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Fuzzy Matching for Cellular Signaling Networks in a Choroidal Melanoma Model. ADVANCES IN INTELLIGENT SYSTEMS AND COMPUTING 2021. [DOI: 10.1007/978-3-030-54568-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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2
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Santos-Buitrago B, Santos-García G, Hernández-Galilea E. Artificial intelligence for modeling uveal melanoma. Artif Intell Cancer 2020; 1:51-65. [DOI: 10.35713/aic.v1.i4.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/05/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Gustavo Santos-García
- IME, University of Salamanca, Salamanca 37007, Spain
- FADoSS Research Unit, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Emiliano Hernández-Galilea
- Department of Ophthalmology, Institute of Biomedicine Investigation of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, Salamanca 37007, Spain
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Reyes ME, Riquelme I, Salvo T, Zanella L, Letelier P, Brebi P. Brown Seaweed Fucoidan in Cancer: Implications in Metastasis and Drug Resistance. Mar Drugs 2020; 18:md18050232. [PMID: 32354032 PMCID: PMC7281670 DOI: 10.3390/md18050232] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/18/2020] [Accepted: 04/19/2020] [Indexed: 12/11/2022] Open
Abstract
Fucoidans are sulphated polysaccharides that can be obtained from brown seaweed and marine invertebrates. They have anti-cancer properties, through their targeting of several signaling pathways and molecular mechanisms within malignant cells. This review describes the chemical structure diversity of fucoidans and their similarity with other molecules such as glycosaminoglycan, which enable them to participation in diverse biological processes. Furthermore, this review summarizes their influence on the development of metastasis and drug resistance, which are the main obstacles to cure cancer. Finally, this article discusses how fucoidans have been used in clinical trials to evaluate their potential synergy with other anti-cancer therapies.
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Affiliation(s)
- María Elena Reyes
- Laboratory of Integrative Biology (LIBi), Center of Excellence in Translational Medicine- Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4710296, Chile
| | - Ismael Riquelme
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco 4810101, Chile
| | - Tomás Salvo
- Laboratory of Integrative Biology (LIBi), Center of Excellence in Translational Medicine- Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4710296, Chile
| | - Louise Zanella
- Laboratory of Integrative Biology (LIBi), Center of Excellence in Translational Medicine- Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4710296, Chile
| | - Pablo Letelier
- Precision Health Research Laboratory, Departamento de Procesos Diagnósticos y Evaluación, Facultad Ciencias de la Salud, Universidad Católica de Temuco, Temuco 4813302, Chile
| | - Priscilla Brebi
- Laboratory of Integrative Biology (LIBi), Center of Excellence in Translational Medicine- Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4710296, Chile
- Correspondence: ; Tel.: +56-9-92659362
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Santos-Buitrago B, Hernández-Galilea E. Signaling Transduction Networks in Choroidal Melanoma: A Symbolic Model Approach. PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 13TH INTERNATIONAL CONFERENCE 2020. [DOI: 10.1007/978-3-030-23873-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Yoo S, Kim K, Nam H, Lee D. Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence. Nutrients 2018; 10:nu10081042. [PMID: 30096807 PMCID: PMC6115900 DOI: 10.3390/nu10081042] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 12/18/2022] Open
Abstract
Identifying the health benefits of phytochemicals is an essential step in drug and functional food development. While many in vitro screening methods have been developed to identify the health effects of phytochemicals, there is still room for improvement because of high cost and low productivity. Therefore, researchers have alternatively proposed in silico methods, primarily based on three types of approaches; utilizing molecular, chemical or ethnopharmacological information. Although each approach has its own strength in analyzing the characteristics of phytochemicals, previous studies have not considered them all together. Here, we apply an integrated in silico analysis to identify the potential health benefits of phytochemicals based on molecular analysis and chemical properties as well as ethnopharmacological evidence. From the molecular analysis, we found an average of 415.6 health effects for 591 phytochemicals. We further investigated ethnopharmacological evidence of phytochemicals and found that on average 129.1 (31%) of the predicted health effects had ethnopharmacological evidence. Lastly, we investigated chemical properties to confirm whether they are orally bio-available, drug available or effective on certain tissues. The evaluation results indicate that the health effects can be predicted more accurately by cooperatively considering the molecular analysis, chemical properties and ethnopharmacological evidence.
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Affiliation(s)
- Sunyong Yoo
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Bio-Synergy Research Center, Daejeon 34141, Korea.
| | - Kwansoo Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Bio-Synergy Research Center, Daejeon 34141, Korea.
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea.
| | - Doheon Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Bio-Synergy Research Center, Daejeon 34141, Korea.
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Yoo S, Noh K, Shin M, Park J, Lee KH, Nam H, Lee D. In silico profiling of systemic effects of drugs to predict unexpected interactions. Sci Rep 2018; 8:1612. [PMID: 29371651 PMCID: PMC5785495 DOI: 10.1038/s41598-018-19614-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/03/2018] [Indexed: 12/16/2022] Open
Abstract
Identifying unexpected drug interactions is an essential step in drug development. Most studies focus on predicting whether a drug pair interacts or is effective on a certain disease without considering the mechanism of action (MoA). Here, we introduce a novel method to infer effects and interactions of drug pairs with MoA based on the profiling of systemic effects of drugs. By investigating propagated drug effects from the molecular and phenotypic networks, we constructed profiles of 5,441 approved and investigational drugs for 3,833 phenotypes. Our analysis indicates that highly connected phenotypes between drug profiles represent the potential effects of drug pairs and the drug pairs with strong potential effects are more likely to interact. When applied to drug interactions with verified effects, both therapeutic and adverse effects have been successfully identified with high specificity and sensitivity. Finally, tracing drug interactions in molecular and phenotypic networks allows us to understand the MoA.
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Affiliation(s)
- Sunyong Yoo
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Republic of Korea
| | - Kyungrin Noh
- Bio-Synergy Research Center, Daejeon, 34141 Republic of Korea
| | - Moonshik Shin
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Republic of Korea
| | - Junseok Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Republic of Korea
| | - Kwang-Hyung Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Republic of Korea
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005 Republic of Korea
| | - Doheon Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Republic of Korea
- Bio-Synergy Research Center, Daejeon, 34141 Republic of Korea
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Riesco A, Santos-Buitrago B, De Las Rivas J, Knapp M, Santos-García G, Talcott C. Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1809513. [PMID: 28191459 PMCID: PMC5278199 DOI: 10.1155/2017/1809513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/30/2016] [Indexed: 12/24/2022]
Abstract
In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation. Signaling is initiated by binding the ligand protein EGF to the membrane-bound receptor EGFR so as to trigger a reactions path which have several linked elements through the cell from the membrane till the nucleus. We present two different types of search for analyzing the EGF/proliferation system with the help of Pathway Logic tool, which provides a knowledge-based development environment to carry out the modeling of the signaling. The first one is a standard (forward) search. The second one is a novel approach based on narrowing, which allows us to trace backwards the causes of a given final state. The analysis allows the identification of critical elements that have to be activated to provoke proliferation.
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Affiliation(s)
| | | | | | - Merrill Knapp
- Biosciences Division, SRI International, Menlo Park, CA, USA
| | | | - Carolyn Talcott
- Computer Science Laboratory, SRI International, Menlo Park, CA, USA
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Reverse Inference in Symbolic Systems Biology. 11TH INTERNATIONAL CONFERENCE ON PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY & BIOINFORMATICS 2017. [DOI: 10.1007/978-3-319-60816-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks. PLoS One 2015; 10:e0140816. [PMID: 26469276 PMCID: PMC4607460 DOI: 10.1371/journal.pone.0140816] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/29/2015] [Indexed: 01/08/2023] Open
Abstract
As pharmacodynamic drug-drug interactions (PD DDIs) could lead to severe adverse effects in patients, it is important to identify potential PD DDIs in drug development. The signaling starting from drug targets is propagated through protein-protein interaction (PPI) networks. PD DDIs could occur by close interference on the same targets or within the same pathways as well as distant interference through cross-talking pathways. However, most of the previous approaches have considered only close interference by measuring distances between drug targets or comparing target neighbors. We have applied a random walk with restart algorithm to simulate signaling propagation from drug targets in order to capture the possibility of their distant interference. Cross validation with DrugBank and Kyoto Encyclopedia of Genes and Genomes DRUG shows that the proposed method outperforms the previous methods significantly. We also provide a web service with which PD DDIs for drug pairs can be analyzed at http://biosoft.kaist.ac.kr/targetrw.
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Analysis of Cellular Proliferation and Survival Signaling by Using Two Ligand/Receptor Systems Modeled by Pathway Logic. HYBRID SYSTEMS BIOLOGY 2015. [DOI: 10.1007/978-3-319-26916-0_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Matuszcak C, Haier J, Hummel R, Lindner K. MicroRNAs: Promising chemoresistance biomarkers in gastric cancer with diagnostic and therapeutic potential. World J Gastroenterol 2014; 20:13658-13666. [PMID: 25320504 PMCID: PMC4194550 DOI: 10.3748/wjg.v20.i38.13658] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/29/2014] [Accepted: 05/26/2014] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is the fourth most common cancer worldwide and ranks second in global cancer mortality statistics. Perioperative chemotherapy plays an important role in the management and treatment of advanced stage disease. However, response to chemotherapy varies widely, with some patients presenting no or only minor response to treatment. Hence, chemotherapy resistance is a major clinical problem that impacts on outcome. Unfortunately, to date there are no reliable biomarkers available that predict response to chemotherapy before the start of the treatment, or that allow modification of chemotherapy resistance. MicroRNAs (miRNAs) could provide an answer to this problem. miRNAs are involved in the initiation and progression of a variety of cancer types, and there is evidence that miRNAs impact on resistance towards chemotherapeutic drugs as well. This current review aims to provide an overview about the potential clinical applicability of miRNAs as biomarkers for chemoresistance in GC. The authors focus in this context on the potential of miRNAs to predict sensitivity towards different chemotherapeutics, and on the potential of miRNAs to modulate sensitivity and resistance towards chemotherapy in GC.
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Santos-García G, De Las Rivas J, Talcott C. A Logic Computational Framework to Query Dynamics on Complex Biological Pathways. 8TH INTERNATIONAL CONFERENCE ON PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY & BIOINFORMATICS (PACBB 2014) 2014. [DOI: 10.1007/978-3-319-07581-5_25] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Identifying the association rules between clinicopathologic factors and higher survival performance in operation-centric oral cancer patients using the Apriori algorithm. BIOMED RESEARCH INTERNATIONAL 2013; 2013:359634. [PMID: 23984353 PMCID: PMC3741931 DOI: 10.1155/2013/359634] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 06/30/2013] [Indexed: 12/11/2022]
Abstract
This study computationally determines the contribution of clinicopathologic factors correlated with 5-year survival in oral squamous cell carcinoma (OSCC) patients primarily treated by surgical operation (OP) followed by other treatments. From 2004 to 2010, the program enrolled 493 OSCC patients at the Kaohsiung Medical Hospital University. The clinicopathologic records were retrospectively reviewed and compared for survival analysis. The Apriori algorithm was applied to mine the association rules between these factors and improved survival. Univariate analysis of demographic data showed that grade/differentiation, clinical tumor size, pathology tumor size, and OP grouping were associated with survival longer than 36 months. Using the Apriori algorithm, multivariate correlation analysis identified the factors that coexistently provide good survival rates with higher lift values, such as grade/differentiation = 2, clinical stage group = early, primary site = tongue, and group = OP. Without the OP, the lift values are lower. In conclusion, this hospital-based analysis suggests that early OP and other treatments starting from OP are the key to improving the survival of OSCC patients, especially for early stage tongue cancer with moderate differentiation, having a better survival (>36 months) with varied OP approaches.
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