peng‐Chao Wang
- Department of UrologyHainan Branch of Chinese PLA General HospitalSanya China
| | - Hong‐Zhao Li
- Department of UrologyChinese PLA General HospitalBeijing China
| | - Xin Ma
- Department of UrologyChinese PLA General HospitalBeijing China
| | - Xu Zhang
- Department of UrologyChinese PLA General HospitalBeijing China
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44
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Shi X, Wang X, Hua Y. LncRNA GACAT1 Promotes Gastric Cancer Cell Growth, Invasion And Migration By Regulating MiR-149-mediated Of ZBTB2 And SP1. J Cancer 2018; 9:3715-3722. [PMID: 30405842 PMCID: PMC6216017 DOI: 10.7150/jca.27546] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) were involved in the progression of gastric cancer (GC). In our study, we have determined that GACAT1 expression was upregulated in GC. Overexpression of GACAT1 promoted GC cell proliferation, invasion and migration. We also determined that miR-149 directly interacts with the target site on GACAT1. Furthermore, we investigated that miR-149 downregulated ZBTB2 and SP1 expressions which were induced by GACAT1, miR-149 inhibited GC cell growth and invasion mediated by GACAT1. In conclusion, we found that miR-149 downregulated ZBTB2 and SP1 expressions, and inhibited GC cell progression mediated by GACAT1. Therefore, we indicated that GACAT1 and miR-149 may be potential therapeutic targets for GC.
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Affiliation(s)
- Xiaoqing Shi
- West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiaoqin Wang
- West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yimin Hua
- West China Second University Hospital, Sichuan University, Chengdu, China
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45
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Sedaghat N, Fathy M, Modarressi MH, Shojaie A. Combining Supervised and Unsupervised Learning for Improved miRNA Target Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1594-1604. [PMID: 28715336 PMCID: PMC7001746 DOI: 10.1109/tcbb.2017.2727042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs which bind to mRNAs and regulate their expression. MiRNAs have been found to be associated with initiation and progression of many complex diseases. Investigating miRNAs and their targets can thus help develop new therapies by designing anti-miRNA oligonucleotides. While existing computational approaches can predict miRNA targets, these predictions have low accuracy. In this paper, we propose a two-step approach to refine the results of sequence-based prediction algorithms. The first step, which is based on our previous work, uses an ensemble learning approach that combines multiple existing methods. The second step utilizes support vector machine (SVM) classifiers in one- and two-class modes to infer miRNA-mRNA interactions based on both binding features, as well as network features extracted from gene regulatory network. Experimental results using two real data sets from TCGA indicate that the use of two-class SVM classification significantly improves the precision of miRNA-mRNA prediction.
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46
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Sun H, Zhou Z, Dong Y, Yang A, Pan Y, Jiang J, Chen Z, Guan X, Wang B, Gao S, Jiang B. In-depth profiling of miRNA regulation in the body wall of sea cucumber Apostichopus japonicus during skin ulceration syndrome progression. FISH & SHELLFISH IMMUNOLOGY 2018; 79:202-208. [PMID: 29763733 DOI: 10.1016/j.fsi.2018.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that mediate mRNA degradation or translation repression. Previous study showed that the expression of miRNAs was significantly changed in the body wall of sea cucumber Apostichopus japonicus after skin ulceration syndrome (SUS) infection, which is a dynamic process. However, the critical miRNAs from body wall that involved in different infection stages of SUS remain unknown. In this study, four cDNA libraries were constructed with the body wall from healthy and three SUS-infected stages of A. japonicus. A total of 248 conserved miRNAs and five novel miRNAs were identified through Illumina HiSeq 2000 platform. Compared to the control, 238 miRNAs showed significant differential expression at three stages of SUS progression. Totally, 3149 miRNA-mRNA pairs were identified by target prediction and 314 miRNA-mRNA pairs showed negative correlation. It is noteworthy that 15 miRNAs and four mRNAs were located at the crucial positions of the network built with the anti-correlated miRNA-mRNA pairs. GO and KEGG enrichment analysis indicated that the predicted targets were involved in many immune-related processes. Deep analysis of miR-31c-5p, miR-29b-3p, NF-kB, mucin 2 and titin showed that they may play important roles in the pathogens attachment and recognition, signaling transduction and lesions repair of A. japonicus after SUS infection. These results would be useful for further investigating the potential roles of critical miRNAs and mRNAs in A. japonicus immune regulation.
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Affiliation(s)
- Hongjuan Sun
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Aifu Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yongjia Pan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zhong Chen
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bai Wang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shan Gao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
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47
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Zhi Y, Zhou H, Mubalake A, Chen Y, Zhang B, Zhang K, Chu X, Wang R. Regulation and functions of MicroRNA-149 in human cancers. Cell Prolif 2018; 51:e12465. [PMID: 29999552 DOI: 10.1111/cpr.12465] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 03/28/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs are small non-coding RNAs that play critical roles in the regulatory mechanisms involving cell differentiation, proliferation, apoptosis and tumorigenesis. Recent research efforts have been conducted to apply these discoveries into clinical functions, including the early diagnosis and therapeutic outcome of patients with cancer. Previous studies have shown that microRNA-149 (miR-149) is dysregulated in various human cancers and exerts its effects on tumorigenesis and tumour progression. In this review, we summarized the potential roles of miR-149 dysregulation and its target genes during tumorigenesis and clinical treatment of human cancers.
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Affiliation(s)
- Yingru Zhi
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Hao Zhou
- Nanjing Medical University, Nanjing, China
| | - Abudoureyimu Mubalake
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Ying Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Bei Zhang
- Nanjing Medical University, Nanjing, China
| | - Kai Zhang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Xiaoyuan Chu
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Rui Wang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
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Lai Y, Zhao L, Hu J, Quan J, Chen P, Xu J, Guan X, Lai Y, Ni L. microRNA‑181a‑5p functions as an oncogene in renal cell carcinoma. Mol Med Rep 2018; 17:8510-8517. [PMID: 29693121 DOI: 10.3892/mmr.2018.8899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 02/23/2018] [Indexed: 11/06/2022] Open
Abstract
Renal cell carcinoma (RCC) is one of the most common urinary tumors. Previous studies have demonstrated that microRNA (miR)‑181a‑5p has an important role in numerous types of cancer. However, the function of miR‑181a‑5p in RCC remains unknown. In the present study, the expression levels of miR‑181a‑5p in RCC tissues and cell lines were investigated using reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) analysis. The results of the RT‑qPCR analyses suggested that the expression of miR‑181a‑5p was upregulated in RCC tissues and cells lines compared with adjacent normal renal tissues and normal renal cell lines. Furthermore, the effect of miR‑181a‑5p on cell proliferation, migration, invasion and apoptosis was investigated in the present study. Overexpression of miR‑181a‑5p was revealed to suppress the apoptosis of 786‑O and ACHN cells, in addition to enhancing the proliferation, migration and invasion abilities of 786‑O and ACHN cells in vitro, thus suggesting that miR‑181a‑5p may function as an oncogene in RCC. However, further studies are required to investigate the underlying mechanism of miR‑181a‑5p and its potential role as a biomarker for early detection and prognosis, in addition to as a therapeutic target in RCC.
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Affiliation(s)
- Yulin Lai
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Liwen Zhao
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Jia Hu
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Jing Quan
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Peijie Chen
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Jinling Xu
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Xin Guan
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Yongqing Lai
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Liangchao Ni
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
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Dadaneh SZ, Qian X, Zhou M. BNP-Seq: Bayesian Nonparametric Differential Expression Analysis of Sequencing Count Data. J Am Stat Assoc 2018. [DOI: 10.1080/01621459.2017.1328358] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Siamak Zamani Dadaneh
- Department of Electrical & Computer Engineering, Center for Bioinformatics & Genomic Systems Engineering, Texas A&M University, College Station, TX
| | - Xiaoning Qian
- Department of Electrical & Computer Engineering, Center for Bioinformatics & Genomic Systems Engineering, Texas A&M University, College Station, TX
- Department of Information, Risk, & Operations Management and Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, TX
| | - Mingyuan Zhou
- Department of Information, Risk, & Operations Management and Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, TX
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