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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: 3] [Impact Index Per Article: 1.5] [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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Byun MR, Kim CH, Lee HS, Choi JW, Lee SK. Repurposing of ginseng extract as topoisomerase I inhibitor based on the comparative analysis of gene expression patterns. PHYTOCHEMISTRY 2019; 164:223-227. [PMID: 31181353 DOI: 10.1016/j.phytochem.2019.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 03/25/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Repositioning of plant extracts and chemical drugs can accelerate drug development. However, its success rate may depend on what the clue is for the repositioning. Recently, repositioning based on correction of unwarranted gene expression pattern has suggested the possibility of new drug development. Here, we designed a similar method for the repositioning of nutraceutical ginseng (Panax ginseng C.A.Mey.), which is one of the most validated natural therapeutic products for various diseases. We analyzed ginseng-induced gene expression profiles using the connectivity map algorithm, which is a database that connects diseases, chemical drugs, and gene expression. Ginseng was predicted to show the same effects as those of topoisomerase I inhibitors. In a subsequent in vitro assay, ginseng extract unwound coiled or supercoiled DNA, an effect comparable to that of the topoisomerase I inhibitor, camptothecin. Furthermore, ginseng extract induced synthetic lethality with suppression of the Werner syndrome gene. The collected data implicate ginseng as a candidate antitumor agent owing to its topoisomerase I inhibitory activity and further validate the usefulness of differentially expressed gene similarity-based repurposing of other natural products.
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Affiliation(s)
- Mi Ran Byun
- College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Cheol Hyun Kim
- College of Korean Medicine, Wonkwang University, Iksan, Cheonbuk, 54538, Republic of Korea
| | - Ho Sub Lee
- Hanbang Cardio-Renal Syndrome Research Center, Wonkwang University, 460, Iksan-daero, Iksan, Jeonbuk, 54538, Republic of Korea; College of Korean Medicine, Wonkwang University, Iksan, Cheonbuk, 54538, Republic of Korea.
| | - Jin Woo Choi
- College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea.
| | - Sang Kwan Lee
- College of Korean Medicine, Wonkwang University, Iksan, Cheonbuk, 54538, Republic of Korea.
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Byun MR, Lee DH, Jang YP, Lee HS, Choi JW, Lee SK. Repurposing natural products as novel HDAC inhibitors by comparative analysis of gene expression profiles. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 59:152900. [PMID: 30974310 DOI: 10.1016/j.phymed.2019.152900] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 03/13/2019] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Extracts derived from natural products have been used to produce health supplements or therapeutic agents in oriental medicine. Although these extracts contain various bioactive compounds, their applications are generally limited to a few previously known diseases. To effectively expand their use for the treatment of other conditions, systematic analysis should be conducted for repurposing. PURPOSE The purpose of the present study was to investigate the new therapeutic efficacies of the Platycodon grandiflorum and ginseng extract using the CMAP-based gene expression analysis. METHODS In the present study, we analyzed the expression patterns of differentially expressed genes (DEGs) from extracts as the basis for drug repurposing. Cells were treated with extracts or single compounds derived from nine natural products. DEG analysis indicated that the gene expression patterns of cells treated with P. grandiflorum and ginseng extracts were highly similar to those of cells treated with different types of Histone deacetylase (HDAC) inhibitors. To identify the new mechanism of these extracts, we carried out cell viability assay, TUNEL assay, HDAC enzyme activity assay and immunoblot analysis. RESULTS In vitro experiments at the dose of 50 µg/ml of each extract did not affect cell death rate but significantly inhibited HDAC activity. Each extract was found to inhibit HDAC enzymatic activity and induce the expression of the p21. Furthermore, our results revealed that each extract stimulated cell death and inhibited cell proliferation. CONCLUSION These findings demonstrate the HDAC-inhibiting activity of P. grandiflorum and ginseng extracts and further validate the effectiveness of DEG similarity-based repurposing of natural products.
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Affiliation(s)
- Mi Ran Byun
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea; Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dae Hoon Lee
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea; Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Young Pyo Jang
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea; Department of Oriental Pharmaceutical Science, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Ho Sub Lee
- College of Korean Medicine, Wonkwang University, Iksan, Cheonbuk 54538, Republic of Korea.
| | - Jin Woo Choi
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea; Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea.
| | - Sang Kwan Lee
- College of Korean Medicine, Wonkwang University, Iksan, Cheonbuk 54538, Republic of Korea.
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Yoo HS, Kim JM, Jo E, Cho CK, Lee SY, Kang HS, Lee MG, Yang PY, Jang IS. Modified Panax ginseng extract regulates autophagy by AMPK signaling in A549 human lung cancer cells. Oncol Rep 2017; 37:3287-3296. [PMID: 28440448 DOI: 10.3892/or.2017.5590] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/17/2016] [Indexed: 11/06/2022] Open
Abstract
Panax ginseng has been used worldwide as a traditional medicine for the treatment of cancer and other diseases. The antiproliferative activity of ginseng has been increased after enzymatic processing of ginseng saponin, which may result in the accumulation of minor saponins, such as Rh2, Rg3, compound K and protopanaxatriol type (PPT) in modified regular ginseng extract (MRGX). In the present study, the anticancer activity and the associated mechanisms of MRGX were investigated using A549 human lung cancer cells. To elucidate the mechanisms underlying the effects of MRGX, we performed a microarray analysis of gene expression in the A549 cells. Molecular mechanisms that were associated with the anticancer activity of MRGX were studied, with a special focus on the autophagy-related multiple signaling pathways in lung cancer cells. Microarray analyses elucidated autophagy-related genes affected by MRGX. Administration of MRGX at 100 µg/ml induced punctate cytoplasmic expression of LC3, Beclin-1 and ATG5 and increased expression of endogenous LC3-II whereas 50 µg/ml did not inhibit the proliferation of A549 cells. Compared to the control cells, in cells treated with MRGX at 100 µg/ml, the level of p-Akt was increased, while that of mTOR-4EBP1 was decreased. Downregulation of mTOR and 4EBP1 in the MRGX-treated cells was found not to be a p-Ulk (S757)-dependent pathway, but a p-Ulk (S317)-dependent autophagic pathway, using AMPK. These data suggest that MRGX regulates AMPK and induces autophagy in lung cancer cells.
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Affiliation(s)
- Hwa-Seung Yoo
- East-West Cancer Center, Dunsan Oriental Hospital of Daejeon University, Daejeon 302-122, Republic of Korea
| | - Jung Min Kim
- NAR Center, Inc. & Genoplan Korea, Inc., Seoul 06221, Republic of Korea
| | - Eunbi Jo
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon 305-333, Republic of Korea
| | - Chong-Kwan Cho
- East-West Cancer Center, Dunsan Oriental Hospital of Daejeon University, Daejeon 302-122, Republic of Korea
| | - Seung-Yeul Lee
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon 305-333, Republic of Korea
| | - Hwan Su Kang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon 305-333, Republic of Korea
| | - Min-Goo Lee
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Pei-Ying Yang
- Departments of Palliative, Rehabilitation and Integrative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ik-Soon Jang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon 305-333, Republic of Korea
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Hwang IH, Kwon YK, Cho CK, Lee YW, Sung JS, Joo JC, Lee KB, Yoo HS, Jang IS. Modified Panax ginseng Extract Inhibits uPAR-Mediated α5β1-Integrin Signaling by Modulating Caveolin-1 to Induce Early Apoptosis in Lung Cancer Cells. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2016; 44:1081-97. [PMID: 27430913 DOI: 10.1142/s0192415x16500609] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Urokinase receptor (uPAR) is enhanced in many human cancer cells and is frequently an indicator of poor prognosis. Activation of [Formula: see text]1-integrin requires caveolin-1 and is regulated by uPAR. However, the underlying molecular mechanism responsible for the interaction between uPAR and [Formula: see text]1-integrin remains obscure. We found that modified regular Panax ginseng extract (MRGX) had a negative modulating effect on the uPAR/[Formula: see text]1-integrin interaction, disrupted the uPAR/integrin interaction by modulating caveoline-1, and caused early apoptosis in cancer cells. Additionally, we found that siRNA-mediated caveoline-1 downregulation inhibited uPAR-mediated [Formula: see text]1-integrin signaling, whereas caveoline-1 up-regulation stimulated the signaling, which suppressed p53 expression, thereby indicating negative crosstalk exists between the integrin [Formula: see text]1 and the p53 pathways. Thus, these findings identify a novel mechanism whereby the inhibition of [Formula: see text]1 integrin and the activation of p53 modulate the expression of the anti-apoptotic proteins that are crucially involved in inducing apoptosis in A549 lung cancer cells. Furthermore, MRGX causes changes in the expressions of members of the Bcl-2 family (Bax and Bcl-2) in a pro-apoptotic manner. In addition, MGRX-mediated inhibition of [Formula: see text]1 integrin attenuates ERK phosphorylation (p-ERK), which up-regulates caspase-8 and Bax. Therefore, ERK may affect mitochondria through a negative regulation of caspase-8 and Bax. Taken together, these findings reveal that MRGX is involved in uPAR-[Formula: see text]1-integrin signaling by modulating caveolin-1 signaling to induce early apoptosis in A549 lung-cancer cells and strongly indicate that MRGX might be useful as a herbal medicine and may lead to the development of new herbal medicine that would suppress the growth of lung-cancer cells.
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Affiliation(s)
- In-Hu Hwang
- Department of Physiology, Korea University College of Medicine, Seoul 136-705, Republic of Korea
| | - Yong-Kyun Kwon
- East-West Cancer Center, Daejeon University, Daejeon 302-120, Republic of Korea
| | - Chong-Kwan Cho
- East-West Cancer Center, Daejeon University, Daejeon 302-120, Republic of Korea
| | - Yeon-Weol Lee
- East-West Cancer Center, Daejeon University, Daejeon 302-120, Republic of Korea
| | - Jung-Suk Sung
- Department of Life Science, Dongguk University, Goyang, Gyeonggi-do 10326, Republic of Korea
| | - Jong-Cheon Joo
- Department of Sasang Constitutional Medicine, Wonkwang University Oriental Medical Hospital, Jeonju 54887, Republic of Korea
| | - Kyung-Bok Lee
- Division of Bioconvergence, Korea Basic Science Institute, Daejeon 305-333, Korea
| | - Hwa-Seung Yoo
- East-West Cancer Center, Daejeon University, Daejeon 302-120, Republic of Korea
| | - Ik-Soon Jang
- Division of Bioconvergence, Korea Basic Science Institute, Daejeon 305-333, Korea
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