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Pan-Cancer Analysis Reveals SH3TC2 as an Oncogene for Colorectal Cancer and Promotes Tumorigenesis via the MAPK Pathway. Cancers (Basel) 2022; 14:cancers14153735. [PMID: 35954399 PMCID: PMC9367385 DOI: 10.3390/cancers14153735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary SH3 domain and tetrapeptide repeat 2 (SH3TC2) is a protein-encoding gene and has previously been described as a critical signaling hub for neurological disorders, but no systematic analysis of SH3TC2 is available in cancer research. We analyzed SH3TC2 in various kinds of cancer to find its tumorigenic role in one or more specific cancers and further explored the mechanism of SH3TC2 in colorectal cancer (CRC). Our research revealed that higher expression of SH3TC2 indicated poor disease-free survival and promoted CRC progression and invasion via the MAPK signaling pathway. Abstract SH3 domain and tetrapeptide repeat 2 (SH3TC2) is a protein-encoding gene and has previously been described as a critical signaling hub for neurological disorders. Although increasing evidence supports a vital role of SH3TC2 in the tumorigenesis of various kinds of cancer, no systematic analysis of SH3TC2 is available. The function and mechanism of SH3TC2 in other cancers remain unknown. Thus, this study aimed to analyze SH3TC2 in various kinds of cancer to find its tumorigenic role in one or more specific cancers. In the current study, we analyzed the expression level and prognostic value of SH3TC2 in different tumors in the TCGA-GTEx pan-cancer dataset. Subsequently, the prognostic role and mechanism of SH3TC2 in colorectal cancer (CRC) were further explored via clinical samples and in vitro and in vivo experiments. We observed differential expression of SH3TC2 in colon adenocarcinoma (COAD), acute myeloid leukemia (LAML), READ (rectum adenocarcinoma), SKCM (skin cutaneous melanoma), and TGCT (testicular germ cell tumors). Subsequently, SH3TC2 showed a significant effect on the clinical stage and prognostic value in CRC, LAML, and SKCM. Moreover, we found in the TCGA database and seven GEO datasets that SH3TC2 was significantly highly expressed in tumor tissue. Through enrichment analysis of SH3TC2 and its co-expressed genes, we found that SH3TC2 may play a role in the MAPK signaling pathway. Correlation analysis indicated that SH3TC2 was significantly associated with multiple key factors in the MAPK signaling pathway. Additionally, higher expression of SH3TC2 was found in tumor tissue in our cohort including 40 CRC patients. Overexpression of SH3TC2 may imply poor prognosis. Knockdown of SH3TC2 significantly inhibited tumor invasion, migration, and proliferation. More importantly, knockdown of SH3TC2 inhibited tumor growth in a CRC mouse model. The study preliminarily conducted a pan-cancer study of SH3TC2 and further explored the mechanism of SH3TC2 in CRC. Our research revealed that higher expression of SH3TC2 may promote CRC progression and invasion via the MAPK signaling pathway.
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Dang S, Zhang R, Tian S, Hou P, Li G, Ji M. MicroRNA‑218 inhibits the malignant phenotypes of glioma by modulating the TNC/AKT/AP‑1/TGFβ1 feedback signaling loop. Int J Mol Med 2021; 48:205. [PMID: 34558654 PMCID: PMC8480380 DOI: 10.3892/ijmm.2021.5038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/30/2021] [Indexed: 01/22/2023] Open
Abstract
Gliomas are the most malignant and common tumors of the human brain, and the prognosis of glioma patients is extremely poor MicroRNAs (miRNAs or miRs) play critical roles in different types of cancer by performing post-transcriptional regulation of gene expression Although miR-218 has been demonstrated to be decreased in gliomas, its role in gliomas remains largely unknown miR-218 expression was analyzed in gliomas and normal brain tissues (control subjects) using a dataset from The Cancer Genome Atlas A series of in vitro and in vivo studies were performed to determine the biological roles of miR-218 in glioma cells Potential targets of miR-218 were identified using a dual-luciferase reporter system Western blot and dual-luciferase reporter system experiments were performed to evaluate the regulatory effect of miR-218 on the tenascin C (TNC)/AKT/activator protein 1 (AP-1)/transforming growth factor β1 (TGFβ1) pathway It was demonstrated that miR-218 was significantly downregulated in gliomas compared with control subjects, and played potent tumor suppressor roles in glioma cells by inhibiting cell proliferation, colony formation, migration, invasion and tumorigenic potential in nude mice, as well as inducing cell cycle arrest and apoptosis Mechanistically, miR-218 inhibited malignant phenotypes of glioma cells by binding to the 3′-untranslated region of its target TNC and subsequently suppressing its expression As a result, miR-218 could reduce AKT phosphorylation and subsequently inhibit transcriptional activity of AP-1 by reducing JNK phosphorylation, downregulating the expression of TGFβ1, while TGFβ1 was able to, in turn, activate the TNC/AKT/AP-1 signaling axis Our data revealed a previously unknown tumor suppressor role of miR-218 by blocking the TNC/AKT/AP-1/TGFβ1-positive feedback loop in glioma
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Affiliation(s)
- Siwen Dang
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Rui Zhang
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Sijia Tian
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Peng Hou
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Gang Li
- Department of Neurosurgery, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Meiju Ji
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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Wu HJ, Chu PY. Epigenetic Regulation of Breast Cancer Stem Cells Contributing to Carcinogenesis and Therapeutic Implications. Int J Mol Sci 2021; 22:ijms22158113. [PMID: 34360879 PMCID: PMC8348144 DOI: 10.3390/ijms22158113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/15/2022] Open
Abstract
Globally, breast cancer has remained the most commonly diagnosed cancer and the leading cause of cancer death among women. Breast cancer is a highly heterogeneous and phenotypically diverse group of diseases, which require different selection of treatments. Breast cancer stem cells (BCSCs), a small subset of cancer cells with stem cell-like properties, play essential roles in breast cancer progression, recurrence, metastasis, chemoresistance and treatments. Epigenetics is defined as inheritable changes in gene expression without alteration in DNA sequence. Epigenetic regulation includes DNA methylation and demethylation, as well as histone modifications. Aberrant epigenetic regulation results in carcinogenesis. In this review, the mechanism of epigenetic regulation involved in carcinogenesis, therapeutic resistance and metastasis of BCSCs will be discussed, and finally, the therapies targeting these biomarkers will be presented.
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Affiliation(s)
- Hsing-Ju Wu
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan;
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua 505, Taiwan
| | - Pei-Yi Chu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
- Correspondence: ; Tel.: +886-975611855; Fax: +886-47227116
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Paço A, de Bessa Garcia SA, Freitas R. Methylation in HOX Clusters and Its Applications in Cancer Therapy. Cells 2020; 9:cells9071613. [PMID: 32635388 PMCID: PMC7408435 DOI: 10.3390/cells9071613] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 02/08/2023] Open
Abstract
HOX genes are commonly known for their role in embryonic development, defining the positional identity of most structures along the anterior–posterior axis. In postembryonic life, HOX gene aberrant expression can affect several processes involved in tumorigenesis such as proliferation, apoptosis, migration and invasion. Epigenetic modifications are implicated in gene expression deregulation, and it is accepted that methylation events affecting HOX gene expression play crucial roles in tumorigenesis. In fact, specific methylation profiles in the HOX gene sequence or in HOX-associated histones are recognized as potential biomarkers in several cancers, helping in the prediction of disease outcomes and adding information for decisions regarding the patient’s treatment. The methylation of some HOX genes can be associated with chemotherapy resistance, and its identification may suggest the use of other treatment options. The use of epigenetic drugs affecting generalized or specific DNA methylation profiles, an approach that now deserves much attention, seems likely to be a promising weapon in cancer therapy in the near future. In this review, we summarize these topics, focusing particularly on how the regulation of epigenetic processes may be used in cancer therapy.
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Affiliation(s)
- Ana Paço
- Centre Bio: Bioindustries, Biorefineries and Bioproducts, BLC3 Association—Technology and Innovation Campus, 3405-169 Oliveira do Hospital, Portugal;
| | | | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal;
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Correspondence:
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Yu P, Lan H, Song X, Pan Z. High Expression of the SH3TC2-DT/SH3TC2 Gene Pair Associated With FLT3 Mutation and Poor Survival in Acute Myeloid Leukemia: An Integrated TCGA Analysis. Front Oncol 2020; 10:829. [PMID: 32637351 PMCID: PMC7318790 DOI: 10.3389/fonc.2020.00829] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/28/2020] [Indexed: 12/21/2022] Open
Abstract
Fms-like tyrosine kinase 3 (FLT3) mutation is one of the most common mutations in acute myeloid leukemia (AML). However, the effect of FLT3 mutation on survival is currently still controversial and the leukemogenic mechanisms are still under further investigation. The aim of our study is to identify differentially expressed genes (DEGs) in FLT3-mutant AML and to find crucial DEGs whose expression level is related to prognosis for further analysis. By mining the TCGA-LAML dataset, 619 differentially expressed lncRNAs (DElncRNAs) and 1,428 differentially expressed mRNAs (DEmRNAs) were identified between FLT3-mutant and FLT3-wildtype samples. Through weighted gene correlation network analysis (WGCNA) and the following Cox proportional hazards regression analysis, we constructed the prognostic risk models to identify the hub DElncRNAs and DEmRNAs associated with AML prognosis. The presence of both SH3TC2 divergent transcript (SH3TC2-DT) and SH3TC2 in respective prognostic risk models promotes us to further study the significance of this gene pair in AML. SH3TC2-DT and SH3TC2 were identified to be coordinately high expressed in FLT3-mutant AML samples. High expression of this gene pair was associated with poor survival. Using logistic regression analysis, we found that high SH3TC2-DT/SH3TC2 expression was associated with FLT3 mutation, high WBC count, and intermediate cytogenetic and molecular–genetic risk. AML with SH3TC2-DT/SH3TC2 high expression showed enrichment of transcripts associated with stemness, quiescence, and leukemogenesis. Our study suggests that the SH3TC2-DT/SH3TC2 gene pair may be a possible biomarker to further optimize AML prognosis and may function in stemness or quiescence of FLT3-mutant leukemic stem cells (LSCs).
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Affiliation(s)
- Pengfei Yu
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Hannover Medical School, Institute of Virology, Hanover, Germany
| | - Haifeng Lan
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xianmin Song
- Department of Hematology, Shanghai General Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Zengkai Pan
- Department of Hematology, Shanghai General Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China.,Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hanover, Germany
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The New Biomarker for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) Based on Public Database Mining. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5478574. [PMID: 32351997 PMCID: PMC7174939 DOI: 10.1155/2020/5478574] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 01/19/2023]
Abstract
To reconstruct the ceRNA biological network of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) and to select an appropriate mRNA as a biomarker that could be used for CESC early diagnosis and prognosis evaluation. We downloaded CESC data from the TCGA public database, and statistical analysis was conducted with the R software to find out differential expressed genes encoding for lncRNAs, miRNAs, and mRNAs. The differentially expressed mRNAs (DEmRNAs) screened in the ceRNA network were analyzed for survival to find the mRNAs with significantly linked to the survival prognosis. These mRNAs were searched in the Pathological Atlas to identify the final appropriate mRNAs. Differential expression analysis revealed 773 lncRNAs, 94 miRNAs, and 2466 mRNAs. Survival analysis of DEmRNAs in the ceRNA network indicated that ADGRF4, ANXA8L1, HCAR3, IRF6, and PDE2A (P < 0.05) were negatively correlated with survival time. Verification of these six DEmRNAs in the Pathology Atlas indicated that PDE2A was a possible biomarker for CESC patients. PDE2A might be a biomarker for early diagnosis and prognosis evaluation of CESC patients, but due to the lack of available data, further studies may be needed for confirmation.
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d'Errico M, Alwers E, Zhang Y, Edelmann D, Brenner H, Hoffmeister M. Identification of prognostic DNA methylation biomarkers in patients with gastrointestinal adenocarcinomas: A systematic review of epigenome-wide studies. Cancer Treat Rev 2020; 82:101933. [DOI: 10.1016/j.ctrv.2019.101933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 02/07/2023]
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8
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Pérez-Pérez D, Reyes-Vidal I, Chávez-Cortez EG, Sotelo J, Magaña-Maldonado R. Methylxanthines: Potential Therapeutic Agents for Glioblastoma. Pharmaceuticals (Basel) 2019; 12:ph12030130. [PMID: 31500285 PMCID: PMC6789489 DOI: 10.3390/ph12030130] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/24/2019] [Accepted: 09/01/2019] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive primary brain tumor. Currently, treatment is ineffective and the median overall survival is 20.9 months. The poor prognosis of GBM is a consequence of several altered signaling pathways that favor the proliferation and survival of neoplastic cells. One of these pathways is the deregulation of phosphodiesterases (PDEs). These enzymes participate in the development of GBM and may have value as therapeutic targets to treat GBM. Methylxanthines (MXTs) such as caffeine, theophylline, and theobromine are PDE inhibitors and constitute a promising therapeutic anti-cancer agent against GBM. MTXs also regulate various cell processes such as proliferation, migration, cell death, and differentiation; these processes are related to cancer progression, making MXTs potential therapeutic agents in GBM.
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Affiliation(s)
- Daniel Pérez-Pérez
- PECEM, Faculty of Medicine, National Autonomous University of México, México City 04510, Mexico
- Neuroimmunology and Neuro-oncology Unit, National Institute of Neurology and Neurosurgery, México City 14269, Mexico
| | - Iannel Reyes-Vidal
- Neuroimmunology and Neuro-oncology Unit, National Institute of Neurology and Neurosurgery, México City 14269, Mexico
| | - Elda Georgina Chávez-Cortez
- Neuroimmunology and Neuro-oncology Unit, National Institute of Neurology and Neurosurgery, México City 14269, Mexico
| | - Julio Sotelo
- Neuroimmunology and Neuro-oncology Unit, National Institute of Neurology and Neurosurgery, México City 14269, Mexico
| | - Roxana Magaña-Maldonado
- Neuroimmunology and Neuro-oncology Unit, National Institute of Neurology and Neurosurgery, México City 14269, Mexico.
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Ma K, Zhang H, Wei G, Dong Z, Zhao H, Han X, Song X, Zhang H, Zong X, Baloch Z, Wang S. Identification of key genes, pathways, and miRNA/mRNA regulatory networks of CUMS-induced depression in nucleus accumbens by integrated bioinformatics analysis. Neuropsychiatr Dis Treat 2019; 15:685-700. [PMID: 30936699 PMCID: PMC6421879 DOI: 10.2147/ndt.s200264] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Major depressive disorder (MDD) is a recurrent, devastating mental disorder, which affects >350 million people worldwide, and exerts substantial public health and financial costs to society. Thus, there is a significant need to discover innovative therapeutics to treat depression efficiently. Stress-induced dysfunction in the subtype of neuronal cells and the change of synaptic plasticity and structural plasticity of nucleus accumbens (NAc) are implicated in depression symptomology. However, the molecular and epigenetic mechanisms and stresses to the NAc pathological changes in depression remain elusive. MATERIALS AND METHODS In this study, treatment group mice were treated continually with the chronic unpredictable mild stress (CUMS) until expression of depression-like behaviors were found. Depression was confirmed with sucrose preference, novelty-suppressed feeding, forced swimming, and tail suspension tests. We applied high-throughput RNA sequencing to assess microRNA expression and transcriptional profiles in the NAc tissue from depression-like behaviors mice and control mice. The regulatory network of miRNAs/mRNAs was constructed based on the high-throughput RNA sequence and bioinformatics software predictions. RESULTS A total of 17 miRNAs and 10 mRNAs were significantly upregulated in the NAc of CUMS-induced mice with depression-like behaviors, and 12 miRNAs and 29 mRNAs were downregulated. A series of bioinformatics analyses showed that these altered miRNAs predicted target mRNA and differentially expressed mRNAs were significantly enriched in the MAPK signaling pathway, GABAergic synapse, dopaminergic synapse, cytokine-cytokine receptor interaction, axon guidance, regulation of autophagy, and so on. Furthermore, dual luciferase report assay and qRT-PCR results validated the miRNA/mRNA regulatory network. CONCLUSION The deteriorations of GABAergic synapses, dopaminergic synapses, neurotransmitter synthesis, as well as autophagy-associated apoptotic pathway are associated with the molecular pathological mechanism of CUMS-induced depression.
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Affiliation(s)
- Ke Ma
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
| | - Hongxiu Zhang
- Institute of Virology, Jinan Center for Disease Control and Prevention, Jinan 250021, People's Republic of China
| | - Guohui Wei
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
| | - Zhenfei Dong
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
| | - Haijun Zhao
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
| | - Xiaochun Han
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
| | - Xiaobin Song
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
| | - Huiling Zhang
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
| | - Xin Zong
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
| | - Zulqarnain Baloch
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China,
| | - Shijun Wang
- Shandong Co-Innovation Center of Classic TCM formula, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China,
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Li Y, Liu X, Ma Y, Wang Y, Zhou W, Hao M, Yuan Z, Liu J, Xiong M, Shugart YY, Wang J, Jin L. knnAUC: an open-source R package for detecting nonlinear dependence between one continuous variable and one binary variable. BMC Bioinformatics 2018; 19:448. [PMID: 30466390 PMCID: PMC6249767 DOI: 10.1186/s12859-018-2427-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 10/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous variable X and one binary dependent variables Y (0 or 1). RESULTS We addressed this problem by using knnAUC (k-nearest neighbors AUC test, the R package is available at https://sourceforge.net/projects/knnauc/ ). In the knnAUC software framework, we first resampled a dataset to get the training and testing dataset according to the sample ratio (from 0 to 1), and then constructed a k-nearest neighbors algorithm classifier to get the yhat estimator (the probability of y = 1) of testy (the true label of testing dataset). Finally, we calculated the AUC (area under the curve of receiver operating characteristic) estimator and tested whether the AUC estimator is greater than 0.5. To evaluate the advantages of knnAUC compared to seven other popular methods, we performed extensive simulations to explore the relationships between eight different methods and compared the false positive rates and statistical power using both simulated and real datasets (Chronic hepatitis B datasets and kidney cancer RNA-seq datasets). CONCLUSIONS We concluded that knnAUC is an efficient R package to test non-linear dependence between one continuous variable and one binary dependent variable especially in computational biology area.
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Affiliation(s)
- Yi Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Six Industrial Research Institute, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaoyu Liu
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yanyun Ma
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Six Industrial Research Institute, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Weichen Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Meng Hao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhenghong Yuan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Medical School, Fudan University, Shanghai, China
| | - Jie Liu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Medical School, Fudan University, Shanghai, China.,Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Momiao Xiong
- Human Genetics Center, School of Public Health, University of Texas Houston Health Sciences Center, Houston, TX, USA
| | - Yin Yao Shugart
- Unit on Statistical Genomics, Division of Intramural Division Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
| | - Jiucun Wang
- Six Industrial Research Institute, Fudan University, Shanghai, China. .,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China. .,Human Phenome Institute, Fudan University, Shanghai, China.
| | - Li Jin
- Six Industrial Research Institute, Fudan University, Shanghai, China. .,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China. .,Human Phenome Institute, Fudan University, Shanghai, China.
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Zhao X, Ren Y, Cui N, Wang X, Cui Y. Identification of key microRNAs and their targets in exosomes of pancreatic cancer using bioinformatics analysis. Medicine (Baltimore) 2018; 97:e12632. [PMID: 30278585 PMCID: PMC6181532 DOI: 10.1097/md.0000000000012632] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pancreatic cancer (PC) is one of the most lethal tumors, due to late diagnosis and limited surgical strategies. It has been reported that serum exosomal microRNAs (S-Exo-miRNAs) play a pivotal role as signaling molecules and serve as noninvasive diagnosis methods for PC. The combination of S-Exo-miRNAs with the corresponding target also plays an important role in the tumor microenvironment.Here we investigated S-Exo-miRNAs involved in PC. The gene expression profile was downloaded from the Gene Expression Omnibus (GEO) database. The analysis was carried out using GEO2R. The targets of differentially expressed serum exosomal miRNAs (DE-S-Exo-miRNAs) were predicted by 4 bioinformatic algorithms (miRanda, miRDB, miRWalk, and Targetscan). Further analysis with gene ontology (GO) and Kyoto Encyclopedia of Genomes pathway (KEGG) enrichment analyses were performed with Cytoscape software version 3.4.0. Subsequently, the interaction regulatory network of target genes was performed with the Search Tool for the Retrieval of Interacting Genes (STRING) database (http://www.string-db.org/) and visualized using Cytoscape software.We downloaded the gene expression profile GSE50632, which was based on an Agilent microarray GPL17660 platform containing 4 eligible samples. In total 467 DE-S-Exo-miRNAs were obtained, including 7 overexpressed miRNAs (1.50%), and 460 remaining underexpressed miRNAs (98.50%). The databases miRWalk, miRDB, miRanda, and TargetScan were used to predict their potential targets, which were subsequently submitted to Cytoscape software version 3.4.0 (www.cytoscape.org). Next the functional and pathway enrichment analysis were used for the KEGG pathway and GO categories analysis. The enrichment analysis identified the genes involved in such processes as developmental and negative regulation of multicellular organismal processes, regulation of anatomical structure morphogenesis, regulation of cell death, apoptotic processes and mitogen-activated protein kinase (MAPK) signaling pathway, transforming growth factor - beta (TGF -β) signaling pathway, cyclic adenosine monophosphate (cAMP) signaling pathway, and the phosphatidylinositol-3 kinases/Akt (PI3K-Akt) signaling pathway. Subsequently according to the protein-protein interaction (PPI) network, the top 10 genes were obtained. The enrichment analyses of the genes involved in a significant module revealed that these genes were related to the TGF-β signaling pathway. After reviewing the literature, we identified the apoptosis genes, and their corresponding miRNAs that have a relationship with apoptosis of the tumor.This analysis provides a comprehensive understanding of the roles of S-Exo-miRNAs and the related targets in the development of PC. Additionally, the present study provides promising candidate targets for early diagnosis and therapeutic intervention. However, these predictions require further experimental validation in future studies.
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Affiliation(s)
- Xin Zhao
- Tianjin Medical University, Tianjin
- Department of Surgery, Tianjin Nankai Hospital, Nankai Clinical School, Tianjin Medical University
| | - Yiming Ren
- Department of Bone and Joint, Tianjin Union Medicine Center, PR China
| | - Naiqiang Cui
- Department of Surgery, Tianjin Nankai Hospital, Nankai Clinical School, Tianjin Medical University
| | - Ximo Wang
- Department of Surgery, Tianjin Nankai Hospital, Nankai Clinical School, Tianjin Medical University
| | - Yunfeng Cui
- Department of Surgery, Tianjin Nankai Hospital, Nankai Clinical School, Tianjin Medical University
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12
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Predicting miRNA targets for head and neck squamous cell carcinoma using an ensemble method. Int J Biol Markers 2018; 33:87-93. [PMID: 28665450 DOI: 10.5301/ijbm.5000285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND This study aimed to uncover potential microRNA (miRNA) targets in head and neck squamous cell carcinoma (HNSCC) using an ensemble method which combined 3 different methods: Pearson's correlation coefficient (PCC), Lasso and a causal inference method (i.e., intervention calculus when the directed acyclic graph (DAG) is absent [IDA]), based on Borda count election. METHODS The Borda count election method was used to integrate the top 100 predicted targets of each miRNA generated by individual methods. Afterwards, to validate the performance ability of our method, we checked the TarBase v6.0, miRecords v2013, miRWalk v2.0 and miRTarBase v4.5 databases to validate predictions for miRNAs. Pathway enrichment analysis of target genes in the top 1,000 miRNA-messenger RNA (mRNA) interactions was conducted to focus on significant KEGG pathways. Finally, we extracted target genes based on occurrence frequency ≥3. RESULTS Based on an absolute value of PCC >0.7, we found 33 miRNAs and 288 mRNAs for further analysis. We extracted 10 target genes with predicted frequencies not less than 3. The target gene MYO5C possessed the highest frequency, which was predicted by 7 different miRNAs. Significantly, a total of 8 pathways were identified; the pathways of cytokine-cytokine receptor interaction and chemokine signaling pathway were the most significant. CONCLUSIONS We successfully predicted target genes and pathways for HNSCC relying on miRNA expression data, mRNA expression profile, an ensemble method and pathway information. Our results may offer new information for the diagnosis and estimation of the prognosis of HNSCC.
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Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep 2018; 23:194-212.e6. [PMID: 29617660 PMCID: PMC6002769 DOI: 10.1016/j.celrep.2018.03.063] [Citation(s) in RCA: 207] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 02/26/2018] [Accepted: 03/15/2018] [Indexed: 12/23/2022] Open
Abstract
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.
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Affiliation(s)
- Joshua D Campbell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Boston University School of Medicine, Boston, MA 02118, USA
| | - Christina Yau
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94115, USA; Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kevin Brennan
- Department of Medicine-Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
| | - Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Alison M Taylor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Chen Wang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Vonn Walter
- Department of Public Health Sciences, Penn State Milton Hershey Medical Center, Hershey, PA 17033, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren Averett Byers
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chad J Creighton
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine and Dan L Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Department of Molecular & Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Juliann Shih
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Olivier Gevaert
- Department of Medicine-Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
| | - Marcos Prunello
- Department of Medicine-Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Pavana Anur
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97201, USA
| | - Jianhong Chen
- Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Hui Cheng
- Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - D Neil Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Chandra Sekhar Pedamallu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Akinyemi I Ojesina
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Hudson Alpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sara Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Christopher Benz
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Andre Schultz
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rupa S Kanchi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carl M Gay
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Apurva Hegde
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wencai Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pavel Sumazin
- Department of Medicine-Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hua-Sheng Chiu
- Department of Medicine-Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ting-Wen Chen
- Department of Medicine-Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Preethi Gunaratne
- Department of Biology & Biochemistry, UH-SeqNEdit Core, University of Houston, Houston, TX 77204, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Larry Donehower
- Center for Comparative Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Janet S Rader
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Department of Pathology, Oklahoma City, OK 73104, USA
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine, Dermatology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77401, USA
| | - Elsa R Flores
- Molecular Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Kenneth Y Tsai
- Departments of Anatomic Pathology and Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Jane H Zhou
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Esther Drill
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronglei Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher K Wong
- Department of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joshua M Stuart
- Department of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Katherine A Hoadley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Myron Peto
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97201, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhong Chen
- Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.
| | - Carter Van Waes
- Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.
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Abstract
Glioblastoma is the most aggressive brain tumor and, even with the current multimodal therapy, is an invariably lethal cancer with a life expectancy that depends on the tumor subtype but, even in the most favorable cases, rarely exceeds 2 years. Epigenetic factors play an important role in gliomagenesis, are strong predictors of outcome, and are important determinants for the resistance to radio- and chemotherapy. The latest addition to the epigenetic machinery is the noncoding RNA (ncRNA), that is, RNA molecules that are not translated into a protein and that exert their function by base pairing with other nucleic acids in a reversible and nonmutational mode. MicroRNAs (miRNA) are a class of ncRNA of about 22 bp that regulate gene expression by binding to complementary sequences in the mRNA and silence its translation into proteins. MicroRNAs reversibly regulate transcription through nonmutational mechanisms; accordingly, they can be considered as epigenetic effectors. In this review, we will discuss the role of miRNA in glioma focusing on their role in drug resistance and on their potential applications in the therapy of this tumor.
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15
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Li L, Zhao J, Huang S, Wang Y, Zhu L, Cao Y, Xiong J, Deng J. MiR-93-5p promotes gastric cancer-cell progression via inactivation of the Hippo signaling pathway. Gene 2017; 641:240-247. [PMID: 29045821 DOI: 10.1016/j.gene.2017.09.071] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 09/01/2017] [Accepted: 09/26/2017] [Indexed: 01/07/2023]
Abstract
MiR-93-5p has been previously found to be associated with gastric cancer (GC) tumorigenesis; however, the current understanding of its function in this context remains largely incomplete. In the present study, we showed that miR-93-5p was upregulated in GC tissues. We also demonstrated that miR-93-5p overexpression promoted the proliferation, migration, invasion, and chemoresistance of SGC-7901 cells in vitro, and conversely, that endogenously silencing miR-93-5p expression induced the opposite effects in HGC-27 cells. Overexpression of miR-93-5p was found to inactivate the Hippo pathway, and furthermore, miR-93-5p knockdown activated Hippo signaling. MiR-93-5p upregulation was also shown to inhibit the expression of two well-characterized Hippo pathway regulators, protocadherin Fat 4 (FAT4), and large tumor suppressors 2 (LATS2), at both the mRNA and protein level. Additionally, the results of bioinformatics analyses and luciferase reporter assays indicated that miR-93-5p directly targets the 3'-UTR of FAT4 and LATS2. Taken together, these results demonstrate that miR-93-5p promotes GC-cell progression via the inactivation of the Hippo signaling pathway, and thus, represents a potential therapeutic target for the treatment of GC.
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Affiliation(s)
- Li Li
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, PR China
| | - Jianguo Zhao
- Department of Oncology, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing 312000, PR China
| | - Shanshan Huang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, PR China
| | - Yi Wang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, PR China
| | - Lingling Zhu
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, PR China
| | - Yuan Cao
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, PR China
| | - Jianping Xiong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, PR China.
| | - Jun Deng
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, PR China.
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16
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Zare M, Bastami M, Solali S, Alivand MR. Aberrant miRNA promoter methylation and EMT‐involving miRNAs in breast cancer metastasis: Diagnosis and therapeutic implications. J Cell Physiol 2017; 233:3729-3744. [DOI: 10.1002/jcp.26116] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 08/01/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Maryam Zare
- Department of BiologyPayame Noor UniversityTehranIran
| | - Milad Bastami
- Drug Applied Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Medical GeneticsFaculty of Medicine, Tabriz University of Medical SciencesTabrizIran
| | - Saeed Solali
- Department of HematologyFaculty of Medicine, Tabriz University of Medical SciencesTabrizIran
- Immunology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohammad Reza Alivand
- Drug Applied Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Medical GeneticsFaculty of Medicine, Tabriz University of Medical SciencesTabrizIran
- Stem Cell Research CenterTabriz University of Medical SciencesTabrizIran
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