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Xiong Z, Li L, Wang G, Guo L, Luo S, Liao X, Liu J, Teng W. Integrated Analysis of scRNA-Seq and Bulk RNA-Seq Reveals Metabolic Reprogramming of Liver Cancer and Establishes a Prognostic Risk Model. Genes (Basel) 2024; 15:755. [PMID: 38927691 PMCID: PMC11203231 DOI: 10.3390/genes15060755] [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: 03/11/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Liver cancer manifests as a profoundly heterogeneous malignancy, posing significant challenges in terms of both therapeutic intervention and prognostic evaluation. Given that the liver is the largest metabolic organ, a prognostic risk model grounded in single-cell transcriptome analysis and a metabolic perspective can facilitate precise prevention and treatment strategies for liver cancer. Hence, we identified 11 cell types in a scRNA-seq profile comprising 105,829 cells and found that the metabolic activity of malignant cells increased significantly. Subsequently, a prognostic risk model incorporating tumor heterogeneity, cell interactions, tumor cell metabolism, and differentially expressed genes was established based on eight genes; this model can accurately distinguish the survival outcomes of liver cancer patients and predict the response to immunotherapy. Analyzing the immune status and drug sensitivity of the high- and low-risk groups identified by the model revealed that the high-risk group had more active immune cell status and greater expression of immune checkpoints, indicating potential risks associated with liver cancer-targeted drugs. In summary, this study provides direct evidence for the stratification and precise treatment of liver cancer patients, and is an important step in establishing reliable predictors of treatment efficacy in liver cancer patients.
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Affiliation(s)
- Zhuang Xiong
- Department of Hepatopancreatobiliary Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China;
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350108, China; (L.G.); (S.L.); (X.L.)
| | - Lizhi Li
- Department of Pediatric Surgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, China;
| | - Guoliang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing 100101, China;
| | - Lei Guo
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350108, China; (L.G.); (S.L.); (X.L.)
| | - Shangyi Luo
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350108, China; (L.G.); (S.L.); (X.L.)
| | - Xiangwen Liao
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350108, China; (L.G.); (S.L.); (X.L.)
| | - Jingfeng Liu
- Department of Hepatopancreatobiliary Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China;
| | - Wenhao Teng
- Department of Hepatopancreatobiliary Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China;
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350108, China; (L.G.); (S.L.); (X.L.)
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Payá-Milans M, Peña-Chilet M, Loucera C, Esteban-Medina M, Dopazo J. Functional Profiling of Soft Tissue Sarcoma Using Mechanistic Models. Int J Mol Sci 2023; 24:14732. [PMID: 37834179 PMCID: PMC10572617 DOI: 10.3390/ijms241914732] [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: 08/10/2023] [Revised: 09/08/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Soft tissue sarcoma is an umbrella term for a group of rare cancers that are difficult to treat. In addition to surgery, neoadjuvant chemotherapy has shown the potential to downstage tumors and prevent micrometastases. However, finding effective therapeutic targets remains a research challenge. Here, a previously developed computational approach called mechanistic models of signaling pathways has been employed to unravel the impact of observed changes at the gene expression level on the ultimate functional behavior of cells. In the context of such a mechanistic model, RNA-Seq counts sourced from the Recount3 resource, from The Cancer Genome Atlas (TCGA) Sarcoma project, and non-diseased sarcomagenic tissues from the Genotype-Tissue Expression (GTEx) project were utilized to investigate signal transduction activity through signaling pathways. This approach provides a precise view of the relationship between sarcoma patient survival and the signaling landscape in tumors and their environment. Despite the distinct regulatory alterations observed in each sarcoma subtype, this study identified 13 signaling circuits, or elementary sub-pathways triggering specific cell functions, present across all subtypes, belonging to eight signaling pathways, which served as predictors for patient survival. Additionally, nine signaling circuits from five signaling pathways that highlighted the modifications tumor samples underwent in comparison to normal tissues were found. These results describe the protective role of the immune system, suggesting an anti-tumorigenic effect in the tumor microenvironment, in the process of tumor cell detachment and migration, or the dysregulation of ion homeostasis. Also, the analysis of signaling circuit intermediary proteins suggests multiple strategies for therapy.
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Affiliation(s)
- Miriam Payá-Milans
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013 Seville, Spain
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - María Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013 Seville, Spain
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Carlos Loucera
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Marina Esteban-Medina
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Joaquín Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013 Seville, Spain
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
- FPS/ELIXIR-ES, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocío, 41013 Sevilla, Spain
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3
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Çubuk C, Loucera C, Peña-Chilet M, Dopazo J. Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer. Int J Mol Sci 2023; 24:ijms24087450. [PMID: 37108611 PMCID: PMC10138666 DOI: 10.3390/ijms24087450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The reprogramming of metabolism is a recognized cancer hallmark. It is well known that different signaling pathways regulate and orchestrate this reprogramming that contributes to cancer initiation and development. However, recent evidence is accumulating, suggesting that several metabolites could play a relevant role in regulating signaling pathways. To assess the potential role of metabolites in the regulation of signaling pathways, both metabolic and signaling pathway activities of Breast invasive Carcinoma (BRCA) have been modeled using mechanistic models. Gaussian Processes, powerful machine learning methods, were used in combination with SHapley Additive exPlanations (SHAP), a recent methodology that conveys causality, to obtain potential causal relationships between the production of metabolites and the regulation of signaling pathways. A total of 317 metabolites were found to have a strong impact on signaling circuits. The results presented here point to the existence of a complex crosstalk between signaling and metabolic pathways more complex than previously was thought.
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Affiliation(s)
- Cankut Çubuk
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Carlos Loucera
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, 41013 Sevilla, Spain
| | - María Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Sevilla, Spain
- FPS, ELIXIR-es, Hospital Virgen del Rocío, 42013 Sevilla, Spain
| | - Joaquin Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Sevilla, Spain
- FPS, ELIXIR-es, Hospital Virgen del Rocío, 42013 Sevilla, Spain
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Has EG, Akçelik N, Akçelik M. Comparative global gene expression analysis of biofilm forms of Salmonella Typhimurium ATCC 14028 and its seqA mutant. Gene X 2023; 853:147094. [PMID: 36470486 DOI: 10.1016/j.gene.2022.147094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
In this study, comparative transcriptomic analyzes (mRNA and miRNA) were performed on the biofilm forms of S. Typhimurium ATCC 14028 wild-type strain and its seqA gene mutant in order to determine the regulation characteristics of the seqA gene in detail. The results of global gene expression analyses showed an increase in the expression level of 54 genes and a decrease in the expression level of 155 genes (p < 0.05) in the seqA mutant compared to the wild-type strain. 10 of the 48 miRNAs identified on behalf of sequence analysis are new miRNA records for Salmonella. Transcripts of 14 miRNAs differed between wild-type strain and seqA mutant (p < 0.05), of which eight were up-regulated and six were down-regulated. Bioinformatic analyzes showed that differentially expressed genes in the wild-type strain and its seqA gene mutant play a role in different metabolic processes as well as biofilm formation, pathogenicity and virulence. When the transcriptomic data were interpreted together with the findings obtained from phenotypic tests such as motility, attachment to host cells and biofilm morphotyping, it was determined that the seqA gene has a critical function especially for the adhesion and colonization stages of biofilm formation, as well as for biofilm stability. Transcriptomic data pointing out that the seqA gene is also a general positive regulator of T3SS effector proteins active in cell invasion in S. Typhimurium wild-type biofilm, proves that this gene is involved in Salmonella host cell invasion.
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Affiliation(s)
- Elif Gamze Has
- Department of Biology, Ankara University, Yenimahalle, 06100 Ankara, Turkey
| | - Nefise Akçelik
- Biotechnology Institute, Ankara University, Keçiören, 06135 Ankara, Turkey
| | - Mustafa Akçelik
- Department of Biology, Ankara University, Yenimahalle, 06100 Ankara, Turkey.
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Keçeli Oğuz S, Has EG, Akçelik N, Akçelik M. Phenotypic impacts and genetic regulation characteristics of the DNA adenine methylase gene (dam) in Salmonella Typhimurium biofilm forms. Res Microbiol 2023; 174:103991. [PMID: 36113833 DOI: 10.1016/j.resmic.2022.103991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
In this study, transcriptional level gene expression changes in biofilm forms of Salmonella Typhimurium ATCC 14028 and its dam mutant were investigated by performing RNAseq analysis. As a result of these analyzes, a total of 233 differentially expressed genes (DEGs) were identified in the dam mutant, of which 145 genes were downregulated and 88 genes were upregulated compared to the wild type. According to data from miRNA sequence analysis, of 13 miRNAs differentially expressed in dam mutant, 9 miRNAs were downregulated and 4 miRNAs were upregulated. These data provide the first evidence that the dam gene is a global regulator of biofilm formation in Salmonella. In addition, phenotypic analyses revealed that bacterial swimming and swarming motility and cellulose production were highly inhibited in the dam mutant. It was determined that bacterial adhesion in Caco-2 and HEp-2 cell lines was significantly reduced in dam mutant. At the end of 90 min, the adhesion rate of wild type strain was 43.3% in Caco-2 cell line, while this rate was 14.9% in dam mutant. In the HEp-2 cell line, while 45.5% adherence was observed in the wild-type strain, this rate decreased to 15.3% in the dam mutant.
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Affiliation(s)
- Selma Keçeli Oğuz
- Department of Biology, Ankara University, Yenimahalle, 06100, Ankara, Turkey.
| | - Elif Gamze Has
- Department of Biology, Ankara University, Yenimahalle, 06100, Ankara, Turkey.
| | - Nefise Akçelik
- Biotechnology Institute, Ankara University, Keçiören, 06135, Ankara, Turkey.
| | - Mustafa Akçelik
- Department of Biology, Ankara University, Yenimahalle, 06100, Ankara, Turkey.
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Transcriptome Analysis Unveils That Exosomes Derived from M1-Polarized Microglia Induce Ferroptosis of Neuronal Cells. Cells 2022; 11:cells11243956. [PMID: 36552720 PMCID: PMC9776787 DOI: 10.3390/cells11243956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
Microglia play a vital role in neurodegenerative diseases. However, the effects of microglia-derived exosomes on neuronal cells are poorly understood. This study aimed to explore the role of M1-polarized microglia exosomes in neuronal cells by transcriptome analysis. Exosomes isolated from resting M0-phenotype BV2 (M0-BV2) microglia and M1-polarized BV2 (M1-BV2) microglia were analyzed using high-throughput sequencing of the transcriptome. Differentially expressed genes (DEGs) between the two types of exosomes were identified by analyzing the sequencing data. The biological functions and pathways regulated by the identified DEGs were then identified using bioinformatics analyses. Finally, we evaluated the effects of exosomes on neuronal cells by coculturing M0-BV2 and M1-BV2 exosomes with primary neuronal cells. Enrichment analyses revealed that DEGs were significantly enriched in the ferroptosis pathway (p = 0.0137). M0-BV2 exosomes had no distinct effects on ferroptosis in neuronal cells, whereas M1-BV2 exosomes significantly reduced ferroptosis suppressor proteins (GPX4, SLC7A11, and FTH1) and elevated the levels of intracellular and mitochondrial ferrous iron and lipid peroxidation in neuronal cells. Polarized M1-BV2 microglia exosomes can induce ferroptosis in neuronal cells, thereby aggravating neuronal damage. Taken together, these findings enhance knowledge of the pathogenesis of neurological disorders and suggest potential therapeutic targets against neurodegenerative diseases.
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Potential Diagnostic and Prognostic Values of CBX8 Expression in Liver Hepatocellular Carcinoma, Kidney Renal Clear Cell Carcinoma, and Ovarian Cancer: A Study Based on TCGA Data Mining. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1372879. [PMID: 35813444 PMCID: PMC9259361 DOI: 10.1155/2022/1372879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022]
Abstract
Background Chromobox protein homolog 8 (CBX8), a transcriptional repressor, participates in many biological processes in various carcinomas. Cell differentiation, aging, and cell cycle progression are examples of such processes. It is critical to investigate CBX8 expression and its relationship with clinicopathological characteristics in liver hepatocellular carcinoma (LIHC), kidney renal clear cell carcinoma (KIRC), and ovarian cancer (OV) to investigate CBX8's potential diagnostic and prognostic values. Methods TCGA and CPTAC databases were used to compare the data between cancer and matched normal tissues on RNA and protein expression profiles and their relevant clinical information to determine the relationship between CBX8 and clinicopathological features. Kaplan–Meier analyses were used to assess CBX8 relationship's with disease-free survival (DFS), relapse-free survival (RFS), and overall survival (OS). The multivariate Cox regression analysis was used to identify independent risk factors which affect prognosis. DNA methylation and genetic changes and their impact on prognoses were evaluated by cBioPortal and MethSurv websites. Spearman's correlation was used to determine the relationship of CBX8 expression with somatic mutation. Tumor immune estimation resource (TIMER) was adopted to investigate the relationship between CBX8 and immune cell infiltration (ICI). CBX8-relevant genes and proteins are analyzed by EnhancedVolcano and STRING databases. The gene set enrichment analysis (GSEA) was performed to investigate the potential functions of CBX8. Results CBX8 RNA and protein overexpression were confirmed in LIHC, KIRC, and OV (p < 0.05). High CBX8 was significantly related to the clinical features and poor prognoses. The CBX8 genetic alteration rate was 3%. DNA methylation was also associated with prognoses. CBX8 closely interacted with ICI, TMB, MSI, purity, and ploidy. GO analyses revealed that CBX8-associated genes were enriched in biological processes, cell cycle regulation, and molecular functions. KEGG analyses exhibited that CBX8 was gathered in signaling pathway regulation. GSEA revealed that cell cycle, DNA replication, and Wnt signaling pathways were differentially enriched in the high CBX8 expression group. Conclusions CBX8 could be a potential diagnostic and prognostic biomarker for LIHC, KIRC, and OV cancers.
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Vergani E, Beretta GL, Aloisi M, Costantino M, Corno C, Frigerio S, Tinelli S, Dugo M, Accattatis FM, Granata A, Arnaboldi L, Rodolfo M, Perego P, Gatti L. Targeting of the Lipid Metabolism Impairs Resistance to BRAF Kinase Inhibitor in Melanoma. Front Cell Dev Biol 2022; 10:927118. [PMID: 35912092 PMCID: PMC9326082 DOI: 10.3389/fcell.2022.927118] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Drug resistance limits the achievement of persistent cures for the treatment of melanoma, in spite of the efficacy of the available drugs. The aim of the present study was to explore the involvement of lipid metabolism in melanoma resistance and assess the effects of its targeting in cellular models of melanoma with acquired resistance to the BRAF-inhibitor PLX4032/Vemurafenib. Since transcriptional profiles pointed to decreased cholesterol and fatty acids synthesis in resistant cells as compared to their parental counterparts, we examined lipid composition profiles of resistant cells, studied cell growth dependence on extracellular lipids, assessed the modulation of enzymes controlling the main nodes in lipid biosynthesis, and evaluated the effects of targeting Acetyl-CoA Acetyltransferase 2 (ACAT2), the first enzyme in the cholesterol synthesis pathway, and Acyl-CoA Cholesterol Acyl Transferase (ACAT/SOAT), which catalyzes the intracellular esterification of cholesterol and the formation of cholesteryl esters. We found a different lipid composition in the resistant cells, which displayed reduced saturated fatty acids (SFA), increased monounsaturated (MUFA) and polyunsaturated (PUFA), and reduced cholesteryl esters (CE) and triglycerides (TG), along with modulated expression of enzymes regulating biosynthetic nodes of the lipid metabolism. The effect of tackling lipid metabolism pathways in resistant cells was evidenced by lipid starvation, which reduced cell growth, increased sensitivity to the BRAF-inhibitor PLX4032, and induced the expression of enzymes involved in fatty acid and cholesterol metabolism. Molecular targeting of ACAT2 or pharmacological inhibition of SOAT by avasimibe showed antiproliferative effects in melanoma cell lines and a synergistic drug interaction with PLX4032, an effect associated to increased ferroptosis. Overall, our findings reveal that lipid metabolism affects melanoma sensitivity to BRAF inhibitors and that extracellular lipid availability may influence tumor cell response to treatment, a relevant finding in the frame of personalized therapy. In addition, our results indicate new candidate targets for drug combination treatments.
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Affiliation(s)
- Elisabetta Vergani
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Giovanni L. Beretta
- Unit of Molecular Pharmacology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mariachiara Aloisi
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Matteo Costantino
- Unit of Molecular Pharmacology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Cristina Corno
- Unit of Molecular Pharmacology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Simona Frigerio
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Stella Tinelli
- Unit of Molecular Pharmacology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Felice Maria Accattatis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Cosenza, Italy
| | - Agnese Granata
- Department of Pharmacological and Biomolecular Sciences DISFeB, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Arnaboldi
- Department of Pharmacological and Biomolecular Sciences DISFeB, Università degli Studi di Milano, Milan, Italy
| | - Monica Rodolfo
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
- *Correspondence: Monica Rodolfo,
| | - Paola Perego
- Unit of Molecular Pharmacology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Laura Gatti
- Neurobiology Laboratory, Department of Clinical Neurosciences, Fondazione IRCSS Istituto Neurologico Carlo Besta, Milan, Italy
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Ng RH, Lee JW, Baloni P, Diener C, Heath JR, Su Y. Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer. Front Oncol 2022; 12:914594. [PMID: 35875150 PMCID: PMC9303011 DOI: 10.3389/fonc.2022.914594] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
The influence of metabolism on signaling, epigenetic markers, and transcription is highly complex yet important for understanding cancer physiology. Despite the development of high-resolution multi-omics technologies, it is difficult to infer metabolic activity from these indirect measurements. Fortunately, genome-scale metabolic models and constraint-based modeling provide a systems biology framework to investigate the metabolic states and define the genotype-phenotype associations by integrations of multi-omics data. Constraint-Based Reconstruction and Analysis (COBRA) methods are used to build and simulate metabolic networks using mathematical representations of biochemical reactions, gene-protein reaction associations, and physiological and biochemical constraints. These methods have led to advancements in metabolic reconstruction, network analysis, perturbation studies as well as prediction of metabolic state. Most computational tools for performing these analyses are written for MATLAB, a proprietary software. In order to increase accessibility and handle more complex datasets and models, community efforts have started to develop similar open-source tools in Python. To date there is a comprehensive set of tools in Python to perform various flux analyses and visualizations; however, there are still missing algorithms in some key areas. This review summarizes the availability of Python software for several components of COBRA methods and their applications in cancer metabolism. These tools are evolving rapidly and should offer a readily accessible, versatile way to model the intricacies of cancer metabolism for identifying cancer-specific metabolic features that constitute potential drug targets.
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Affiliation(s)
- Rachel H. Ng
- Institute for Systems Biology, Seattle, WA, United States
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Jihoon W. Lee
- Medical Scientist Training Program, University of Washington, Seattle, WA, United States
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | | | | | - James R. Heath
- Institute for Systems Biology, Seattle, WA, United States
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Yapeng Su
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Herbold Computational Biology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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Park S, Kim OH, Lee K, Park IB, Kim NH, Moon S, Im J, Sharma SP, Oh BC, Nam S, Lee DH. Plasma and urinary extracellular vesicle microRNAs and their related pathways in diabetic kidney disease. Genomics 2022; 114:110407. [PMID: 35716820 DOI: 10.1016/j.ygeno.2022.110407] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/22/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
To explore extracellular vesicle microRNAs (EV miRNAs) and their target mRNAs in relation to diabetic kidney disease (DKD), we performed paired plasma and urinary EV small RNA sequencing (n = 18) in patients with type 2 diabetes and DKD (n = 5) and healthy subjects (n = 4) and metabolic network analyses using our own miRNA and public mRNA datasets. We found 13 common differentially expressed EV miRNAs in both fluids and 17 target mRNAs, including RRM2, NT5E, and UGDH. Because succinate dehydrogenase B was suggested to interact with proteins encoded by these three genes, we measured urinary succinate and adenosine in a validation study (n = 194). These two urinary metabolite concentrations were associated with DKD progression. In addition, renal expressions of NT5E and UGDH proteins were increased in db/db mice with DKD compared to control mice. In conclusion, we profiled DKD-related EV miRNAs in plasma and urine samples and found their relevant target pathways.
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Affiliation(s)
- Sungjin Park
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Republic of Korea
| | - Ok-Hee Kim
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, Incheon, Republic of Korea
| | - Kiyoung Lee
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Republic of Korea; Department of Internal Medicine, Gachon University College of Medicine, Incheon, Republic of Korea
| | - Ie Byung Park
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Republic of Korea; Department of Internal Medicine, Gachon University College of Medicine, Incheon, Republic of Korea
| | - Nan Hee Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seongryeol Moon
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, Republic of Korea
| | - Jaebeen Im
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, Republic of Korea
| | - Satya Priya Sharma
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Republic of Korea
| | - Byung-Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, Incheon, Republic of Korea
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Republic of Korea; Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, Republic of Korea.
| | - Dae Ho Lee
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Republic of Korea; Department of Internal Medicine, Gachon University College of Medicine, Incheon, Republic of Korea; Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, Republic of Korea.
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11
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Genome-Scale Metabolic Model Analysis of Metabolic Differences between Lauren Diffuse and Intestinal Subtypes in Gastric Cancer. Cancers (Basel) 2022; 14:cancers14092340. [PMID: 35565469 PMCID: PMC9104812 DOI: 10.3390/cancers14092340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 01/01/2023] Open
Abstract
Gastric cancer (GC) is one of the most lethal cancers worldwide; it has a high mortality rate, particularly in East Asia. Recently, genetic events (e.g., mutations and copy number alterations) and molecular signaling associated with histologically different GC subtypes (diffuse and intestinal) have been elucidated. However, metabolic differences among the histological GC subtypes have not been studied systematically. In this study, we utilized transcriptome-based genome-scale metabolic models (GEMs) to identify differential metabolic pathways between Lauren diffuse and intestinal subtypes. We found that diverse metabolic pathways, including cholesterol homeostasis, xenobiotic metabolism, fatty acid metabolism, the MTORC1 pathway, and glycolysis, were dysregulated between the diffuse and intestinal subtypes. Our study provides an overview of the metabolic differences between the two subtypes, possibly leading to an understanding of metabolism in GC heterogeneity.
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12
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Hrovatin K, Fischer DS, Theis FJ. Toward modeling metabolic state from single-cell transcriptomics. Mol Metab 2022; 57:101396. [PMID: 34785394 PMCID: PMC8829761 DOI: 10.1016/j.molmet.2021.101396] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Single-cell metabolic studies bring new insights into cellular function, which can often not be captured on other omics layers. Metabolic information has wide applicability, such as for the study of cellular heterogeneity or for the understanding of drug mechanisms and biomarker development. However, metabolic measurements on single-cell level are limited by insufficient scalability and sensitivity, as well as resource intensiveness, and are currently not possible in parallel with measuring transcript state, commonly used to identify cell types. Nevertheless, because omics layers are strongly intertwined, it is possible to make metabolic predictions based on measured data of more easily measurable omics layers together with prior metabolic network knowledge. SCOPE OF REVIEW We summarize the current state of single-cell metabolic measurement and modeling approaches, motivating the use of computational techniques. We review three main classes of computational methods used for prediction of single-cell metabolism: pathway-level analysis, constraint-based modeling, and kinetic modeling. We describe the unique challenges arising when transitioning from bulk to single-cell modeling. Finally, we propose potential model extensions and computational methods that could be leveraged to achieve these goals. MAJOR CONCLUSIONS Single-cell metabolic modeling is a rising field that provides a new perspective for understanding cellular functions. The presented modeling approaches vary in terms of input requirements and assumptions, scalability, modeled metabolic layers, and newly gained insights. We believe that the use of prior metabolic knowledge will lead to more robust predictions and will pave the way for mechanistic and interpretable machine-learning models.
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Affiliation(s)
- Karin Hrovatin
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstaedter Landstraße 1, Neuherberg, 85764, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, Freising, 85354, Germany.
| | - David S Fischer
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstaedter Landstraße 1, Neuherberg, 85764, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, Freising, 85354, Germany.
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstaedter Landstraße 1, Neuherberg, 85764, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, Freising, 85354, Germany; Department of Mathematics, Technical University of Munich, Boltzmannstr. 3, Garching bei München, 85748, Germany.
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13
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Golriz Khatami S, Mubeen S, Bharadhwaj VS, Kodamullil AT, Hofmann-Apitius M, Domingo-Fernández D. Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures. NPJ Syst Biol Appl 2021; 7:40. [PMID: 34707117 PMCID: PMC8551267 DOI: 10.1038/s41540-021-00199-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/21/2021] [Indexed: 11/21/2022] Open
Abstract
The utility of pathway signatures lies in their capability to determine whether a specific pathway or biological process is dysregulated in a given patient. These signatures have been widely used in machine learning (ML) methods for a variety of applications including precision medicine, drug repurposing, and drug discovery. In this work, we leverage highly predictive ML models for drug response simulation in individual patients by calibrating the pathway activity scores of disease samples. Using these ML models and an intuitive scoring algorithm to modify the signatures of patients, we evaluate whether a given sample that was formerly classified as diseased, could be predicted as normal following drug treatment simulation. We then use this technique as a proxy for the identification of potential drug candidates. Furthermore, we demonstrate the ability of our methodology to successfully identify approved and clinically investigated drugs for four different cancers, outperforming six comparable state-of-the-art methods. We also show how this approach can deconvolute a drugs' mechanism of action and propose combination therapies. Taken together, our methodology could be promising to support clinical decision-making in personalized medicine by simulating a drugs' effect on a given patient.
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Affiliation(s)
- Sepehr Golriz Khatami
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, 53757, Germany.
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115, Bonn, Germany.
| | - Sarah Mubeen
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, 53757, Germany
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115, Bonn, Germany
- Fraunhofer Center for Machine Learning, Sankt Augustin, Germany
| | - Vinay Srinivas Bharadhwaj
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, 53757, Germany
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115, Bonn, Germany
| | - Alpha Tom Kodamullil
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, 53757, Germany
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, 53757, Germany
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115, Bonn, Germany
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, 53757, Germany.
- Fraunhofer Center for Machine Learning, Sankt Augustin, Germany.
- Enveda Biosciences, Boulder, CO, 80301, USA.
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14
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Vallée A, Lecarpentier Y, Vallée JN. Opposed Interplay between IDH1 Mutations and the WNT/β-Catenin Pathway: Added Information for Glioma Classification. Biomedicines 2021; 9:biomedicines9060619. [PMID: 34070746 PMCID: PMC8229353 DOI: 10.3390/biomedicines9060619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/23/2022] Open
Abstract
Gliomas are the main common primary intraparenchymal brain tumor in the central nervous system (CNS), with approximately 7% of the death caused by cancers. In the WHO 2016 classification, molecular dysregulations are part of the definition of particular brain tumor entities for the first time. Nevertheless, the underlying molecular mechanisms remain unclear. Several studies have shown that 75% to 80% of secondary glioblastoma (GBM) showed IDH1 mutations, whereas only 5% of primary GBM have IDH1 mutations. IDH1 mutations lead to better overall survival in gliomas patients. IDH1 mutations are associated with lower stimulation of the HIF-1α a, aerobic glycolysis and angiogenesis. The stimulation of HIF-1α and the process of angiogenesis appears to be activated only when hypoxia occurs in IDH1-mutated gliomas. In contrast, the observed upregulation of the canonical WNT/β-catenin pathway in gliomas is associated with proliferation, invasion, aggressive-ness and angiogenesis.. Molecular pathways of the malignancy process are involved in early stages of WNT/β-catenin pathway-activated-gliomas, and this even under normoxic conditions. IDH1 mutations lead to decreased activity of the WNT/β-catenin pathway and its enzymatic targets. The opposed interplay between IDH1 mutations and the canonical WNT/β-catenin pathway in gliomas could participate in better understanding of the observed evolution of different tumors and could reinforce the glioma classification.
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Affiliation(s)
- Alexandre Vallée
- Department of Clinical Research and Innovation, Foch Hospital, 92150 Suresnes, France
- Correspondence:
| | - Yves Lecarpentier
- Centre de Recherche Clinique, Grand Hôpital de l’Est Francilien (GHEF), 77100 Meaux, France;
| | - Jean-Noël Vallée
- Centre Hospitalier Universitaire (CHU) Amiens Picardie, Université Picardie Jules Verne (UPJV), 80000 Amiens, France;
- Laboratoire de Mathématiques et Applications (LMA), UMR CNRS 7348, Université de Poitiers, 86000 Poitiers, France
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15
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Virtuoso A, Giovannoni R, De Luca C, Gargano F, Cerasuolo M, Maggio N, Lavitrano M, Papa M. The Glioblastoma Microenvironment: Morphology, Metabolism, and Molecular Signature of Glial Dynamics to Discover Metabolic Rewiring Sequence. Int J Mol Sci 2021; 22:3301. [PMID: 33804873 PMCID: PMC8036663 DOI: 10.3390/ijms22073301] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Different functional states determine glioblastoma (GBM) heterogeneity. Brain cancer cells coexist with the glial cells in a functional syncytium based on a continuous metabolic rewiring. However, standard glioma therapies do not account for the effects of the glial cells within the tumor microenvironment. This may be a possible reason for the lack of improvements in patients with high-grade gliomas therapies. Cell metabolism and bioenergetic fitness depend on the availability of nutrients and interactions in the microenvironment. It is strictly related to the cell location in the tumor mass, proximity to blood vessels, biochemical gradients, and tumor evolution, underlying the influence of the context and the timeline in anti-tumor therapeutic approaches. Besides the cancer metabolic strategies, here we review the modifications found in the GBM-associated glia, focusing on morphological, molecular, and metabolic features. We propose to analyze the GBM metabolic rewiring processes from a systems biology perspective. We aim at defining the crosstalk between GBM and the glial cells as modules. The complex networking may be expressed by metabolic modules corresponding to the GBM growth and spreading phases. Variation in the oxidative phosphorylation (OXPHOS) rate and regulation appears to be the most important part of the metabolic and functional heterogeneity, correlating with glycolysis and response to hypoxia. Integrated metabolic modules along with molecular and morphological features could allow the identification of key factors for controlling the GBM-stroma metabolism in multi-targeted, time-dependent therapies.
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Affiliation(s)
- Assunta Virtuoso
- Laboratory of Neuronal Networks, Department of Mental and Physical Health and Preventive Medicine, University of Campania ‘‘Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (F.G.); (M.C.); (M.P.)
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | | | - Ciro De Luca
- Laboratory of Neuronal Networks, Department of Mental and Physical Health and Preventive Medicine, University of Campania ‘‘Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (F.G.); (M.C.); (M.P.)
| | - Francesca Gargano
- Laboratory of Neuronal Networks, Department of Mental and Physical Health and Preventive Medicine, University of Campania ‘‘Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (F.G.); (M.C.); (M.P.)
| | - Michele Cerasuolo
- Laboratory of Neuronal Networks, Department of Mental and Physical Health and Preventive Medicine, University of Campania ‘‘Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (F.G.); (M.C.); (M.P.)
| | - Nicola Maggio
- Department of Neurology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel;
- Department of Neurology, The Chaim Sheba Medical Center, Ramat Gan 5211401, Israel
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Michele Papa
- Laboratory of Neuronal Networks, Department of Mental and Physical Health and Preventive Medicine, University of Campania ‘‘Luigi Vanvitelli”, 80138 Naples, Italy; (A.V.); (F.G.); (M.C.); (M.P.)
- SYSBIO Centre of Systems Biology ISBE-IT, University of Milano-Bicocca, 20126 Milan, Italy
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16
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Auslander N, Gussow AB, Koonin EV. Incorporating Machine Learning into Established Bioinformatics Frameworks. Int J Mol Sci 2021; 22:2903. [PMID: 33809353 PMCID: PMC8000113 DOI: 10.3390/ijms22062903] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/23/2022] Open
Abstract
The exponential growth of biomedical data in recent years has urged the application of numerous machine learning techniques to address emerging problems in biology and clinical research. By enabling the automatic feature extraction, selection, and generation of predictive models, these methods can be used to efficiently study complex biological systems. Machine learning techniques are frequently integrated with bioinformatic methods, as well as curated databases and biological networks, to enhance training and validation, identify the best interpretable features, and enable feature and model investigation. Here, we review recently developed methods that incorporate machine learning within the same framework with techniques from molecular evolution, protein structure analysis, systems biology, and disease genomics. We outline the challenges posed for machine learning, and, in particular, deep learning in biomedicine, and suggest unique opportunities for machine learning techniques integrated with established bioinformatics approaches to overcome some of these challenges.
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Affiliation(s)
| | | | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA;
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17
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Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J. Mechanistic modeling of the SARS-CoV-2 disease map. BioData Min 2021; 14:5. [PMID: 33478554 PMCID: PMC7817765 DOI: 10.1186/s13040-021-00234-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map. In this framework, the detailed activity of the human signaling circuits related to the viral infection, covering from the entry and replication mechanisms to the downstream consequences as inflammation and antigenic response, can be inferred from gene expression experiments. Moreover, the effect of potential interventions, such as knock-downs, or drug effects (currently the system models the effect of more than 8000 DrugBank drugs) can be studied. This freely available tool not only provides an unprecedentedly detailed view of the mechanisms of viral invasion and the consequences in the cell but has also the potential of becoming an invaluable asset in the search for efficient antiviral treatments.
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Affiliation(s)
- Kinza Rian
- Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain
| | - Marina Esteban-Medina
- Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain
| | - Marta R Hidalgo
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain
| | - Cankut Çubuk
- Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain
| | - Matias M Falco
- Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
| | - Carlos Loucera
- Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain
| | - Devrim Gunyel
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - María Peña-Chilet
- Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain.
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain.
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain.
| | - Joaquín Dopazo
- Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain.
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain.
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain.
- Functional Genomics Node (INB-ELIXIR-es), Sevilla, Spain.
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18
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Transcriptomic Analysis of a Diabetic Skin-Humanized Mouse Model Dissects Molecular Pathways Underlying the Delayed Wound Healing Response. Genes (Basel) 2020; 12:genes12010047. [PMID: 33396192 PMCID: PMC7824036 DOI: 10.3390/genes12010047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
Defective healing leading to cutaneous ulcer formation is one of the most feared complications of diabetes due to its consequences on patients' quality of life and on the healthcare system. A more in-depth analysis of the underlying molecular pathophysiology is required to develop effective healing-promoting therapies for those patients. Major architectural and functional differences with human epidermis limit extrapolation of results coming from rodents and other small mammal-healing models. Therefore, the search for reliable humanized models has become mandatory. Previously, we developed a diabetes-induced delayed humanized wound healing model that faithfully recapitulated the major histological features of such skin repair-deficient condition. Herein, we present the results of a transcriptomic and functional enrichment analysis followed by a mechanistic analysis performed in such humanized wound healing model. The deregulation of genes implicated in functions such as angiogenesis, apoptosis, and inflammatory signaling processes were evidenced, confirming published data in diabetic patients that in fact might also underlie some of the histological features previously reported in the delayed skin-humanized healing model. Altogether, these molecular findings support the utility of such preclinical model as a valuable tool to gain insight into the molecular basis of the delayed diabetic healing with potential impact in the translational medicine field.
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19
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Chowdhury S, Fong SS. Leveraging genome-scale metabolic models for human health applications. Curr Opin Biotechnol 2020; 66:267-276. [PMID: 33120253 DOI: 10.1016/j.copbio.2020.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023]
Abstract
Genome-scale metabolic modeling is a scalable and extensible computational method for analyzing and predicting biological function. With the ongoing improvements in computational methods and experimental capabilities, genome-scale metabolic models (GEMs) are demonstrating utility in addressing human health applications. The initial areas of highest impact are likely to be health applications where disease states involve metabolic changes. In this review, we focus on recent application of GEMs to studying cancer and the human microbiome by describing the enabling methodologies and outcomes of these studies. We conclude with proposing some areas of research that are likely to arise as a result of recent methodological advances.
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Affiliation(s)
- Shomeek Chowdhury
- Integrative Life Sciences, Virginia Commonwealth University, 1000 West Main Street, Richmond, 23284, VA, USA
| | - Stephen S Fong
- Integrative Life Sciences, Virginia Commonwealth University, 1000 West Main Street, Richmond, 23284, VA, USA; Chemical and Life Science Engineering, Virginia Commonwealth University, 601 West Main Street, Richmond, 23284, VA, USA.
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20
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Çubuk C, Can FE, Peña-Chilet M, Dopazo J. Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments. Cells 2020; 9:E1579. [PMID: 32610626 PMCID: PMC7408716 DOI: 10.3390/cells9071579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022] Open
Abstract
Despite the existence of differences in gene expression across numerous genes between males and females having been known for a long time, these have been mostly ignored in many studies, including drug development and its therapeutic use. In fact, the consequences of such differences over the disease mechanisms or the drug action mechanisms are completely unknown. Here we applied mechanistic mathematical models of signaling activity to reveal the ultimate functional consequences that gender-specific gene expression activities have over cell functionality and fate. Moreover, we also used the mechanistic modeling framework to simulate the drug interventions and unravel how drug action mechanisms are affected by gender-specific differential gene expression. Interestingly, some cancers have many biological processes significantly affected by these gender-specific differences (e.g., bladder or head and neck carcinomas), while others (e.g., glioblastoma or rectum cancer) are almost insensitive to them. We found that many of these gender-specific differences affect cancer-specific pathways or in physiological signaling pathways, also involved in cancer origin and development. Finally, mechanistic models have the potential to be used for finding alternative therapeutic interventions on the pathways targeted by the drug, which lead to similar results compensating the downstream consequences of gender-specific differences in gene expression.
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Affiliation(s)
- Cankut Çubuk
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain; (C.Ç.); (F.E.C.); (M.P.-C.)
- Division of Genetics and Epidemiology, Institute of Cancer Research, London SW7 3RP, UK
- William Harvey Research Institute, Queen Mary University, London EC1M 6BQ, UK
| | - Fatma E. Can
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain; (C.Ç.); (F.E.C.); (M.P.-C.)
- Department of Biostatistics, Faculty of Medicine, Izmir Katip Celebi University, 35620 Balatçık, Turkey
| | - María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain; (C.Ç.); (F.E.C.); (M.P.-C.)
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), 41013 Sevilla, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain; (C.Ç.); (F.E.C.); (M.P.-C.)
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), 41013 Sevilla, Spain
- FPS-ELIXIR-ES, Hospital Virgen del Rocío, 41013 Sevilla, Spain
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21
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Falco MM, Peña-Chilet M, Loucera C, Hidalgo MR, Dopazo J. Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape. NAR Cancer 2020; 2:zcaa011. [PMID: 34316686 PMCID: PMC8210212 DOI: 10.1093/narcan/zcaa011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023] Open
Abstract
Single-cell RNA sequencing is revealing an unexpectedly large degree of heterogeneity in gene expression levels across cell populations. However, little is known on the functional consequences of this heterogeneity and the contribution of individual cell fate decisions to the collective behavior of the tissues these cells are part of. Here, we use mechanistic modeling of signaling circuits, which reveals a complex functional landscape at single-cell level. Different clusters of neoplastic glioblastoma cells have been defined according to their differences in signaling circuit activity profiles triggering specific cancer hallmarks, which suggest different functional strategies with distinct degrees of aggressiveness. Moreover, mechanistic modeling of effects of targeted drug inhibitions at single-cell level revealed, how in some cells, the substitution of VEGFA, the target of bevacizumab, by other expressed proteins, like PDGFD, KITLG and FGF2, keeps the VEGF pathway active, insensitive to the VEGFA inhibition by the drug. Here, we describe for the first time mechanisms that individual cells use to avoid the effect of a targeted therapy, providing an explanation for the innate resistance to the treatment displayed by some cells. Our results suggest that mechanistic modeling could become an important asset for the definition of personalized therapeutic interventions.
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Affiliation(s)
- Matías M Falco
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, 41013 Sevilla, Spain
| | - María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, 41013 Sevilla, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, 41013 Sevilla, Spain
| | - Marta R Hidalgo
- Unidad de Bioinformática y Bioestadística, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, 41013 Sevilla, Spain
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Roy H, Nandi S. In-Silico Modeling in Drug Metabolism and Interaction: Current Strategies of Lead Discovery. Curr Pharm Des 2020; 25:3292-3305. [PMID: 31481001 DOI: 10.2174/1381612825666190903155935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/01/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Drug metabolism is a complex mechanism of human body systems to detoxify foreign particles, chemicals, and drugs through bio alterations. It involves many biochemical reactions carried out by invivo enzyme systems present in the liver, kidney, intestine, lungs, and plasma. After drug administration, it crosses several biological membranes to reach into the target site for binding and produces the therapeutic response. After that, it may undergo detoxification and excretion to get rid of the biological systems. Most of the drugs and its metabolites are excreted through kidney via urination. Some drugs and their metabolites enter into intestinal mucosa and excrete through feces. Few of the drugs enter into hepatic circulation where they go into the intestinal tract. The drug leaves the liver via the bile duct and is excreted through feces. Therefore, the study of total methodology of drug biotransformation and interactions with various targets is costly. METHODS To minimize time and cost, in-silico algorithms have been utilized for lead-like drug discovery. Insilico modeling is the process where a computer model with a suitable algorithm is developed to perform a controlled experiment. It involves the combination of both in-vivo and in-vitro experimentation with virtual trials, eliminating the non-significant variables from a large number of variable parameters. Whereas, the major challenge for the experimenter is the selection and validation of the preferred model, as well as precise simulation in real physiological status. RESULTS The present review discussed the application of in-silico models to predict absorption, distribution, metabolism, and excretion (ADME) properties of drug molecules and also access the net rate of metabolism of a compound. CONCLUSION It helps with the identification of enzyme isoforms; which are likely to metabolize a compound, as well as the concentration dependence of metabolism and the identification of expected metabolites. In terms of drug-drug interactions (DDIs), models have been described for the inhibition of metabolism of one compound by another, and for the compound-dependent induction of drug-metabolizing enzymes.
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Affiliation(s)
- Harekrishna Roy
- Nirmala College of Pharmacy, Mangalagiri, Guntur, Affiliated to Acharya Nagarjuna University, Andhra Pradesh-522503, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research, Affiliated to Uttarakhand Technical University, Kashipur-244713, India
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23
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Celentano A, Glurich I, Borgnakke WS, Farah CS. World Workshop on Oral Medicine VII: Prognostic biomarkers in oral leukoplakia and proliferative verrucous leukoplakia-A systematic review of retrospective studies. Oral Dis 2020; 27:848-880. [PMID: 32306449 DOI: 10.1111/odi.13363] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/06/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To systematically review retrospective studies examining prognostic potentials of candidate biomarkers to stratify malignant progression of oral leukoplakia (OL) and proliferative verrucous leukoplakia (PVL). MATERIALS AND METHODS A systematic literature search of PubMed, EMBASE, Evidence-Based Medicine and Web of Science databases targeted literature published through 29 March 2018. Inter-rater agreement was ascertained during title, abstract and full-text reviews. Eligibility evaluation and data abstraction from eligible studies were guided by predefined PICO questions and bias assessment by the Quality in Prognosis Studies tool. Reporting followed Preferred Reporting Items for Systematic Review and Meta-Analysis criteria. Biomarkers were stratified based on cancer hallmarks. RESULTS Eligible studies (n = 54/3,415) evaluated 109 unique biomarkers in tissue specimens from 2,762 cases (2,713 OL, 49 PVL). No biomarker achieved benchmarks for clinical application to detect malignant transformation. Inter-rater reliability was high, but 65% of included studies had high "Study Confounding" bias risk. CONCLUSION There was no evidence to support translation of candidate biomarkers predictive of malignant transformation of OL and PVL. Systematically designed, large, optimally controlled, collaborative, prospective and longitudinal studies with a priori-specified methods to identify, recruit, prospectively follow and test for malignant transformation are needed to enhance feasibility of prognostic biomarkers predicting malignant OL or PVL transformation.
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Affiliation(s)
- Antonio Celentano
- Melbourne Dental School, The University of Melbourne, Melbourne, Vic., Australia
| | - Ingrid Glurich
- Center for Oral and Systemic Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Wenche S Borgnakke
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Camile S Farah
- Australian Centre for Oral Oncology Research & Education, Perth, WA, Australia.,Oral, Maxillofacial and Dental Surgery, Fiona Stanley Hospital, Murdoch, WA, Australia
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24
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Humayun F, Domingo-Fernández D, Paul George AA, Hopp MT, Syllwasschy BF, Detzel MS, Hoyt CT, Hofmann-Apitius M, Imhof D. A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders. Front Bioeng Biotechnol 2020; 8:74. [PMID: 32211383 PMCID: PMC7069124 DOI: 10.3389/fbioe.2020.00074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/28/2020] [Indexed: 01/07/2023] Open
Abstract
Heme is an iron ion-containing molecule found within hemoproteins such as hemoglobin and cytochromes that participates in diverse biological processes. Although excessive heme has been implicated in several diseases including malaria, sepsis, ischemia-reperfusion, and disseminated intravascular coagulation, little is known about its regulatory and signaling functions. Furthermore, the limited understanding of heme's role in regulatory and signaling functions is in part due to the lack of curated pathway resources for heme cell biology. Here, we present two resources aimed to exploit this unexplored information to model heme biology. The first resource is a terminology covering heme-specific terms not yet included in standard controlled vocabularies. Using this terminology, we curated and modeled the second resource, a mechanistic knowledge graph representing the heme's interactome based on a corpus of 46 scientific articles. Finally, we demonstrated the utility of these resources by investigating the role of heme in the Toll-like receptor signaling pathway. Our analysis proposed a series of crosstalk events that could explain the role of heme in activating the TLR4 signaling pathway. In summary, the presented work opens the door to the scientific community for exploring the published knowledge on heme biology.
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Affiliation(s)
- Farah Humayun
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Ajay Abisheck Paul George
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Marie-Thérèse Hopp
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Benjamin F. Syllwasschy
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Milena S. Detzel
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Charles Tapley Hoyt
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany
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25
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Peña-Chilet M, Esteban-Medina M, Falco MM, Rian K, Hidalgo MR, Loucera C, Dopazo J. Using mechanistic models for the clinical interpretation of complex genomic variation. Sci Rep 2019; 9:18937. [PMID: 31831811 PMCID: PMC6908734 DOI: 10.1038/s41598-019-55454-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023] Open
Abstract
The sustained generation of genomic data in the last decade has increased the knowledge on the causal mutations of a large number of diseases, especially for highly penetrant Mendelian diseases, typically caused by a unique or a few genes. However, the discovery of causal genes in complex diseases has been far less successful. Many complex diseases are actually a consequence of the failure of complex biological modules, composed by interrelated proteins, which can happen in many different ways, which conferring a multigenic nature to the condition that can hardly be attributed to one or a few genes. We present a mechanistic model, Hipathia, implemented in a web server that allows estimating the effect that mutations, or changes in the expression of genes, have over the whole system of human signaling and the corresponding functional consequences. We show several use cases where we demonstrate how different the ultimate impact of mutations with similar loss-of-function potential can be and how the potential pathological role of a damaged gene can be inferred within the context of a signaling network. The use of systems biology-based approaches, such as mechanistic models, allows estimating the potential impact of loss-of-function mutations occurring in proteins that are part of complex biological interaction networks, such as signaling pathways. This holistic approach provides an elegant alternative to gene-centric approaches that can open new avenues in the interpretation of the genomic variability in complex diseases.
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Affiliation(s)
- María Peña-Chilet
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocío, 41013, Sevilla, Spain
- Bioinformatics in RareDiseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain
| | - Marina Esteban-Medina
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocío, 41013, Sevilla, Spain
| | - Matias M Falco
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocío, 41013, Sevilla, Spain
- Bioinformatics in RareDiseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain
| | - Kinza Rian
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocío, 41013, Sevilla, Spain
| | - Marta R Hidalgo
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocío, 41013, Sevilla, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocío, 41013, Sevilla, Spain.
- Bioinformatics in RareDiseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain.
- INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, Sevilla, 42013, Spain.
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26
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Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM. Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform 2019; 22:109-126. [PMID: 31813964 DOI: 10.1093/bib/bbz104] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION Biological systems function through dynamic interactions among genes and their products, regulatory circuits and metabolic networks. Our development of the Pathway Tools software was motivated by the need to construct biological knowledge resources that combine these many types of data, and that enable users to find and comprehend data of interest as quickly as possible through query and visualization tools. Further, we sought to support the development of metabolic flux models from pathway databases, and to use pathway information to leverage the interpretation of high-throughput data sets. RESULTS In the past 4 years we have enhanced the already extensive Pathway Tools software in several respects. It can now support metabolic-model execution through the Web, it provides a more accurate gap filler for metabolic models; it supports development of models for organism communities distributed across a spatial grid; and model results may be visualized graphically. Pathway Tools supports several new omics-data analysis tools including the Omics Dashboard, multi-pathway diagrams called pathway collages, a pathway-covering algorithm for metabolomics data analysis and an algorithm for generating mechanistic explanations of multi-omics data. We have also improved the core pathway/genome databases management capabilities of the software, providing new multi-organism search tools for organism communities, improved graphics rendering, faster performance and re-designed gene and metabolite pages. AVAILABILITY The software is free for academic use; a fee is required for commercial use. See http://pathwaytools.com. CONTACT pkarp@ai.sri.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
- Peter D Karp
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | - Peter E Midford
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | - Richard Billington
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | - Anamika Kothari
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | | | - Mario Latendresse
- Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
| | - Wai Kit Ong
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | - Pallavi Subhraveti
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | - Ron Caspi
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | - Carol Fulcher
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | - Ingrid M Keseler
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
| | - Suzanne M Paley
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
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27
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Petkevicius K, Virtue S, Bidault G, Jenkins B, Çubuk C, Morgantini C, Aouadi M, Dopazo J, Serlie MJ, Koulman A, Vidal-Puig A. Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity. eLife 2019; 8:e47990. [PMID: 31418690 PMCID: PMC6748830 DOI: 10.7554/elife.47990] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/15/2019] [Indexed: 12/28/2022] Open
Abstract
White adipose tissue (WAT) inflammation contributes to the development of insulin resistance in obesity. While the role of adipose tissue macrophage (ATM) pro-inflammatory signalling in the development of insulin resistance has been established, it is less clear how WAT inflammation is initiated. Here, we show that ATMs isolated from obese mice and humans exhibit markers of increased rate of de novo phosphatidylcholine (PC) biosynthesis. Macrophage-specific knockout of phosphocholine cytidylyltransferase A (CCTα), the rate-limiting enzyme of de novo PC biosynthesis pathway, alleviated obesity-induced WAT inflammation and insulin resistance. Mechanistically, CCTα-deficient macrophages showed reduced ER stress and inflammation in response to palmitate. Surprisingly, this was not due to lower exogenous palmitate incorporation into cellular PCs. Instead, CCTα-null macrophages had lower membrane PC turnover, leading to elevated membrane polyunsaturated fatty acid levels that negated the pro-inflammatory effects of palmitate. Our results reveal a causal link between obesity-associated increase in de novo PC synthesis, accelerated PC turnover and pro-inflammatory activation of ATMs.
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Affiliation(s)
- Kasparas Petkevicius
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRCCambridgeUnited Kingdom
| | - Sam Virtue
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRCCambridgeUnited Kingdom
| | - Guillaume Bidault
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRCCambridgeUnited Kingdom
| | - Benjamin Jenkins
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRCCambridgeUnited Kingdom
| | - Cankut Çubuk
- Clinical Bioinformatics AreaFundación Progreso y Salud, CDCA, Hospital Virgen del RocioSevillaSpain
- Functional Genomics NodeINB-ELIXIR-es, FPS, Hospital Virgen del RocioSevillaSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del RocioSevillaSpain
| | - Cecilia Morgantini
- Department of Medicine, Integrated Cardio Metabolic CentreKarolinska InstitutetHuddingeSweden
| | - Myriam Aouadi
- Department of Medicine, Integrated Cardio Metabolic CentreKarolinska InstitutetHuddingeSweden
| | - Joaquin Dopazo
- Clinical Bioinformatics AreaFundación Progreso y Salud, CDCA, Hospital Virgen del RocioSevillaSpain
- Functional Genomics NodeINB-ELIXIR-es, FPS, Hospital Virgen del RocioSevillaSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del RocioSevillaSpain
| | - Mireille J Serlie
- Department of Endocrinology and MetabolismAmsterdam University Medical CenterAmsterdamNetherlands
| | - Albert Koulman
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRCCambridgeUnited Kingdom
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRCCambridgeUnited Kingdom
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
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28
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Esteban-Medina M, Peña-Chilet M, Loucera C, Dopazo J. Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. BMC Bioinformatics 2019; 20:370. [PMID: 31266445 PMCID: PMC6604281 DOI: 10.1186/s12859-019-2969-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensionality, given the disbalance between samples and candidate genes. And this is especially dramatic in scenarios in which the availability of samples is difficult, such as the case of rare diseases. RESULTS The application of multi-output regression machine learning methodologies to predict the potential effect of external proteins over the signaling circuits that trigger Fanconi anemia related cell functionalities, inferred with a mechanistic model, allowed us to detect over 20 potential therapeutic targets. CONCLUSIONS The use of artificial intelligence methods for the prediction of potentially causal relationships between proteins of interest and cell activities related with disease-related phenotypes opens promising avenues for the systematic search of new targets in rare diseases.
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Affiliation(s)
- Marina Esteban-Medina
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - María Peña-Chilet
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013 Sevilla, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013 Sevilla, Spain
- INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, 42013 Sevilla, Spain
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