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Wang CY, Chao YJ, Chen YL, Wang TW, Phan NN, Hsu HP, Shan YS, Lai MD. Upregulation of peroxisome proliferator-activated receptor-α and the lipid metabolism pathway promotes carcinogenesis of ampullary cancer. Int J Med Sci 2021; 18:256-269. [PMID: 33390794 PMCID: PMC7738964 DOI: 10.7150/ijms.48123] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
Ampullary cancer is a rare periampullary cancer currently with no targeted therapeutic agent. It is important to develop a deeper understanding of the carcinogenesis of ampullary cancer. We attempted to explore the characteristics of ampullary cancer in our dataset and a public database, followed by a search for potential drugs. We used a bioinformatics pipeline to analyze complementary (c)DNA microarray data of ampullary cancer and surrounding normal duodenal tissues from five patients. A public database from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) was applied for external validation. Bioinformatics tools used included the Gene Set Enrichment Analysis (GSEA), Database for Annotation, Visualization and Integrated Discovery (DAVID), MetaCore, Kyoto Encyclopedia of Genes and Genomes (KEGG), Hallmark, BioCarta, Reactome, and Connectivity Map (CMap). In total, 9097 genes were upregulated in the five ampullary cancer samples compared to normal duodenal tissues. From the MetaCore analysis, genes of peroxisome proliferator-activated receptor alpha (PPARA) and retinoid X receptor (RXR)-regulated lipid metabolism were overexpressed in ampullary cancer tissues. Further a GSEA of the KEGG, Hallmark, Reactome, and Gene Ontology databases revealed that PPARA and lipid metabolism-related genes were enriched in our specimens of ampullary cancer and in the NCBI GSE39409 database. Expressions of PPARA messenger (m)RNA and the PPAR-α protein were higher in clinical samples and cell lines of ampullary cancer. US Food and Drug Administration (FDA)-approved drugs, including alvespimycin, trichostatin A (a histone deacetylase inhibitor), and cytochalasin B, may have novel therapeutic effects in ampullary cancer patients as predicted by the CMap analysis. Trichostatin A was the most potent agent for ampullary cancer with a half maximal inhibitory concentration of < 0.3 μM. According to our results, upregulation of PPARA and lipid metabolism-related genes are potential pathways in the carcinogenesis and development of ampullary cancer. Results from the CMap analysis suggested potential drugs for patients with ampullary cancer.
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Affiliation(s)
- Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.,Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Ying-Jui Chao
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan.,Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yi-Ling Chen
- Senior Citizen Service Management, Chia-Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Tzu-Wen Wang
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Nam Nhut Phan
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan.,Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yan-Shen Shan
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Ming-Derg Lai
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.,Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 70101, Taiwan.,Center for Infectious Diseases and Signaling Research, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
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Cortesi M, Liverani C, Mercatali L, Ibrahim T, Giordano E. An in-silico study of cancer cell survival and spatial distribution within a 3D microenvironment. Sci Rep 2020; 10:12976. [PMID: 32737377 PMCID: PMC7395763 DOI: 10.1038/s41598-020-69862-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
3D cell cultures are in-vitro models representing a significant improvement with respect to traditional monolayers. Their diffusion and applicability, however, are hampered by the complexity of 3D systems, that add new physical variables for experimental analyses. In order to account for these additional features and improve the study of 3D cultures, we here present SALSA (ScAffoLd SimulAtor), a general purpose computational tool that can simulate the behavior of a population of cells cultured in a 3D scaffold. This software allows for the complete customization of both the polymeric template structure and the cell population behavior and characteristics. In the following the technical description of SALSA will be presented, together with its validation and an example of how it could be used to optimize the experimental analysis of two breast cancer cell lines cultured in collagen scaffolds. This work contributes to the growing field of integrated in-silico/in-vitro analysis of biological systems, which have great potential for the study of complex cell population behaviours and could lead to improve and facilitate the effectiveness and diffusion of 3D cell culture models.
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Affiliation(s)
- Marilisa Cortesi
- Department of Electrical, Electronic and Information Engineering "G. Marconi", University of Bologna, Cesena, FC, Italy.
| | - Chiara Liverani
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo Per Lo Studio E La Cura Dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Laura Mercatali
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo Per Lo Studio E La Cura Dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Toni Ibrahim
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo Per Lo Studio E La Cura Dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Emanuele Giordano
- Department of Electrical, Electronic and Information Engineering "G. Marconi", University of Bologna, Cesena, FC, Italy.,Advanced Research Center On Electronic Systems (ARCES), University of Bologna, Bologna, BO, Italy.,BioEngLab, Health Science and Technology, Interdepartmental Center for Industrial Research (HST-CIRI), University of Bologna, Ozzano Emilia, BO, Italy
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Ung MH, Varn FS, Cheng C. In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics. Expert Opin Drug Discov 2016; 11:1213-1222. [PMID: 27689915 DOI: 10.1080/17460441.2016.1243524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Leukemia is a collection of highly heterogeneous cancers that arise from neoplastic transformation and clonal expansion of immature hematopoietic cells. Post-treatment recurrence is high, especially among elderly patients, thus necessitating more effective treatment modalities. Development of novel anti-leukemic compounds relies heavily on traditional in vitro screens which require extensive resources and time. Therefore, integration of in silico screens prior to experimental validation can improve the efficiency of pre-clinical drug development. Areas covered: This article reviews different methods and frameworks used to computationally screen for anti-leukemic agents. In particular, three approaches are discussed including molecular docking, transcriptomic integration, and network analysis. Expert opinion: Today's data deluge presents novel opportunities to develop computational tools and pipelines to screen for likely therapeutic candidates in the treatment of leukemia. Formal integration of these methodologies can accelerate and improve the efficiency of modern day anti-leukemic drug discovery and ease the economic and healthcare burden associated with it.
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Affiliation(s)
- Matthew H Ung
- a Department of Molecular and Systems Biology , Geisel School of Medicine at Dartmouth , Hanover , NH , USA
| | - Frederick S Varn
- a Department of Molecular and Systems Biology , Geisel School of Medicine at Dartmouth , Hanover , NH , USA
| | - Chao Cheng
- a Department of Molecular and Systems Biology , Geisel School of Medicine at Dartmouth , Hanover , NH , USA.,b Department of Biomedical Data Science , Geisel School of Medicine at Dartmouth , Lebanon , NH , USA.,c Norris Cotton Cancer Center , Lebanon , NH , USA
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