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Silva MC, Eugénio P, Faria D, Pesquita C. Ontologies and Knowledge Graphs in Oncology Research. Cancers (Basel) 2022; 14:cancers14081906. [PMID: 35454813 PMCID: PMC9029532 DOI: 10.3390/cancers14081906] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
The complexity of cancer research stems from leaning on several biomedical disciplines for relevant sources of data, many of which are complex in their own right. A holistic view of cancer—which is critical for precision medicine approaches—hinges on integrating a variety of heterogeneous data sources under a cohesive knowledge model, a role which biomedical ontologies can fill. This study reviews the application of ontologies and knowledge graphs in cancer research. In total, our review encompasses 141 published works, which we categorized under 14 hierarchical categories according to their usage of ontologies and knowledge graphs. We also review the most commonly used ontologies and newly developed ones. Our review highlights the growing traction of ontologies in biomedical research in general, and cancer research in particular. Ontologies enable data accessibility, interoperability and integration, support data analysis, facilitate data interpretation and data mining, and more recently, with the emergence of the knowledge graph paradigm, support the application of Artificial Intelligence methods to unlock new knowledge from a holistic view of the available large volumes of heterogeneous data.
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Bioinformatics Analysis Identified Key Molecular Changes in Bladder Cancer Development and Recurrence. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3917982. [PMID: 31828101 PMCID: PMC6881748 DOI: 10.1155/2019/3917982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/16/2019] [Accepted: 09/27/2019] [Indexed: 12/29/2022]
Abstract
Background and Objectives: Bladder cancer (BC) is a complex tumor associated with high recurrence and mortality. To discover key molecular changes in BC, we analyzed next-generation sequencing data of BC and surrounding tissue samples from clinical specimens. Methods. Gene expression profiling datasets of bladder cancer were analyzed online. The Database for Annotation, Visualization, and Integrated Discovery (DAVID, https://david.ncifcrf.gov/) was used to perform Gene Ontology (GO) functional and KEGG pathway enrichment analyses. Molecular Complex Detection (MCODE) in Cytoscape software (Cytoscape_v3.6.1) was applied to identify hub genes. Protein expression and survival data were downloaded from OncoLnc (http://www.oncolnc.org/). Gene expression data were obtained from the ONCOMINE website (https://www.oncomine.org/). Results. We identified 4211 differentially expressed genes (DEGs) by analysis of surrounding tissue vs. cancer tissue (SC analysis) and 410 DEGs by analysis of cancer tissue vs. recurrent tissue cluster (CR analysis). GO function analysis revealed enrichment of DEGs in genes related to the cytoplasm and nucleoplasm for both clusters, and KEGG pathway analysis showed enrichment of DEGs in the PI3K-Akt signaling pathway. We defined the 20 genes with the highest degree of connectivity as the hub genes. Cox regression revealed CCNB1, ESPL1, CENPM, BLM, and ASPM were related to overall survival. The expression levels of CCNB1, ESPL1, CENPM, BLM, and ASPM were 4.795-, 5.028-, 8.691-, 2.083-, and 3.725-fold higher in BC than the levels in normal tissues, respectively. Conclusions. The results suggested that the functions of CCNB1, ESPL1, CENPM, BLM, and ASPM may contribute to BC development and the functions of CCNB1, ESPL1, CENPM, and BLM may also contribute to BC recurrence.
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Hahn O, Stubbs TM, Reik W, Grönke S, Beyer A, Partridge L. Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity. PLoS Genet 2018; 14:e1007766. [PMID: 30462643 PMCID: PMC6281273 DOI: 10.1371/journal.pgen.1007766] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 12/05/2018] [Accepted: 11/08/2018] [Indexed: 12/30/2022] Open
Abstract
Dietary, pharmacological and genetic interventions can extend health- and lifespan in diverse mammalian species. DNA methylation has been implicated in mediating the beneficial effects of these interventions; methylation patterns deteriorate during ageing, and this is prevented by lifespan-extending interventions. However, whether these interventions also actively shape the epigenome, and whether such epigenetic reprogramming contributes to improved health at old age, remains underexplored. We analysed published, whole-genome, BS-seq data sets from mouse liver to explore DNA methylation patterns in aged mice in response to three lifespan-extending interventions: dietary restriction (DR), reduced TOR signaling (rapamycin), and reduced growth (Ames dwarf mice). Dwarf mice show enhanced DNA hypermethylation in the body of key genes in lipid biosynthesis, cell proliferation and somatotropic signaling, which strongly correlates with the pattern of transcriptional repression. Remarkably, DR causes a similar hypermethylation in lipid biosynthesis genes, while rapamycin treatment increases methylation signatures in genes coding for growth factor and growth hormone receptors. Shared changes of DNA methylation were restricted to hypermethylated regions, and they were not merely a consequence of slowed ageing, thus suggesting an active mechanism driving their formation. By comparing the overlap in ageing-independent hypermethylated patterns between all three interventions, we identified four regions, which, independent of genetic background or gender, may serve as novel biomarkers for longevity-extending interventions. In summary, we identified gene body hypermethylation as a novel and partly conserved signature of lifespan-extending interventions in mouse, highlighting epigenetic reprogramming as a possible intervention to improve health at old age.
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Affiliation(s)
- Oliver Hahn
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cellular Networks and Systems Biology, CECAD, University of Cologne, Cologne, Germany
| | - Thomas M. Stubbs
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Andreas Beyer
- Cellular Networks and Systems Biology, CECAD, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom
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Falzone L, Candido S, Salemi R, Basile MS, Scalisi A, McCubrey JA, Torino F, Signorelli SS, Montella M, Libra M. Computational identification of microRNAs associated to both epithelial to mesenchymal transition and NGAL/MMP-9 pathways in bladder cancer. Oncotarget 2018; 7:72758-72766. [PMID: 27602581 PMCID: PMC5341942 DOI: 10.18632/oncotarget.11805] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/25/2016] [Indexed: 12/20/2022] Open
Abstract
Bladder cancer is one of the leading cancer of the urinary tract. It is often diagnosed at advanced stage of the disease. To date, no specific and effective early detection biomarkers are available. Cancer development and progression are associated with the involvement of both epithelial-mesenchymal transition (EMT) and tumor microenvironment of which NGAL/MMP-9 complex represents the main player in bladder cancer. It is known that change in microRNAs (miRNAs) expression may result in gene modulation. Therefore, the identification of specific miRNAs associated with EMT pathway and NGAL/MMP-9 complex may be useful to detect the development of bladder cancer at early stages. On this ground, the expression levels of miRNAs in public available datasets of bladder cancer containing data of non-coding RNA profiling was evaluated. This analysis revealed a group of 16 miRNAs differentially expressed between bladder cancer patients and related healthy controls. By miRNA prediction tool (mirDIP), the relationship between the identified miRNAs and the EMT genes was established. Using the DIANA-mirPath (v.2) software, miRNAs, able to modulate the expression of NGAL and MMP-9 genes, were recognized. The results of this study provide evidence that the downregulated hsa-miR-145-5p and hsa-miR-214-3p may modulate the expression of both EMT and NGAL/MMP-9 pathways. Therefore, further validation analyses may confirm the usefulness of these selected miRNAs for predicting the development of bladder cancer at the early stage of the disease.
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Affiliation(s)
- Luca Falzone
- Department of Biomedical and Biotechnological Sciences, Laboratory of Translational Oncology and Functional Genomics, Section of General and Clinical Pathology and Oncology, University of Catania, Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, Laboratory of Translational Oncology and Functional Genomics, Section of General and Clinical Pathology and Oncology, University of Catania, Catania, Italy
| | - Rossella Salemi
- Department of Biomedical and Biotechnological Sciences, Laboratory of Translational Oncology and Functional Genomics, Section of General and Clinical Pathology and Oncology, University of Catania, Catania, Italy
| | - Maria S Basile
- Department of Biomedical and Biotechnological Sciences, Laboratory of Translational Oncology and Functional Genomics, Section of General and Clinical Pathology and Oncology, University of Catania, Catania, Italy
| | | | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Francesco Torino
- Department of Systems Medicine, Chair of Medical Oncology, Tor Vergata University of Rome, Rome, Italy
| | - Salvatore S Signorelli
- Department of Clinical and Experimental Medicine, University of Catania, Medical Angiology Unit, Garibaldi Hospital, Catania, Italy
| | - Maurizio Montella
- Unit of Epidemiology, 'Fondazione G. Pascale', Istituto Nazionale Tumori, Naples, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, Laboratory of Translational Oncology and Functional Genomics, Section of General and Clinical Pathology and Oncology, University of Catania, Catania, Italy
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Kuo JH, Huang AC, Lin JJ, Lai KC, Wu RSC, Yang JL, Ji BC, Yang MD, Chu YL, Chung JG. Cantharidin alters the expression of genes associated with the NKG2D-associated immune response in TSGH-8301 human bladder carcinoma cells. Oncol Lett 2017; 14:234-240. [PMID: 28693159 PMCID: PMC5494876 DOI: 10.3892/ol.2017.6168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 02/03/2017] [Indexed: 12/29/2022] Open
Abstract
Cantharidin (CTD) is a natural toxin in beetles of the Mylabris genus (blister beetle), which has been revealed to induce cell death in various types of human cancer cells. However, to the best of our knowledge, no previous studies have investigated the effect of CTD on the expression of genes and their associated signaling pathways in human bladder carcinoma cells. In the present study, CTD-induced cell morphological changes and apoptosis were observed using phase-contrast microscopy and the terminal deoxynucleotidyl transferase dUTP nick end labeling assay, respectively, in TSGH-8301 human bladder carcinoma cells. In addition, a complementary DNA microarray analysis demonstrated that CTD treatment led to a >2-fold upregulation of 269 genes. For example, the DNA damage-associated gene DNA-damage-inducible transcript 3 had a 4.75-fold upregulation. Furthermore, another 286 genes were >2-fold downregulated in response to CTD treatment. Matrix-remodeling associated 5, which is associated with cell migration and invasion, was downregulated 7.98-fold.
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Affiliation(s)
- Jehn-Hwa Kuo
- Special Class of Healthcare, Industry Management, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan, R.O.C.,Department of Urology, Jen-Ai Hospital, Taichung 412, Taiwan, R.O.C
| | - An-Cheng Huang
- Department of Nursing, St. Mary's Junior College of Medicine, Nursing and Management, Yilan 26644, Taiwan, R.O.C
| | - Jen-Jyh Lin
- Division of Cardiology, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Kuang-Chi Lai
- School of Medicine, China Medical University, Taichung 404, Taiwan, R.O.C.,Department of Surgery, China Medical University Beigang Hospital, Yunlin 651, Taiwan, R.O.C
| | - Rick Sai-Chuen Wu
- School of Medicine, China Medical University, Taichung 404, Taiwan, R.O.C.,Department of Anesthesiology, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Jiun-Long Yang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung 404, Taiwan, R.O.C
| | - Bin-Chuan Ji
- Division of Chest Medicine, Department of Internal Medicine, Changhua Christian Hospital, Changhua 500, Taiwan, R.O.C
| | - Mei-Due Yang
- Department of Surgery, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Yung-Lin Chu
- International Master's Degree Program in Food Science, Department of Food Science, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan, R.O.C
| | - Jing-Gung Chung
- Department of Biological Science and Technology, China Medical University, Taichung 404, Taiwan, R.O.C.,Department of Biotechnology, Asia University, Taichung 413, Taiwan, R.O.C
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Chang L, Qi H, Xiao Y, Li C, Wang Y, Guo T, Liu Z, Liu Q. Integrated analysis of noncoding RNAs and mRNAs reveals their potential roles in the biological activities of the growth hormone receptor. Growth Horm IGF Res 2016; 29:11-20. [PMID: 27064376 DOI: 10.1016/j.ghir.2016.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 02/14/2016] [Accepted: 03/18/2016] [Indexed: 11/28/2022]
Abstract
Accumulating evidence has indicated that noncoding RNAs (ncRNAs) have important regulatory potential in various biological processes. The molecular mechanisms by which growth hormone receptor (GHR) deficiency protects against age-related pathologies, reduces the incidence and delays the occurrence of fatal neoplasms are unclear. The aim of this study was to investigate miRNA, lncRNA and mRNA expression profiles and the potential functional roles of these RNA molecules in GHR knockout (GHR-KO) mice. Microarray expression profiles of miRNAs, lncRNAs and mRNAs were determined in wild type control mice and in GHR-KO mice. Differential expression, pathway and gene network analyses were developed to identify the possible biological roles of functional RNA molecules. Compared to wild type control mice, 1695 lncRNAs, 914 mRNAs and 9 miRNAs were upregulated and 1747 lncRNAs, 786 mRNAs and 21 miRNAs were downregulated in female GHR-KO mice. Moreover, 1265 lncRNAs, 724 mRNAs and 41 miRNAs were upregulated and 1377 lncRNAs, 765 mRNAs and 16 miRNAs were downregulated in male GHR-KO mice compared to wild type mice. Co-expression analysis of mRNAs, lncRNAs, and miRNAs showed that mRNAs including Hemxi2, Ero1Ib, 4933434i20RIK, Pde7a and Lgals1, lncRNAs including ASMM9PARTA014848, EL605414-P1, ASMM9PARTA051724, ASMM9PARTA045378 and ASMM9PARTA049185, and miRNAs including miR-188-3p, miR-690, miR-709 and miR-710 are situated at the core position of a three-dimensional lncRNA-mRNA-miRNA regulatory network. KEGG analysis showed that the most significantly regulated pathway was steroid hormone biosynthesis. We identified a set of lncRNAs, miRNAs and mRNAs that were aberrantly expressed in GHR-KO mice. Our results provide a foundation and an expansive view of the biological activities of the GHR.
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Affiliation(s)
- Lei Chang
- Department of General Surgery, Zhongnan Hospital, Wuhan University, Donghu Road 169, Wuhan 430071, PR China
| | - Haolong Qi
- Department of General Surgery, Zhongnan Hospital, Wuhan University, Donghu Road 169, Wuhan 430071, PR China
| | - Yusha Xiao
- Department of General Surgery, Zhongnan Hospital, Wuhan University, Donghu Road 169, Wuhan 430071, PR China
| | - Changsheng Li
- Department of General Surgery, Zhongnan Hospital, Wuhan University, Donghu Road 169, Wuhan 430071, PR China
| | - Yitao Wang
- Department of General Surgery, Zhongnan Hospital, Wuhan University, Donghu Road 169, Wuhan 430071, PR China
| | - Tao Guo
- Department of General Surgery, Zhongnan Hospital, Wuhan University, Donghu Road 169, Wuhan 430071, PR China
| | - Zhisu Liu
- Department of General Surgery, Zhongnan Hospital, Wuhan University, Donghu Road 169, Wuhan 430071, PR China
| | - Quanyan Liu
- Department of General Surgery, Zhongnan Hospital, Wuhan University, Donghu Road 169, Wuhan 430071, PR China.
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Luo J, Chen B, Ji XX, Zhou SW, Zheng D. Overexpression of miR-100 inhibits cancer growth, migration, and chemosensitivity in human NSCLC cells through fibroblast growth factor receptor 3. Tumour Biol 2015; 37:15517-15524. [PMID: 26314855 DOI: 10.1007/s13277-015-3850-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 07/24/2015] [Indexed: 01/08/2023] Open
Abstract
Nonsmall cell lung cancer (NSCLC) is a commonly occurring lung cancer. A combination of molecular biological treatments with regular chemotherapy may result in improved therapeutic outcome. Here, we reported significantly higher levels of fibroblast growth factor receptor 3 (FGFR3) and significantly lower levels of miR-100 in the NSCLC specimen, compared to the paired NSCLC-adjacent normal lung tissues. Moreover, the levels of FGFR3 and miR-100 were inversely correlated. Bioinformatics analyses followed by luciferase reporter assay showed that miR-100 bound to the 3'-UTR of FGFR3 messenger RNA (mRNA) to inhibit its translation. Overexpression of miR-100 in NSCLC cells decreased FGFR3 protein levels, whereas inhibition of miR-100 increased FGFR3 protein levels, without affecting FGFR3 mRNA levels. Furthermore, overexpression of miR-100 suppressed cancer growth, migration, and chemosensitivity in NSCLC cells, while inhibition of miR-100 significantly facilitated them. Taken together, our data demonstrate that miR-100 may inhibit NSCLC through FGFR3.
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Affiliation(s)
- Jie Luo
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai, 200433, China
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