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Mesén-Porras S, Rojas-Céspedes A, Molina-Mora JA, Vega-Baudrit J, Siles F, Quiros S, Mora-Rodríguez R. Sphingolipid-Based Synergistic Interactions to Enhance Chemosensitivity in Lung Cancer Cells. Cells 2023; 12:2588. [PMID: 37998323 PMCID: PMC10670127 DOI: 10.3390/cells12222588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
Tumor heterogeneity leads to drug resistance in cancer treatment with the crucial role of sphingolipids in cell fate and stress signaling. We analyzed sphingolipid metabolism and autophagic flux to study chemotherapeutic interactions on the A549 lung cancer model. Loaded cells with fluorescent sphingomyelin analog (BODIPY) and mCherry-EGFP-LC3B were used to track autophagic flux and assess cytotoxicity when cells are exposed to chemotherapy (epirubicin, cisplatin, and paclitaxel) together with sphingolipid pathway inhibitors and autophagy modulators. Our cell model approach employed fluorescent sphingolipid biosensors and a Gaussian Mixture Model of cell heterogeneity profiles to map the influence of chemotherapy on the sphingolipid pathway and infer potential synergistic interactions. Results showed significant synergy, especially when combining epirubicin with autophagy inducers (rapamycin and Torin), reducing cell viability. Cisplatin also synergized with a ceramidase inhibitor. However, paclitaxel often led to antagonistic effects. Our mapping model suggests that combining chemotherapies with autophagy inducers increases vesicle formation, possibly linked to ceramide accumulation, triggering cell death. However, the in silico model proposed ceramide accumulation in autophagosomes, and kinetic analysis provided evidence of sphingolipid colocalization in autophagosomes. Further research is needed to identify specific sphingolipids accumulating in autophagosomes. These findings offer insights into potential strategies for overcoming chemotherapy resistance by targeting the sphingolipid pathway.
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Affiliation(s)
- Susana Mesén-Porras
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
- Master Program in Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica
- National Laboratory of Nanotechnology (LANOTEC), National Center of High Technology (CeNAT), Pavas, San José 1174-1200, Costa Rica;
| | - Andrea Rojas-Céspedes
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
| | - José Arturo Molina-Mora
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
| | - José Vega-Baudrit
- National Laboratory of Nanotechnology (LANOTEC), National Center of High Technology (CeNAT), Pavas, San José 1174-1200, Costa Rica;
| | - Francisco Siles
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
- Pattern Recognition and Intelligent Systems Laboratory (PRIS-Lab), Department and Postgraduate Studies in Electrical Engineering, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Steve Quiros
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
| | - Rodrigo Mora-Rodríguez
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
- Master Program in Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica
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Quiros-Fernandez I, Figueroa-Protti L, Arias-Arias JL, Brenes-Cordero N, Siles F, Mora J, Mora-Rodríguez RA. Perturbation-Based Modeling Unveils the Autophagic Modulation of Chemosensitivity and Immunogenicity in Breast Cancer Cells. Metabolites 2021; 11:637. [PMID: 34564453 PMCID: PMC8469554 DOI: 10.3390/metabo11090637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 01/18/2023] Open
Abstract
In the absence of new therapeutic strategies, chemotherapeutic drugs are the most widely used strategy against metastatic breast cancer, in spite of eliciting multiple adverse effects and having low responses with an average 5-year patient survival rate. Among the new therapeutic targets that are currently in clinical trials, here, we addressed the association between the regulation of the metabolic process of autophagy and the exposure of damage-associated molecular patterns associated (DAMPs) to immunogenic cell death (ICD), which has not been previously studied. After validating an mCHR-GFP tandem LC3 sensor capacity to report dynamic changes of the autophagic metabolic flux in response to external stimuli and demonstrating that both basal autophagy levels and response to diverse autophagy regulators fluctuate among different cell lines, we explored the interaction between autophagy modulators and chemotherapeutic agents in regards of cytotoxicity and ICD using three different breast cancer cell lines. Since these interactions are very complex and variable throughout different cell lines, we designed a perturbation-based model in which we propose specific modes of action of chemotherapeutic agents on the autophagic flux and the corresponding strategies of modulation to enhance the response to chemotherapy. Our results point towards a promising therapeutic potential of the metabolic regulation of autophagy to overcome chemotherapy resistance by eliciting ICD.
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Affiliation(s)
- Isaac Quiros-Fernandez
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
- Master’s Program in Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Lucía Figueroa-Protti
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Jorge L. Arias-Arias
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- Dulbecco Laboratory Studio, Residencial Lisboa 2G, Alajuela 20102, Costa Rica
| | - Norman Brenes-Cordero
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
| | - Francisco Siles
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
- Pattern Recognition and Intelligent Systems Laboratory (PRIS-Lab), Department of Electrical Engineering and Postgraduate Studies in Electrical Engineering, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Javier Mora
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Rodrigo Antonio Mora-Rodríguez
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
- Master’s Program in Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica
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Molina Mora JA, Montero-Manso P, García-Batán R, Campos-Sánchez R, Vilar-Fernández J, García F. A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach. Biosystems 2021; 205:104411. [PMID: 33757842 DOI: 10.1016/j.biosystems.2021.104411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/27/2023]
Abstract
Tolerance to stress conditions is vital for organismal survival, including bacteria under specific environmental conditions, antibiotics, and other perturbations. Some studies have described common modulation and shared genes during stress response to different types of disturbances (termed as perturbome), leading to the idea of central control at the molecular level. We implemented a robust machine learning approach to identify and describe genes associated with multiple perturbations or perturbome in a Pseudomonas aeruginosa PAO1 model. Using microarray datasets from the Gene Expression Omnibus (GEO), we evaluated six approaches to rank and select genes: using two methodologies, data single partition (SP method) or multiple partitions (MP method) for training and testing datasets, we evaluated three classification algorithms (SVM Support Vector Machine, KNN K-Nearest neighbor and RF Random Forest). Gene expression patterns and topological features at the systems level were included to describe the perturbome elements. We were able to select and describe 46 core response genes associated with multiple perturbations in P. aeruginosa PAO1 and it can be considered a first report of the P. aeruginosa perturbome. Molecular annotations, patterns in expression levels, and topological features in molecular networks revealed biological functions of biosynthesis, binding, and metabolism, many of them related to DNA damage repair and aerobic respiration in the context of tolerance to stress. We also discuss different issues related to implemented and assessed algorithms, including data partitioning, classification approaches, and metrics. Altogether, this work offers a different and robust framework to select genes using a machine learning approach.
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Affiliation(s)
- Jose Arturo Molina Mora
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
| | | | - Raquel García-Batán
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, Costa Rica.
| | | | - Fernando García
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
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Snider JM, Trayssac M, Clarke CJ, Schwartz N, Snider AJ, Obeid LM, Luberto C, Hannun YA. Multiple actions of doxorubicin on the sphingolipid network revealed by flux analysis. J Lipid Res 2019; 60:819-831. [PMID: 30573560 PMCID: PMC6446699 DOI: 10.1194/jlr.m089714] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/18/2018] [Indexed: 12/16/2022] Open
Abstract
Sphingolipids (SLs) have been implicated in numerous important cellular biologies; however, their study has been hindered by the complexities of SL metabolism. Furthermore, enzymes of SL metabolism represent a dynamic and interconnected network in which one metabolite can be transformed into other bioactive SLs through further metabolism, resulting in diverse cellular responses. Here we explore the effects of both lethal and sublethal doses of doxorubicin (Dox) in MCF-7 cells. The two concentrations of Dox resulted in the regulation of SLs, including accumulations in sphingosine, sphingosine-1-phosphate, dihydroceramide, and ceramide, as well as reduced levels of hexosylceramide. To further define the effects of Dox on SLs, metabolic flux experiments utilizing a d17 dihydrosphingosine probe were conducted. Results indicated the regulation of ceramidases and sphingomyelin synthase components specifically in response to the cytostatic dose. The results also unexpectedly demonstrated dose-dependent inhibition of dihydroceramide desaturase and glucosylceramide synthase in response to Dox. Taken together, this study uncovers novel targets in the SL network for the action of Dox, and the results reveal the significant complexity of SL response to even a single agent. This approach helps to define the role of specific SL enzymes, their metabolic products, and the resulting biologies in response to chemotherapeutics and other stimuli.
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Affiliation(s)
- Justin M Snider
- Molecular and Cellular Biology and Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY; Departments of Medicine, Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY
| | - Magali Trayssac
- Departments of Medicine, Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY
| | - Christopher J Clarke
- Departments of Medicine, Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY
| | - Nicholas Schwartz
- Departments of Medicine, Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY
| | - Ashley J Snider
- Departments of Medicine, Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY; Northport Veterans Affairs Medical Center, Northport, NY
| | - Lina M Obeid
- Departments of Medicine, Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY; Northport Veterans Affairs Medical Center, Northport, NY
| | - Chiara Luberto
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY; Departments of Physiology and Biophysics, Stony Brook University, Stony Brook, NY.
| | - Yusuf A Hannun
- Departments of Medicine, Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY; Departments of Biochemistry, Stony Brook University, Stony Brook, NY; Departments of Pharmacology, Stony Brook University, Stony Brook, NY; Departments of Pathology, Stony Brook University, Stony Brook, NY.
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