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Weinstein N, Carlsen J, Schulz S, Stapleton T, Henriksen HH, Travnik E, Johansson PI. A Lifelike guided journey through the pathophysiology of pulmonary hypertension-from measured metabolites to the mechanism of action of drugs. Front Cardiovasc Med 2024; 11:1341145. [PMID: 38845688 PMCID: PMC11153715 DOI: 10.3389/fcvm.2024.1341145] [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: 11/19/2023] [Accepted: 04/12/2024] [Indexed: 06/09/2024] Open
Abstract
Introduction Pulmonary hypertension (PH) is a pathological condition that affects approximately 1% of the population. The prognosis for many patients is poor, even after treatment. Our knowledge about the pathophysiological mechanisms that cause or are involved in the progression of PH is incomplete. Additionally, the mechanism of action of many drugs used to treat pulmonary hypertension, including sotatercept, requires elucidation. Methods Using our graph-powered knowledge mining software Lifelike in combination with a very small patient metabolite data set, we demonstrate how we derive detailed mechanistic hypotheses on the mechanisms of PH pathophysiology and clinical drugs. Results In PH patients, the concentration of hypoxanthine, 12(S)-HETE, glutamic acid, and sphingosine 1 phosphate is significantly higher, while the concentration of L-arginine and L-histidine is lower than in healthy controls. Using the graph-based data analysis, gene ontology, and semantic association capabilities of Lifelike, led us to connect the differentially expressed metabolites with G-protein signaling and SRC. Then, we associated SRC with IL6 signaling. Subsequently, we found associations that connect SRC, and IL6 to activin and BMP signaling. Lastly, we analyzed the mechanisms of action of several existing and novel pharmacological treatments for PH. Lifelike elucidated the interplay between G-protein, IL6, activin, and BMP signaling. Those pathways regulate hallmark pathophysiological processes of PH, including vasoconstriction, endothelial barrier function, cell proliferation, and apoptosis. Discussion The results highlight the importance of SRC, ERK1, AKT, and MLC activity in PH. The molecular pathways affected by existing and novel treatments for PH also converge on these molecules. Importantly, sotatercept affects SRC, ERK1, AKT, and MLC simultaneously. The present study shows the power of mining knowledge graphs using Lifelike's diverse set of data analytics functionalities for developing knowledge-driven hypotheses on PH pathophysiological and drug mechanisms and their interactions. We believe that Lifelike and our presented approach will be valuable for future mechanistic studies of PH, other diseases, and drugs.
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Affiliation(s)
- Nathan Weinstein
- CAG Center for Endotheliomics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Jørn Carlsen
- CAG Center for Endotheliomics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Sebastian Schulz
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Timothy Stapleton
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Hanne H. Henriksen
- CAG Center for Endotheliomics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Evelyn Travnik
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pär Ingemar Johansson
- CAG Center for Endotheliomics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Israr J, Alam S, Kumar A. System biology approaches for drug repurposing. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:221-245. [PMID: 38789180 DOI: 10.1016/bs.pmbts.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Drug repurposing, or drug repositioning, refers to the identification of alternative therapeutic applications for established medications that go beyond their initial indications. This strategy has becoming increasingly popular since it has the potential to significantly reduce the overall costs of drug development by around $300 million. System biology methodologies have been employed to facilitate medication repurposing, encompassing computational techniques such as signature matching and network-based strategies. These techniques utilize pre-existing drug-related data types and databases to find prospective repurposed medications that have minimal or acceptable harmful effects on patients. The primary benefit of medication repurposing in comparison to drug development lies in the fact that approved pharmaceuticals have already undergone multiple phases of clinical studies, thereby possessing well-established safety and pharmacokinetic properties. Utilizing system biology methodologies in medication repurposing offers the capacity to expedite the discovery of viable candidates for drug repurposing and offer novel perspectives for structure-based drug design.
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Affiliation(s)
- Juveriya Israr
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, Uttar Pradesh, India; Department of Biotechnology Era University, Lucknow, Uttar Pradesh, India
| | - Shabroz Alam
- Department of Biotechnology Era University, Lucknow, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Mandhana, Kanpur, Uttar Pradesh, India.
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Philip A, Dwivedi PSR, Shastry CS, Utagi B. Guideline directed medical therapy induced nephrotoxicity in HFrEF patients; an insight to its mechanism. J Biomol Struct Dyn 2024:1-15. [PMID: 38466079 DOI: 10.1080/07391102.2024.2326193] [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: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/12/2024]
Abstract
Guideline Directed Medical Therapy (GDMT) has been the standard pharmacotherapy for the treatment of Heart Failure patients with reduced Ejection Fraction (HFrEF) recommended by the European Society of Cardiology (ESC). However, patients on GDMT are likely to possess nephrotoxicity as an adverse effect. We utilized multiple system biology tools like ADVER-Pred, gene enrichment analysis, molecular docking, molecular dynamic simulations, and MMPBSA analysis to predict a possible molecular mechanism of how selected combinations of GDMT may cause nephrotoxicity. As per the ACC/AHA/ESC guidelines, we categorized the drugs as category 1 including β-blockers (BB), angiotensin receptor blockers (ARB), and sodium-glucose cotransporter-2 inhibitors (SGLT2I), category 2 includes BB's, SGLT2I, and angiotensin receptor-neprilysin inhibitors (ARNI), and category 3 includes BB's, SGLT2I, and angiotensin-converting enzyme (ACE) inhibitors. Enrichment analysis predicted category 2 drugs to possess the highest number of proteins to be involved in the development of nephrotoxicity i.e. 79.41%. The targets HBA1, CBR1, ATG5, and SLC6A3 were the top hub genes with an edge count of 7 followed by GPX1 with an edge count of 6. Molecular docking studies revealed candesartan-SLC6A3 to possess the highest binding affinity of -10.2 kcal/mol. In addition, simulation studies displayed empagliflozin-CBR1 to possess the highest stability followed by candesartan-ATG5. A combination of β-blockers, ARBs, and SGLT2I are predicted to likely possess nephrotoxicity which may be due to the modulation of HBA1, CBR1, ATG5, and GPX1. In conclusion, candesartan and empagliflozin are most likely to cause nephrotoxicity via the modulation of HBA1, CBR1, ATG5, and GPX1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anu Philip
- Department of Pharmacy Practice, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India
| | - Prarambh S R Dwivedi
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India
| | - C S Shastry
- Department of Pharmacy Practice, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India
| | - Basavaraj Utagi
- Department of Cardiology, KS Hegde Medical Academy (KSHEMA), Nitte (Deemed to be University), Mangalore, India
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4
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Ahmed F, Samantasinghar A, Manzoor Soomro A, Kim S, Hyun Choi K. A systematic review of computational approaches to understand cancer biology for informed drug repurposing. J Biomed Inform 2023; 142:104373. [PMID: 37120047 DOI: 10.1016/j.jbi.2023.104373] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
Cancer is the second leading cause of death globally, trailing only heart disease. In the United States alone, 1.9 million new cancer cases and 609,360 deaths were recorded for 2022. Unfortunately, the success rate for new cancer drug development remains less than 10%, making the disease particularly challenging. This low success rate is largely attributed to the complex and poorly understood nature of cancer etiology. Therefore, it is critical to find alternative approaches to understanding cancer biology and developing effective treatments. One such approach is drug repurposing, which offers a shorter drug development timeline and lower costs while increasing the likelihood of success. In this review, we provide a comprehensive analysis of computational approaches for understanding cancer biology, including systems biology, multi-omics, and pathway analysis. Additionally, we examine the use of these methods for drug repurposing in cancer, including the databases and tools that are used for cancer research. Finally, we present case studies of drug repurposing, discussing their limitations and offering recommendations for future research in this area.
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Affiliation(s)
- Faheem Ahmed
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea
| | | | | | - Sejong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Kyung Hyun Choi
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea.
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Stamhuis E, Evangelista L, van der Voort S, Mele AM, Spiller E, Demir E, Pin A, Heine K. From bottleneck to enabler: a new approach to regulating data-driven medical research. Clin Transl Imaging 2023. [DOI: 10.1007/s40336-023-00546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Perico D, Di Silvestre D, Imamichi S, Sanada Y, Masutani M, Mauri PL. Systems Biology Approach to Investigate Biomarkers, Boron-10 Carriers, and Mechanisms Useful for Improving Boron Neutron Capture Therapy. Cancer Biother Radiopharm 2022; 38:152-159. [PMID: 36269655 DOI: 10.1089/cbr.2022.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Systems biology approach, carried out with high-throughput omics technologies, has become a fundamental aspect of the study of complex diseases like cancer. It can molecularly characterize subjects, physiopathological conditions, and interactions, allowing a precise description, to reach personalized medicine. In particular, proteomics, typically performed with liquid chromatography coupled to mass spectrometry, is a powerful tool for systems biology, giving the possibility to perform diagnosis, patient stratification, and prediction of therapy effects. Boron Neutron Capture Therapy (BNCT) is a selective antitumoral radiotherapy based on a nuclear reaction that occurs when 10B atoms are irradiated by low-energy thermal neutrons, leading to cell death, thanks to the production of high-energy α particles. Since BNCT is recently becoming an important therapy for the treatment of different types of solid tumors such as gliomas, head and neck cancers, and others, it can take advantage of molecular investigation to improve the understanding of effects and mechanisms and so help its clinical applications. In this context, proteomics can provide a better understanding of mechanisms related to BNCT effect, identify potential biomarkers, and individuate differential responses by specific patients, stratifying responders and nonresponders. Another key aspect of BNCT is the study of new potential Boron-10 carriers to improve the selectivity of Boron delivery to tumors and proteomics can be important in this application, studying the effectiveness of new boron delivery agents, including protein-based carriers, also using computational studies that can investigate new molecules, such as boronated monoclonal antibodies, for improving BNCT.
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Affiliation(s)
- Davide Perico
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Shoji Imamichi
- Department of Molecular and Genomic Biomedicine, School of Biomedical Sciences, Nagasaki University Graduate, Nagasaki, Japan.,Central Radioisotope Division, National Cancer Center Research Institute, Tokyo, Japan.,Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Japan
| | - Yu Sanada
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Japan
| | - Mitsuko Masutani
- Department of Molecular and Genomic Biomedicine, School of Biomedical Sciences, Nagasaki University Graduate, Nagasaki, Japan.,Central Radioisotope Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Pier Luigi Mauri
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy.,Institute of Life Science, Scuola Superiore Sant'Anna, Pisa, Italy
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Kalantari E, Kouchaki S, Miaskowski C, Kober K, Barnaghi P. Network analysis to identify symptoms clusters and temporal interconnections in oncology patients. Sci Rep 2022; 12:17052. [PMID: 36224203 PMCID: PMC9556713 DOI: 10.1038/s41598-022-21140-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 09/22/2022] [Indexed: 12/30/2022] Open
Abstract
Oncology patients experience numerous co-occurring symptoms during their treatment. The identification of sentinel/core symptoms is a vital prerequisite for therapeutic interventions. In this study, using Network Analysis, we investigated the inter-relationships among 38 common symptoms over time (i.e., a total of six time points over two cycles of chemotherapy) in 987 oncology patients with four different types of cancer (i.e., breast, gastrointestinal, gynaecological, and lung). In addition, we evaluated the associations between and among symptoms and symptoms clusters and examined the strength of these interactions over time. Eight unique symptom clusters were identified within the networks. Findings from this research suggest that changes occur in the relationships and interconnections between and among co-occurring symptoms and symptoms clusters that depend on the time point in the chemotherapy cycle and the type of cancer. The evaluation of the centrality measures provides new insights into the relative importance of individual symptoms within various networks that can be considered as potential targets for symptom management interventions.
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Affiliation(s)
- Elaheh Kalantari
- grid.5475.30000 0004 0407 4824Centre for Vision, Speech and Signal Processing (CVSSP), University of Surrey, Guildford, UK ,grid.7445.20000 0001 2113 8111UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, London, UK
| | - Samaneh Kouchaki
- grid.5475.30000 0004 0407 4824Centre for Vision, Speech and Signal Processing (CVSSP), University of Surrey, Guildford, UK ,grid.7445.20000 0001 2113 8111UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, London, UK
| | - Christine Miaskowski
- grid.266102.10000 0001 2297 6811Department of Physiological Nursing, University of California San Francisco, San Francisco, CA USA
| | - Kord Kober
- grid.266102.10000 0001 2297 6811Department of Physiological Nursing, University of California San Francisco, San Francisco, CA USA
| | - Payam Barnaghi
- grid.7445.20000 0001 2113 8111Department of Brain Sciences, Imperial College London, London, UK ,grid.7445.20000 0001 2113 8111UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, London, UK
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La Ferlita A, Alaimo S, Ferro A, Pulvirenti A. Pathway Analysis for Cancer Research and Precision Oncology Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:143-161. [DOI: 10.1007/978-3-030-91836-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Gutiérrez-Casares JR, Quintero J, Jorba G, Junet V, Martínez V, Pozo-Rubio T, Oliva B, Daura X, Mas JM, Montoto C. Methods to Develop an in silico Clinical Trial: Computational Head-to-Head Comparison of Lisdexamfetamine and Methylphenidate. Front Psychiatry 2021; 12:741170. [PMID: 34803764 PMCID: PMC8595241 DOI: 10.3389/fpsyt.2021.741170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Regulatory agencies encourage computer modeling and simulation to reduce the time and cost of clinical trials. Although still not classified in formal guidelines, system biology-based models represent a powerful tool for generating hypotheses with great molecular detail. Herein, we have applied a mechanistic head-to-head in silico clinical trial (ISCT) between two treatments for attention-deficit/hyperactivity disorder, to wit lisdexamfetamine (LDX) and methylphenidate (MPH). The ISCT was generated through three phases comprising (i) the molecular characterization of drugs and pathologies, (ii) the generation of adult and children virtual populations (vPOPs) totaling 2,600 individuals and the creation of physiologically based pharmacokinetic (PBPK) and quantitative systems pharmacology (QSP) models, and (iii) data analysis with artificial intelligence methods. The characteristics of our vPOPs were in close agreement with real reference populations extracted from clinical trials, as did our PBPK models with in vivo parameters. The mechanisms of action of LDX and MPH were obtained from QSP models combining PBPK modeling of dosing schemes and systems biology-based modeling technology, i.e., therapeutic performance mapping system. The step-by-step process described here to undertake a head-to-head ISCT would allow obtaining mechanistic conclusions that could be extrapolated or used for predictions to a certain extent at the clinical level. Altogether, these computational techniques are proven an excellent tool for hypothesis-generation and would help reach a personalized medicine.
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Affiliation(s)
- José Ramón Gutiérrez-Casares
- Unidad Ambulatoria de Psiquiatría y Salud Mental de la Infancia, Niñez y Adolescencia, Hospital Perpetuo Socorro, Badajoz, Spain
| | - Javier Quintero
- Servicio de Psiquiatría, Hospital Universitario Infanta Leonor, Universidad Complutense, Madrid, Spain
| | - Guillem Jorba
- Anaxomics Biotech, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Valentin Junet
- Anaxomics Biotech, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | | | - Baldomero Oliva
- Research Programme on Biomedical Informatics (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | | | - Carmen Montoto
- Medical Department, Takeda Farmacéutica España, Madrid, Spain
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Welch N, Singh SS, Kumar A, Dhruba SR, Mishra S, Sekar J, Bellar A, Attaway AH, Chelluboyina A, Willard BB, Li L, Huo Z, Karnik SS, Esser K, Longworth MS, Shah YM, Davuluri G, Pal R, Dasarathy S. Integrated multiomics analysis identifies molecular landscape perturbations during hyperammonemia in skeletal muscle and myotubes. J Biol Chem 2021; 297:101023. [PMID: 34343564 PMCID: PMC8424232 DOI: 10.1016/j.jbc.2021.101023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/16/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
Ammonia is a cytotoxic molecule generated during normal cellular functions. Dysregulated ammonia metabolism, which is evident in many chronic diseases such as liver cirrhosis, heart failure, and chronic obstructive pulmonary disease, initiates a hyperammonemic stress response in tissues including skeletal muscle and in myotubes. Perturbations in levels of specific regulatory molecules have been reported, but the global responses to hyperammonemia are unclear. In this study, we used a multiomics approach to vertically integrate unbiased data generated using an assay for transposase-accessible chromatin with high-throughput sequencing, RNA-Seq, and proteomics. We then horizontally integrated these data across different models of hyperammonemia, including myotubes and mouse and human muscle tissues. Changes in chromatin accessibility and/or expression of genes resulted in distinct clusters of temporal molecular changes including transient, persistent, and delayed responses during hyperammonemia in myotubes. Known responses to hyperammonemia, including mitochondrial and oxidative dysfunction, protein homeostasis disruption, and oxidative stress pathway activation, were enriched in our datasets. During hyperammonemia, pathways that impact skeletal muscle structure and function that were consistently enriched were those that contribute to mitochondrial dysfunction, oxidative stress, and senescence. We made several novel observations, including an enrichment in antiapoptotic B-cell leukemia/lymphoma 2 family protein expression, increased calcium flux, and increased protein glycosylation in myotubes and muscle tissue upon hyperammonemia. Critical molecules in these pathways were validated experimentally. Human skeletal muscle from patients with cirrhosis displayed similar responses, establishing translational relevance. These data demonstrate complex molecular interactions during adaptive and maladaptive responses during the cellular stress response to hyperammonemia.
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Affiliation(s)
- Nicole Welch
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shashi Shekhar Singh
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Avinash Kumar
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Saugato Rahman Dhruba
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas, USA
| | - Saurabh Mishra
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jinendiran Sekar
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Annette Bellar
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Amy H Attaway
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pulmonary Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Aruna Chelluboyina
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Belinda B Willard
- Proteomics Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ling Li
- Proteomics Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Public Health and Health Profession, University of Florida, Gainesville, Florida, USA
| | - Sadashiva S Karnik
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Karyn Esser
- Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Michelle S Longworth
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology and Department of Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gangarao Davuluri
- Integrated Physiology and Molecular Metabolism, Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA
| | - Ranadip Pal
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas, USA.
| | - Srinivasan Dasarathy
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA.
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Anchang CG, Xu C, Raimondo MG, Atreya R, Maier A, Schett G, Zaburdaev V, Rauber S, Ramming A. The Potential of OMICs Technologies for the Treatment of Immune-Mediated Inflammatory Diseases. Int J Mol Sci 2021; 22:ijms22147506. [PMID: 34299122 PMCID: PMC8306614 DOI: 10.3390/ijms22147506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
Immune-mediated inflammatory diseases (IMIDs), such as inflammatory bowel diseases and inflammatory arthritis (e.g., rheumatoid arthritis, psoriatic arthritis), are marked by increasing worldwide incidence rates. Apart from irreversible damage of the affected tissue, the systemic nature of these diseases heightens the incidence of cardiovascular insults and colitis-associated neoplasia. Only 40–60% of patients respond to currently used standard-of-care immunotherapies. In addition to this limited long-term effectiveness, all current therapies have to be given on a lifelong basis as they are unable to specifically reprogram the inflammatory process and thus achieve a true cure of the disease. On the other hand, the development of various OMICs technologies is considered as “the great hope” for improving the treatment of IMIDs. This review sheds light on the progressive development and the numerous approaches from basic science that gradually lead to the transfer from “bench to bedside” and the implementation into general patient care procedures.
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Affiliation(s)
- Charles Gwellem Anchang
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Cong Xu
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Maria Gabriella Raimondo
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Raja Atreya
- Department of Internal Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany;
| | - Andreas Maier
- Computer Science, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
| | - Georg Schett
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Vasily Zaburdaev
- Max-Planck-Zentrum für Physik und Medizin, 91054 Erlangen, Germany;
- Department of Biology, Mathematics in Life Sciences, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Simon Rauber
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Andreas Ramming
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
- Correspondence: ; Tel.: +49-9131-8543048; Fax: +49-9131-8536448
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Alaimo S, Rapicavoli RV, Marceca GP, La Ferlita A, Serebrennikova OB, Tsichlis PN, Mishra B, Pulvirenti A, Ferro A. PHENSIM: Phenotype Simulator. PLoS Comput Biol 2021; 17:e1009069. [PMID: 34166365 PMCID: PMC8224893 DOI: 10.1371/journal.pcbi.1009069] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 05/12/2021] [Indexed: 11/21/2022] Open
Abstract
Despite the unprecedented growth in our understanding of cell biology, it still remains challenging to connect it to experimental data obtained with cells and tissues’ physiopathological status under precise circumstances. This knowledge gap often results in difficulties in designing validation experiments, which are usually labor-intensive, expensive to perform, and hard to interpret. Here we propose PHENSIM, a computational tool using a systems biology approach to simulate how cell phenotypes are affected by the activation/inhibition of one or multiple biomolecules, and it does so by exploiting signaling pathways. Our tool’s applications include predicting the outcome of drug administration, knockdown experiments, gene transduction, and exposure to exosomal cargo. Importantly, PHENSIM enables the user to make inferences on well-defined cell lines and includes pathway maps from three different model organisms. To assess our approach’s reliability, we built a benchmark from transcriptomics data gathered from NCBI GEO and performed four case studies on known biological experiments. Our results show high prediction accuracy, thus highlighting the capabilities of this methodology. PHENSIM standalone Java application is available at https://github.com/alaimos/phensim, along with all data and source codes for benchmarking. A web-based user interface is accessible at https://phensim.tech/. Despite the unprecedented growth in our understanding of cell biology, it still remains challenging to connect it to experimental data obtained with cells and tissues’ physiopathological status under precise circumstances. This knowledge gap often results in difficulties in designing validation experiments, which are usually labor-intensive, expensive to perform, and hard to interpret. In this context, ’in silico’ simulations can be extensively applied in massive scales, testing thousands of hypotheses under various conditions, which is usually experimentally infeasible. At present, many simulation models have become available. However, complex biological networks might pose challenges to their performance. We propose PHENSIM, a computational tool using a systems biology approach to simulate how cell phenotypes are affected by the activation/inhibition of one or multiple biomolecules, and it does so by exploiting signaling pathways. We implemented our tool as a freely accessible web application, hoping to allow ’in silico’ simulations to play a more central role in the modeling and understanding of biological phenomena.
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Affiliation(s)
- Salvatore Alaimo
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- * E-mail: (SA); (AF)
| | - Rosaria Valentina Rapicavoli
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Gioacchino P. Marceca
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alessandro La Ferlita
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Oksana B. Serebrennikova
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Philip N. Tsichlis
- Department of Cancer Biology and Genetics and the James Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Bud Mishra
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
| | - Alfredo Pulvirenti
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alfredo Ferro
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- * E-mail: (SA); (AF)
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13
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Trappe A, Donnelly SC, McNally P, Coppinger JA. Role of extracellular vesicles in chronic lung disease. Thorax 2021; 76:1047-1056. [PMID: 33712504 PMCID: PMC8461402 DOI: 10.1136/thoraxjnl-2020-216370] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
To explore the role of extracellular vesicles (EVs) in chronic lung diseases. EVs are emerging as mediators of intercellular communication and possible diagnostic markers of disease. EVs harbour cargo molecules including RNA, lipids and proteins that they transfer to recipient cells. EVs are intercellular communicators within the lung microenvironment. Due to their disease-specific cargoes, EVs have the promise to be all-in-one complex multimodal biomarkers. EVs also have potential as drug carriers in chronic lung disease. Descriptive discussion of key studies of EVs as contributors to disease pathology, as biomarkers and as potential therapies with a focus on chronic obstructive pulmonary disorder (COPD), cystic fibrosis (CF), asthma, idiopathic pulmonary fibrosis and lung cancer. We provide a broad overview of the roles of EV in chronic respiratory disease. Recent advances in profiling EVs have shown their potential as biomarker candidates. Further studies have provided insight into their disease pathology, particularly in inflammatory processes across a spectrum of lung diseases. EVs are on the horizon as new modes of drug delivery and as therapies themselves in cell-based therapeutics. EVs are relatively untapped sources of information in the clinic that can help further detail the full translational nature of chronic lung disorders.
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Affiliation(s)
- Anne Trappe
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland.,CF Research Group, National Children's Research Centre, Childrens Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
| | - Seamas C Donnelly
- Department of Medicine, Trinity College Dublin & Tallaght University Hospital, Dublin, Ireland
| | - Paul McNally
- CF Research Group, National Children's Research Centre, Childrens Health Ireland (CHI) at Crumlin, Dublin 12, Ireland.,Department of Paediatrics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Judith A Coppinger
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland .,CF Research Group, National Children's Research Centre, Childrens Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
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14
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Uppal K. Models of Metabolomic Networks. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11615-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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15
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Ciccocioppo R, Comoli P, Astori G, Del Bufalo F, Prapa M, Dominici M, Locatelli F. Developing cell therapies as drug products. Br J Pharmacol 2020; 178:262-279. [PMID: 33140850 DOI: 10.1111/bph.15305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
In the last 20 years, the global regulatory frameworks for drug assessment have been managing the challenges posed by using cellular products as new therapeutic tools. Currently, they are defined as "Advanced Therapy Medicinal Products", comprising a large group of cellular types that either alone or in combination with gene and tissue engineering technology. They have the potential to change the natural course of still lethal or highly debilitating diseases, including cancers, opportunistic infections and chronic inflammatory conditions. Globally, more than 50 cell-based products have obtained market authorization. This overview describes the advantages and unsolved challenges on developing cells as innovative therapeutic vehicles. The main cell therapy players and the legal framework are discussed, starting from chimeric antigen receptor T-cells for leukaemia and solid tumours, dealing then with lymphocytes as potent anti-microbiological tools and then focusing on mesenchymal stem/stromal cells whose role covers regenerative medicine, immunology and anti-tumour therapy.
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Affiliation(s)
- Rachele Ciccocioppo
- Gastroenterology Unit, Department of Medicine, A.O.U.I. Policlinico G.B. Rossi & University of Verona, Verona, Italy
| | - Patrizia Comoli
- Cell Factory and Paediatric Haematology/Oncology Unit, Fondazione I.R.C.C.S. Policlinico San Matteo, Pavia, Italy
| | - Giuseppe Astori
- Laboratory of Advanced Cellular Therapies, Haematology Unit, San Bortolo Hospital, A.U.L.S.S. 8 "Berica", Vicenza, Italy
| | - Francesca Del Bufalo
- Department of Paediatric Haematology and Oncology and Cell and Gene Therapy, I.R.C.C.S. Bambino Gesù Children's Hospital, Rome, Italy
| | - Malvina Prapa
- Division of Oncology, Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Massimo Dominici
- Division of Oncology, Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology and Oncology and Cell and Gene Therapy, I.R.C.C.S. Bambino Gesù Children's Hospital, Rome, Italy.,Department of Paediatrics, Sapienza University of Rome, Rome, Italy
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16
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Stalidzans E, Zanin M, Tieri P, Castiglione F, Polster A, Scheiner S, Pahle J, Stres B, List M, Baumbach J, Lautizi M, Van Steen K, Schmidt HH. Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice. NETWORK AND SYSTEMS MEDICINE 2020. [DOI: 10.1089/nsm.2020.0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Egils Stalidzans
- Computational Systems Biology Group, University of Latvia, Riga, Latvia
- Latvian Biomedical Reasearch and Study Centre, Riga, Latvia
| | - Massimiliano Zanin
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Paolo Tieri
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | - Filippo Castiglione
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | | | - Stefan Scheiner
- Institute for Mechanics of Materials and Structures, Vienna University of Technology, Vienna, Austria
| | - Jürgen Pahle
- BioQuant, Heidelberg University, Heidelberg, Germany
| | - Blaž Stres
- Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Markus List
- Big Data in BioMedicine Research Group, Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Manuela Lautizi
- Computational Systems Medicine Research Group, Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Kristel Van Steen
- BIO-Systems Genetics, GIGA-R, University of Liège, Liège, Belgium
- BIO3—Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Harald H.H.W. Schmidt
- Department of Pharmacology and Personalised Medicine, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, The Netherlands
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17
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Maron BA. Pulmonary arterial hypertension: Cellular and molecular changes in the lung. Glob Cardiol Sci Pract 2020; 2020:e202003. [PMID: 33150148 PMCID: PMC7590941 DOI: 10.21542/gcsp.2020.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The range of cell types identified in the pathogenesis of pulmonary arterial hypertension (PAH) has expanded substantially since the first pathological descriptions of this disease. This, in turn, has provided needed clarity on the gamut of molecular mechanisms that regulate vascular remodeling and promote characteristic cardiopulmonary hemodynamic changes that define PAH clinically. Insight derived from these scientific advances suggest that the PAH arteriopathy is due to the convergence of numerous molecular mechanisms driving cornerstone endophenotypes, such as plexigenic, hypertrophic, and fibrotic histopathological changes. Interestingly, while some endophenotypes are observed commonly in multiple cell types, such as dysregulated metabolism, other events such as endothelial-mesenchymal transition are cell type-specific. Integrating data from classical PAH vascular cell types with fresh information in pericytes, adventitial fibroblasts, and other PAH contributors recognized more recently has enriched the field with deeper understanding on the molecular basis of this disease. This added complexity, however, also serves as the basis for utilizing novel analytical strategies that emphasize functional signaling pathways when extracting information from big datasets. With these concepts as the backdrop, the current work offers a concise summary of cellular and molecular changes in the lung that drive PAH and may, thus, be important for discovering novel therapeutic targets or applications to clarify PAH onset and disease trajectory.
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Affiliation(s)
- Bradley A Maron
- Department of Medicine, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA, USA.,The Boston VA Healthcare System, West Roxbury, MA, USA
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18
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Manzoni C, Lewis PA, Ferrari R. Network Analysis for Complex Neurodegenerative Diseases. CURRENT GENETIC MEDICINE REPORTS 2020. [DOI: 10.1007/s40142-020-00181-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Purpose of Review
Biomedicine is witnessing a paradigm shift in the way complex disorders are investigated. In particular, the need for big data interpretation has led to the development of pipelines that require the cooperation of different fields of expertise, including medicine, functional biology, informatics, mathematics and systems biology. This review sits at the crossroad of different disciplines and surveys the recent developments in the use of graph theory (in the form of network analysis) to interpret large and different datasets in the context of complex neurodegenerative diseases. It aims at a professional audience with different backgrounds.
Recent Findings
Biomedicine has entered the era of big data, and this is actively changing the way we approach and perform research. The increase in size and power of biomedical studies has led to the establishment of multi-centre, international working groups coordinating open access platforms for data generation, storage and analysis. Particularly, pipelines for data interpretation are under development, and network analysis is gaining momentum since it represents a versatile approach to study complex systems made of interconnected multiple players.
Summary
We will describe the era of big data in biomedicine and survey the major freely accessible multi-omics datasets. We will then introduce the principles of graph theory and provide examples of network analysis applied to the interpretation of complex neurodegenerative disorders.
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19
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Tretter F, Löffler-Stastka H. Medical knowledge integration and "systems medicine": Needs, ambitions, limitations and options. Med Hypotheses 2019; 133:109386. [PMID: 31541780 DOI: 10.1016/j.mehy.2019.109386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/22/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Medicine today is an extremely heterogeneous field of knowledge, based on clinical observations and action knowledge and on data from the biological, behavioral and social sciences. We hypothesize at first that medicine suffers from a disciplinary hyper-diversity compared to the level of conceptual interdisciplinary integration. With the claim to "understand" and cure diseases, currently with the label "Systems Medicine" new forms of molecular medicine promise a general new bottom-up directed precise, personalized, predictive, preventive, translational, participatory, etc. medicine. Our second hypothesis rejects this claim because of conceptual, methodological and theoretical weaknesses. In contrary, this is our third hypothesis; we suggest that top-down organismic systems medicine, related to general system theory, opens better options for an integrative scientific understanding of processes of health and disease.
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Affiliation(s)
- Felix Tretter
- Bertalanffy Center for the Study of Systems Science, Vienna, Austria
| | - Henriette Löffler-Stastka
- Dept. of Psychanalysis and Psychotherapy, and Postgraduate Unit, Medical University Vienna, Austria.
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20
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Gupta V, Crudu A, Matsuoka Y, Ghosh S, Rozot R, Marat X, Jäger S, Kitano H, Breton L. Multi-dimensional computational pipeline for large-scale deep screening of compound effect assessment: an in silico case study on ageing-related compounds. NPJ Syst Biol Appl 2019; 5:42. [PMID: 31798962 PMCID: PMC6879499 DOI: 10.1038/s41540-019-0119-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/23/2019] [Indexed: 12/18/2022] Open
Abstract
Designing alternative approaches to efficiently screen chemicals on the efficacy landscape is a challenging yet indispensable task in the current compound profiling methods. Particularly, increasing regulatory restrictions underscore the need to develop advanced computational pipelines for efficacy assessment of chemical compounds as alternative means to reduce and/or replace in vivo experiments. Here, we present an innovative computational pipeline for large-scale assessment of chemical compounds by analysing and clustering chemical compounds on the basis of multiple dimensions-structural similarity, binding profiles and their network effects across pathways and molecular interaction maps-to generate testable hypotheses on the pharmacological landscapes as well as identify potential mechanisms of efficacy on phenomenological processes. Further, we elucidate the application of the pipeline on a screen of anti-ageing-related compounds to cluster the candidates based on their structure, docking profile and network effects on fundamental metabolic/molecular pathways associated with the cell vitality, highlighting emergent insights on compounds activities based on the multi-dimensional deep screen pipeline.
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Affiliation(s)
| | - Alina Crudu
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | | | | | - Roger Rozot
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Xavier Marat
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Sibylle Jäger
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Hiroaki Kitano
- The Systems Biology Institute, Tokyo, Japan
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Lionel Breton
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
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21
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Peedicayil J. Identification of Biomarkers in Neuropsychiatric Disorders Based on Systems Biology and Epigenetics. Front Genet 2019; 10:985. [PMID: 31681422 PMCID: PMC6801306 DOI: 10.3389/fgene.2019.00985] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
Clinically useful biomarkers are available for some neuropsychiatric disorders like fragile X syndrome, Rett syndrome, and Huntington’s disease. Despite many decades of research on the pathogenesis of neuropsychiatric disorders like schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD), the exact pathogenesis of these disorders remains unclear, and there are no clinically useful biomarkers for these disorders. However, there is increasing evidence that abnormal epigenetic mechanisms of gene expression contribute to the pathogenesis of SZ, BD, and MDD. Both systems (or network) biology and epigenetics (a component of systems biology) attempt to make sense of biological systems that are highly dynamic and multi-compartmental. This article suggests that systems biology, emphasizing the epigenetic component of systems biology, could help identify clinically useful biomarkers in neuropsychiatric disorders like SZ, BD, and MDD.
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Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, India
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22
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Optimised lyophilisation-based method for different biomolecule single-extractions from the same rat brain sample: Suitability for RNA and protein expression analyses after ischemic stroke. J Neurosci Methods 2019; 327:108402. [PMID: 31445114 DOI: 10.1016/j.jneumeth.2019.108402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 11/23/2022]
Abstract
BACKGROUND Optimisation of tissue processing procedures in preclinical studies reduces the number of animals used and allows integrated multilevel study in the same sample. Multiple extraction of different biomolecules from the same sample has several limitations. NEW METHOD Using brain samples from rats subjected to ischemic stroke, we combined lyophilisation of flash-frozen tissue, mechanical pulverisation and cryopreservation in a method to optimise tissue handling and preservation for independent RNA or protein single-extract methods, and subsequent RT-qPCR or Western blot analyses. RESULTS Lyophilisation resulted in 70% tissue weight loss. RNA (OD260/280∼1.8) and protein yields were similar in non-ischemic and ischemic brain samples, subjected to either flash freezing (FF) or flash freezing followed by lyophilisation (FF + Lyo). RNA transcription of reference genes (Actb and Rn18s), expression of housekeeping proteins (β-actin and α-tubulin), and mRNA overexpression of stroke-regulated genes (Nos2, Mmp9 and Tnfa) was similar in FF and FF + Lyo samples. COMPARISON WITH EXISTING METHOD(S) Contrary to high heat stress of baking method in a drying oven, lyophilisation maintains the integrity of dried samples for subsequent extractions and analyses. Sample lyophilisation allows different manual representative extractions/analyses from the same rat, it is much cheaper than using commercial kits, and shows higher yields that multiple manual or kit-based extractions. CONCLUSIONS The lyophilisation-based method for different biomolecule single-extractions from tissue powder aliquots, representing the same rat brain sample, is sample saving, contributes to the reduction principle in animal research, and allows coordinated analysis for accurate correlations between the transcriptome and proteome in stroke and other neuroscience research.
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23
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Culver DA, Behr J, Belperio JA, Corte TJ, de Andrade JA, Flaherty KR, Gulati M, Huie TJ, Lancaster LH, Roman J, Ryerson CJ, Kim HJ. Patient Registries in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2019; 200:160-167. [PMID: 31034241 PMCID: PMC6635784 DOI: 10.1164/rccm.201902-0431ci] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/24/2019] [Indexed: 01/06/2023] Open
Abstract
Over the past decade, several large registries of patients with idiopathic pulmonary fibrosis (IPF) have been established. These registries are collecting a wealth of longitudinal data on thousands of patients with this rare disease. The data collected in these registries will be complementary to data collected in clinical trials because the patient populations studied in registries have a broader spectrum of disease severity and comorbidities and can be followed for a longer period of time. Maintaining the quality and completeness of registry databases presents administrative and resourcing challenges, but it is important to ensuring the robustness of the analyses. Data from patient registries have already helped improve understanding of the clinical characteristics of patients with IPF, the impact that the disease has on their quality of life and survival, and current practices in diagnosis and management. In the future, analyses of biospecimens linked to detailed patient profiles will provide the opportunity to identify biomarkers linked to disease progression, facilitating the development of precision medicine approaches for prognosis and therapy in patients with IPF.
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Affiliation(s)
| | - Jürgen Behr
- Department of Internal Medicine V, Ludwig-Maximilians University of Munich, Munich, Germany
- Asklepios Clinic Gauting, Member of the German Center for Lung Research, Gauting, Germany
| | - John A. Belperio
- David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California
| | - Tamera J. Corte
- Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | | | - Kevin R. Flaherty
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Mridu Gulati
- Yale University School of Medicine, New Haven, Connecticut
| | | | | | - Jesse Roman
- Jane and Leonard Korman Respiratory Institute, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Hyun J. Kim
- University of Minnesota, Minneapolis, Minnesota
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24
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Walker MJ, Bourke J, Hutchison K. Evidence for personalised medicine: mechanisms, correlation, and new kinds of black box. THEORETICAL MEDICINE AND BIOETHICS 2019; 40:103-121. [PMID: 30771062 DOI: 10.1007/s11017-019-09482-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Personalised medicine (PM) has been discussed as a medical paradigm shift that will improve health while reducing inefficiency and waste. At the same time, it raises new practical, regulatory, and ethical challenges. In this paper, we examine PM strategies epistemologically in order to develop capacities to address these challenges, focusing on a recently proposed strategy for developing patient-specific models from induced pluripotent stem cells (iPSCs) so as to make individualised treatment predictions. We compare this strategy to two main PM strategies-stratified medicine and computational models. Drawing on epistemological work in the philosophy of medicine, we explain why these two methods, while powerful, are neither truly personalised nor, epistemologically speaking, novel strategies. Both are forms of correlational black box. We then argue that the iPSC models would count as a new kind of black box. They would not rely entirely on mechanistic knowledge, and they would utilise correlational evidence in a different way from other strategies-a way that would enable personalised predictions. In arguing that the iPSC models would present a novel method of gaining evidence for clinical practice, we provide an epistemic analysis that can help to inform the practical, regulatory, and ethical challenges of developing an iPSC system.
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Affiliation(s)
- Mary Jean Walker
- Monash University, Clayton, VIC, Australia.
- Australian Research Council Centre of Excellence for Electromaterials Science, Wollongong, NSW, Australia.
| | - Justin Bourke
- University of Melbourne, Parkville, VIC, Australia
- Australian Research Council Centre of Excellence for Electromaterials Science, Wollongong, NSW, Australia
| | - Katrina Hutchison
- Macquarie University, North Ryde, NSW, Australia
- Australian Research Council Centre of Excellence for Electromaterials Science, Wollongong, NSW, Australia
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25
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Lucignani G, Neri E. Integration of imaging biomarkers into systems biomedicine: a renaissance for medical imaging. Clin Transl Imaging 2019. [DOI: 10.1007/s40336-019-00320-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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26
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Papachristou N, Barnaghi P, Cooper B, Kober KM, Maguire R, Paul SM, Hammer M, Wright F, Armes J, Furlong EP, McCann L, Conley YP, Patiraki E, Katsaragakis S, Levine JD, Miaskowski C. Network Analysis of the Multidimensional Symptom Experience of Oncology. Sci Rep 2019; 9:2258. [PMID: 30783135 PMCID: PMC6381090 DOI: 10.1038/s41598-018-36973-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023] Open
Abstract
Oncology patients undergoing cancer treatment experience an average of fifteen unrelieved symptoms that are highly variable in both their severity and distress. Recent advances in Network Analysis (NA) provide a novel approach to gain insights into the complex nature of co-occurring symptoms and symptom clusters and identify core symptoms. We present findings from the first study that used NA to examine the relationships among 38 common symptoms in a large sample of oncology patients undergoing chemotherapy. Using two different models of Pairwise Markov Random Fields (PMRF), we examined the nature and structure of interactions for three different dimensions of patients’ symptom experience (i.e., occurrence, severity, distress). Findings from this study provide the first direct evidence that the connections between and among symptoms differ depending on the symptom dimension used to create the network. Based on an evaluation of the centrality indices, nausea appears to be a structurally important node in all three networks. Our findings can be used to guide the development of symptom management interventions based on the identification of core symptoms and symptom clusters within a network.
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Affiliation(s)
- Nikolaos Papachristou
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, UK.
| | - Payam Barnaghi
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, UK.
| | | | | | | | | | - Marilyn Hammer
- Department of Nursing, Mount Sinai Medical Center, New York, USA
| | - Fay Wright
- School of Nursing, Yale University, New Haven, USA
| | - Jo Armes
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, UK.,School of Health Sciences, University of Surrey, Guildford, UK
| | - Eileen P Furlong
- School of Nursing, Midwifery and Health Systems, University College Dublin, Dublin, Ireland
| | - Lisa McCann
- University of Strathclyde, Glasgow, Scotland
| | - Yvette P Conley
- School of Nursing, University of Pittsburgh, Pittsburgh, USA
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Wang RS, Oldham WM, Maron BA, Loscalzo J. Systems Biology Approaches to Redox Metabolism in Stress and Disease States. Antioxid Redox Signal 2018; 29:953-972. [PMID: 29121773 PMCID: PMC6104248 DOI: 10.1089/ars.2017.7256] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/12/2017] [Accepted: 11/04/2017] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE All cellular metabolic processes are tied to the cellular redox environment. Therefore, maintaining redox homeostasis is critically important for normal cell function. Indeed, redox stress contributes to the pathobiology of many human diseases. The cellular redox response system is composed of numerous interconnected components, including free radicals, redox couples, protein thiols, enzymes, metabolites, and transcription factors. Moreover, interactions between and among these factors are regulated in time and space. Owing to their complexity, systems biology approaches to the characterization of the cellular redox response system may provide insights into novel homeostatic mechanisms and methods of therapeutic reprogramming. Recent Advances: The emergence and development of systems biology has brought forth a set of innovative technologies that provide new avenues for studying redox metabolism. This article will review these systems biology approaches and their potential application to the study of redox metabolism in stress and disease states. CRITICAL ISSUES Clarifying the scope of biological intermediaries affected by dysregulated redox metabolism requires methods that are suitable for analyzing big datasets as classical methods that do not account for multiple interactions are unlikely to portray the totality of perturbed metabolic systems. FUTURE DIRECTIONS Given the diverse redox microenvironments within cells, it will be important to improve the spatial resolution of omic approaches. Futures studies on the integration of multiple systems-based methods and heterogeneous omics data for redox metabolism are required to accelerate the development of the field of redox systems biology. Antioxid. Redox Signal. 29, 953-972.
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Affiliation(s)
- Rui-Sheng Wang
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - William M. Oldham
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bradley A. Maron
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Section of Cardiology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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28
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Berlin R, Gruen R, Best J. Systems Medicine Disease: Disease Classification and Scalability Beyond Networks and Boundary Conditions. Front Bioeng Biotechnol 2018; 6:112. [PMID: 30131956 PMCID: PMC6090066 DOI: 10.3389/fbioe.2018.00112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/18/2018] [Indexed: 12/26/2022] Open
Abstract
In order to accommodate the forthcoming wealth of health and disease related information, from genome to body sensors to population and the environment, the approach to disease description and definition demands re-examination. Traditional classification methods remain trapped by history; to provide the descriptive features that are required for a comprehensive description of disease, systems science, which realizes dynamic processes, adaptive response, and asynchronous communication channels, must be applied (Wolkenhauer et al., 2013). When Disease is viewed beyond the thresholds of lines and threshold boundaries, disease definition is not only the result of reductionist, mechanistic categories which reluctantly face re-composition. Disease is process and synergy as the characteristics of Systems Biology and Systems Medicine are included. To capture the wealth of information and contribute meaningfully to medical practice and biology research, Disease classification goes beyond a single spatial biologic level or static time assignment to include the interface of Disease process and organism response (Bechtel, 2017a; Green et al., 2017).
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Affiliation(s)
- Richard Berlin
- Department of Computer Science, University of Illinois, Urbana, IL, United States
| | - Russell Gruen
- Department of Surgery, Nanyang Institute of Technology in Health and Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - James Best
- Lee Kong China School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College, London, United Kingdom
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29
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Kramer F, Just S, Zeller T. New perspectives: systems medicine in cardiovascular disease. BMC SYSTEMS BIOLOGY 2018; 12:57. [PMID: 29699591 PMCID: PMC5921396 DOI: 10.1186/s12918-018-0579-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/28/2018] [Indexed: 01/22/2023]
Abstract
Background Cardiovascular diseases (CVD) represent one of the most important causes of morbidity and mortality worldwide. Innovative approaches to increase the understanding of the underpinnings of CVD promise to enhance CVD risk assessment and might pave the way to tailored therapies. Within the last years, systems medicine has emerged as a novel tool to study the genetic, molecular and physiological interactions. Conclusion In this review, we provide an overview of the current molecular-experimental, epidemiological and bioinformatical tools applied in systems medicine in the cardiovascular field. We will discuss the status and challenges in implementing interdisciplinary systems medicine approaches in CVD.
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Affiliation(s)
- Frank Kramer
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee, 32, Göttingen, Germany
| | - Steffen Just
- Molecular Cardiology, Department of Medicine II, University of Ulm, Ulm, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany. .,German Center for Cardiovascular Research (DZHK e.V.), Partner Site Hamburg, Lübeck, Kiel, Hamburg, Germany.
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30
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Moerenhout T, Devisch I, Cornelis GC. E-health beyond technology: analyzing the paradigm shift that lies beneath. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2018; 21:31-41. [PMID: 28551772 DOI: 10.1007/s11019-017-9780-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Information and computer technology has come to play an increasingly important role in medicine, to the extent that e-health has been described as a disruptive innovation or revolution in healthcare. The attention is very much focused on the technology itself, and advances that have been made in genetics and biology. This leads to the question: What is changing in medicine today concerning e-health? To what degree could these changes be characterized as a 'revolution'? We will apply the work of Thomas Kuhn, Larry Laudan, Michel Foucault and other philosophers-which offers an alternative understanding of progress and revolution in medicine to the classic discovery-oriented approach-to our analysis. Nowadays, the long-standing curative or reactive paradigm in medicine is facing a crisis due to an aging population, a significant increase in chronic diseases and the development of more expensive diagnostic tools and therapies. This promotes the evolution towards a new paradigm with an emphasis on preventive medicine. E-health constitutes an essential part of this new paradigm that seeks to solve the challenges presented by an aging population, skyrocketing costs and so forth. Our approach changes the focus from the technology itself toward the underlying paradigm shift in medicine. We will discuss the relevance of this approach by applying it to the surge in digital self-tracking through health apps and wearables: the recognition of the underlying paradigm shift leads to a more comprehensive understanding of self-tracking than a solely discovery-oriented or technology-focused view can provide.
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Affiliation(s)
- Tania Moerenhout
- Department of Family Medicine and Primary Health Care, Research Unit Ethics, Autonomy and Responsibility in Health Care, University of Gent, De Pintelaan 185 - Building 6K3, 9000, Ghent, Belgium.
- Department of Philosophy and Moral Sciences, University of Gent, Blandijnberg 2, 9000, Ghent, Belgium.
- Visiting Researcher at the Center for Bioethics and Health Law, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Ignaas Devisch
- Department of Family Medicine and Primary Health Care, Research Unit Ethics, Autonomy and Responsibility in Health Care, University of Gent, De Pintelaan 185 - Building 6K3, 9000, Ghent, Belgium
| | - Gustaaf C Cornelis
- Department of Philosophy and Moral Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Ixelles, Belgium
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31
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Gosak M, Markovič R, Dolenšek J, Slak Rupnik M, Marhl M, Stožer A, Perc M. Network science of biological systems at different scales: A review. Phys Life Rev 2018; 24:118-135. [DOI: 10.1016/j.plrev.2017.11.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/13/2017] [Accepted: 10/15/2017] [Indexed: 12/20/2022]
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32
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Whole-Transcriptome Sequencing: a Powerful Tool for Vascular Tissue Engineering and Endothelial Mechanobiology. High Throughput 2018; 7:ht7010005. [PMID: 29485616 PMCID: PMC5876531 DOI: 10.3390/ht7010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/18/2018] [Accepted: 02/19/2018] [Indexed: 02/07/2023] Open
Abstract
Among applicable high-throughput techniques in cardiovascular biology, whole-transcriptome sequencing is of particular use. By utilizing RNA that is isolated from virtually all cells and tissues, the entire transcriptome can be evaluated. In comparison with other high-throughput approaches, RNA sequencing is characterized by a relatively low-cost and large data output, which permits a comprehensive analysis of spatiotemporal variation in the gene expression profile. Both shear stress and cyclic strain exert hemodynamic force upon the arterial endothelium and are considered to be crucial determinants of endothelial physiology. Laminar blood flow results in a high shear stress that promotes atheroresistant endothelial phenotype, while a turbulent, oscillatory flow yields a pathologically low shear stress that disturbs endothelial homeostasis, making respective arterial segments prone to atherosclerosis. Severe atherosclerosis significantly impairs blood supply to the organs and frequently requires bypass surgery or an arterial replacement surgery that requires tissue-engineered vascular grafts. To provide insight into patterns of gene expression in endothelial cells in native or bioartificial arteries under different biomechanical conditions, this article discusses applications of whole-transcriptome sequencing in endothelial mechanobiology and vascular tissue engineering.
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Abstract
No therapies have been shown to improve outcomes in patients with acute kidney injury (AKI). Given the high morbidity and mortality associated with AKI this represents an important unmet medical need. A common feature of all of the therapeutic development efforts for AKI is that none were driven by target selection or preclinical modeling that was based primarily on human data. This is important when considering a heterogeneous and dynamic condition such as AKI, in which in the absence of more accurate molecular classifications, clinical cohorts are likely to include patients with different types of injury at different stages in the injury and repair continuum. The National Institutes of Health precision medicine initiative offers an opportunity to address this. By creating a molecular tissue atlas of AKI, defining patient subgroups, and identifying critical cells and pathways involved in human AKI, this initiative has the potential to transform our current approach to therapeutic discovery. In this review, we discuss the opportunities and challenges that this initiative presents, with a specific focus on AKI, what additional efforts will be needed to apply these discoveries to therapeutic development, and how we believe this effort might lead to the development of new therapeutics for subsets of patients with AKI.
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Affiliation(s)
- Mark de Caestecker
- Nephrology Division, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - Raymond Harris
- Nephrology Division, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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34
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Austin ED, West J, Loyd JE, Hemnes AR. Translational Advances in the Field of Pulmonary Hypertension Molecular Medicine of Pulmonary Arterial Hypertension. From Population Genetics to Precision Medicine and Gene Editing. Am J Respir Crit Care Med 2017; 195:23-31. [PMID: 27398627 DOI: 10.1164/rccm.201605-0905pp] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
| | - James West
- 2 Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James E Loyd
- 2 Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anna R Hemnes
- 2 Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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35
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Maron BA, Abman SH. Translational Advances in the Field of Pulmonary Hypertension. Focusing on Developmental Origins and Disease Inception for the Prevention of Pulmonary Hypertension. Am J Respir Crit Care Med 2017; 195:292-301. [PMID: 27854133 DOI: 10.1164/rccm.201604-0882pp] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bradley A Maron
- 1 Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,2 Department of Cardiology, Boston VA Healthcare System, Boston, Massachusetts; and
| | - Steven H Abman
- 3 Section of Pulmonary Medicine and.,4 Pediatric Heart Lung Center, Department of Pediatrics, University of Colorado Denver Anschutz Medical Center and Children's Hospital Colorado, Aurora, Colorado
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36
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Finocchiaro G, Magavern E, Sinagra G, Ashley E, Papadakis M, Tome-Esteban M, Sharma S, Olivotto I. Impact of Demographic Features, Lifestyle, and Comorbidities on the Clinical Expression of Hypertrophic Cardiomyopathy. J Am Heart Assoc 2017; 6:JAHA.117.007161. [PMID: 29237589 PMCID: PMC5779031 DOI: 10.1161/jaha.117.007161] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Gherardo Finocchiaro
- Molecular and Clinical Sciences Research Institute Cardiology Clinical Academic Group, St George's, University of London, London, United Kingdom
| | - Emma Magavern
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, United Kingdom
| | | | | | - Michael Papadakis
- Molecular and Clinical Sciences Research Institute Cardiology Clinical Academic Group, St George's, University of London, London, United Kingdom
| | - Maite Tome-Esteban
- Molecular and Clinical Sciences Research Institute Cardiology Clinical Academic Group, St George's, University of London, London, United Kingdom
| | - Sanjay Sharma
- Molecular and Clinical Sciences Research Institute Cardiology Clinical Academic Group, St George's, University of London, London, United Kingdom
| | - Iacopo Olivotto
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
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37
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Abstract
OBJECTIVE The goals of this review are to provide background information on the definitions and applications of the general term "biomarker" and to highlight the specific roles of breast imaging biomarkers in research and clinical breast cancer care. A search was conducted of the main electronic biomedical databases (PubMed, Cochrane, Embase, MEDLINE [Ovid], Scopus, and Web of Science). The search was focused on review literature in general radiology and biomedical sciences and on reviews and primary research articles on biomarkers in breast imaging over the 15 years ending in June 2017. The keywords included "biomarker," "trial endpoints," "breast imaging," "breast cancer," "radiomics," and "precision medicine" in the titles and abstracts of the papers. CONCLUSION Clinical breast care and breast cancer-related research rely on imaging biomarkers for decision support. In the era of precision medicine and big data, the practice of radiology is likely to change. A closer integration of breast imaging with related biomedical fields and the creation of large integrated and shareable databases of clinical, molecular, and imaging biomarkers should allow the field to continue guiding breast cancer care and research.
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38
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Métris A, Sudhakar P, Fazekas D, Demeter A, Ari E, Olbei M, Branchu P, Kingsley RA, Baranyi J, Korcsmáros T. SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. NPJ Syst Biol Appl 2017; 3:31. [PMID: 29057095 PMCID: PMC5647365 DOI: 10.1038/s41540-017-0034-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/31/2022] Open
Abstract
Salmonella enterica is a prominent bacterial pathogen with implications on human and animal health. Salmonella serovars could be classified as gastro-intestinal or extra-intestinal. Genome-wide comparisons revealed that extra-intestinal strains are closer relatives of gastro-intestinal strains than to each other indicating a parallel evolution of this trait. Given the complexity of the differences, a systems-level comparison could reveal key mechanisms enabling extra-intestinal serovars to cause systemic infections. Accordingly, in this work, we introduce a unique resource, SalmoNet, which combines manual curation, high-throughput data and computational predictions to provide an integrated network for Salmonella at the metabolic, transcriptional regulatory and protein-protein interaction levels. SalmoNet provides the networks separately for five gastro-intestinal and five extra-intestinal strains. As a multi-layered, multi-strain database containing experimental data, SalmoNet is the first dedicated network resource for Salmonella. It comprehensively contains interactions between proteins encoded in Salmonella pathogenicity islands, as well as regulatory mechanisms of metabolic processes with the option to zoom-in and analyze the interactions at specific loci in more detail. Application of SalmoNet is not limited to strain comparisons as it also provides a Salmonella resource for biochemical network modeling, host-pathogen interaction studies, drug discovery, experimental validation of novel interactions, uncovering new pathological mechanisms from emergent properties and epidemiological studies. SalmoNet is available at http://salmonet.org.
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Affiliation(s)
- Aline Métris
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Present Address: Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire UK
| | - Padhmanand Sudhakar
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - David Fazekas
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK.,Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117 Budapest, Hungary
| | - Amanda Demeter
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK.,Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117 Budapest, Hungary
| | - Eszter Ari
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117 Budapest, Hungary.,Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Marton Olbei
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Rob A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK
| | - Jozsef Baranyi
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK
| | - Tamas Korcsmáros
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
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39
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(Re-)programming of subtype specific cardiomyocytes. Adv Drug Deliv Rev 2017; 120:142-167. [PMID: 28916499 DOI: 10.1016/j.addr.2017.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 01/10/2023]
Abstract
Adult cardiomyocytes (CMs) possess a highly restricted intrinsic regenerative potential - a major barrier to the effective treatment of a range of chronic degenerative cardiac disorders characterized by cellular loss and/or irreversible dysfunction and which underlies the majority of deaths in developed countries. Both stem cell programming and direct cell reprogramming hold promise as novel, potentially curative approaches to address this therapeutic challenge. The advent of induced pluripotent stem cells (iPSCs) has introduced a second pluripotent stem cell source besides embryonic stem cells (ESCs), enabling even autologous cardiomyocyte production. In addition, the recent achievement of directly reprogramming somatic cells into cardiomyocytes is likely to become of great importance. In either case, different clinical scenarios will require the generation of highly pure, specific cardiac cellular-subtypes. In this review, we discuss these themes as related to the cardiovascular stem cell and programming field, including a focus on the emergent topic of pacemaker cell generation for the development of biological pacemakers and in vitro drug testing.
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40
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Gomez-Cabrero D, Marabita F, Tarazona S, Cano I, Roca J, Conesa A, Sabatier P, Tegnér J. Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology. Cell Syst 2017; 5:168-175. [PMID: 28843483 DOI: 10.1016/j.cels.2017.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/21/2017] [Accepted: 05/31/2017] [Indexed: 12/15/2022]
Abstract
Systems medicine and systems biology have inherent educational challenges. These have largely been addressed either by providing new masters programs or by redesigning undergraduate programs. In contrast, short courses can respond to a different need: they can provide condensed updates for professionals across academia, the clinic, and industry. These courses have received less attention. Here, we share our experiences in developing and providing such courses to current and future leaders in systems biology and systems medicine. We present guidelines for how to reproduce our courses, and we offer suggestions for how to select students who will nurture an interdisciplinary learning environment and thrive there.
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Affiliation(s)
- David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, L8, 17176 Stockholm, Sweden; Science for Life Laboratory, 17121 Solna, Sweden; Mucosal and Salivary Biology Division, King's College London Dental Institute, London SE1 9RT, UK.
| | - Francesco Marabita
- Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, L8, 17176 Stockholm, Sweden; Science for Life Laboratory, 17121 Solna, Sweden
| | - Sonia Tarazona
- Centro de Investigacion Principe Felipe, 46012 Valencia, Spain; Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Camí de Vera, 46022 Valencia, Spain
| | - Isaac Cano
- Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08007 Barcelona, Spain; Center for Biomedical Network Research in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Josep Roca
- Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08007 Barcelona, Spain; Center for Biomedical Network Research in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Ana Conesa
- Centro de Investigacion Principe Felipe, 46012 Valencia, Spain; Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Philippe Sabatier
- TIMC-IMAG Laboratory, UMR 5525, Centre National de la Recherche Scientifique, Vetagro Sup, Université Grenoble-Alpes, 38400 Saint-Martin-d'Hères, France
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, L8, 17176 Stockholm, Sweden; Science for Life Laboratory, 17121 Solna, Sweden; Biological and Environmental Sciences and Engineering Division (BESE), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
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41
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Schäuble S, Stavrum AK, Bockwoldt M, Puntervoll P, Heiland I. SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. BMC Bioinformatics 2017. [PMID: 28646877 PMCID: PMC5483284 DOI: 10.1186/s12859-017-1722-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Background Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. Results We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models. Subsequent steady state analysis is readily accessible via the web service COPASIWS. We illustrate the utility of SBMLmod by integrating gene expression data from different healthy tissues as well as from a cancer dataset into a previously published model of mammalian tryptophan metabolism. Conclusion SBMLmod is a user-friendly platform for model modification and simulation. The web application is available at http://sbmlmod.uit.no, whereas the WSDL definition file for the web service is accessible via http://sbmlmod.uit.no/SBMLmod.wsdl. Furthermore, the entire package can be downloaded from https://github.com/MolecularBioinformatics/sbml-mod-ws. We envision that SBMLmod will make automated model modification and simulation available to a broader research community. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1722-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sascha Schäuble
- Jena University Language & Information Engineering (JULIE) Lab, Friedrich-Schiller-University Jena, Jena, Germany
| | | | - Mathias Bockwoldt
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Pål Puntervoll
- Centre for Applied Biotechnology, Uni Research Environment, Bergen, Norway
| | - Ines Heiland
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.
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42
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Wang RS, Hall KT, Giulianini F, Passow D, Kaptchuk TJ, Loscalzo J. Network analysis of the genomic basis of the placebo effect. JCI Insight 2017; 2:93911. [PMID: 28570268 DOI: 10.1172/jci.insight.93911] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/02/2017] [Indexed: 12/13/2022] Open
Abstract
The placebo effect is a phenomenon in which patients who are given an inactive treatment (e.g., inert pill) show a perceived or actual improvement in a medical condition. Placebo effects in clinical trials have been investigated for many years especially because placebo treatments often serve as the control arm of randomized clinical trial designs. Recent observations suggest that placebo effects may be modified by genetics. This observation has given rise to the term "placebome," which refers to a group of genome-related mediators that affect an individual's response to placebo treatments. In this study, we conduct a network analysis of the placebome and identify a placebome module in the comprehensive human interactome using a seed-connector algorithm. The placebome module is significantly enriched with neurotransmitter signaling pathways and brain-specific proteins. We validate the placebome module using a large cohort of the Women's Genome Health Study (WGHS) trial and demonstrate that the placebome module is significantly enriched with genes whose SNPs modify the outcome in the placebo arm of the trial. To gain insights into placebo effects in different diseases and drug treatments, we use a network proximity measure to examine the closeness of the placebome module to different disease modules and drug target modules. The results demonstrate that the network proximity of the placebome module to disease modules in the interactome significantly correlates with the strength of the placebo effect in the corresponding diseases. The proximity of the placebome module to molecular pathways affected by certain drug classes indicates the existence of placebo-drug interactions. This study is helpful for understanding the molecular mechanisms mediating the placebo response, and sets the stage for minimizing its effects in clinical trials and for developing therapeutic strategies that intentionally engage it.
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Affiliation(s)
| | - Kathryn T Hall
- Department of Medicine and.,Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Franco Giulianini
- Department of Medicine and.,Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Dani Passow
- Program in Placebo Studies, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Ted J Kaptchuk
- Program in Placebo Studies, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
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Gomez-Cabrero D, Tegnér J. Iterative Systems Biology for Medicine – Time for advancing from network signatures to mechanistic equations. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Contreras AV, Cocom-Chan B, Hernandez-Montes G, Portillo-Bobadilla T, Resendis-Antonio O. Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine. Front Physiol 2016; 7:606. [PMID: 28018236 PMCID: PMC5145879 DOI: 10.3389/fphys.2016.00606] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/21/2016] [Indexed: 12/19/2022] Open
Abstract
It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer. Although this latter disease has been thoroughly studied using different high-throughput (HT) technologies, its heterogeneous nature makes its understanding and proper treatment in patients a remaining challenge in clinical settings. Notably, given the outstanding role of host-microbiome interactions, the ecological interactions with microorganisms have become a new significant aspect in the systems that can contribute to the diagnosis and potential treatment of solid cancers. As a part of expanding precision medicine in the area of cancer research, efforts aimed at effective treatments for various kinds of cancer based on the knowledge of genetics, biology of the disease and host-microbiome interactions might improve the prediction of disease risk and implement potential microbiota-directed therapeutics. In this review, we present the state of the art of sequencing and metabolome technologies, computational methods and schemes in systems biology that have addressed recent breakthroughs of uncovering relationships or associations between microorganisms and cancer. Together, microbiome studies extend the horizon of new personalized treatments against cancer from the perspective of precision medicine through a synergistic strategy integrating clinical knowledge, HT data, bioinformatics, and systems biology.
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Affiliation(s)
| | - Benjamin Cocom-Chan
- Instituto Nacional de Medicina GenómicaMexico City, Mexico; Human Systems Biology Laboratory, Instituto Nacional de Medicina GenómicaMexico City, Mexico
| | - Georgina Hernandez-Montes
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM) Mexico City, Mexico
| | - Tobias Portillo-Bobadilla
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM) Mexico City, Mexico
| | - Osbaldo Resendis-Antonio
- Instituto Nacional de Medicina GenómicaMexico City, Mexico; Human Systems Biology Laboratory, Instituto Nacional de Medicina GenómicaMexico City, Mexico; Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM)Mexico City, Mexico
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45
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Vogt H, Hofmann B, Getz L. Personalized medicine: evidence of normativity in its quantitative definition of health. THEORETICAL MEDICINE AND BIOETHICS 2016; 37:401-16. [PMID: 27638683 PMCID: PMC5035650 DOI: 10.1007/s11017-016-9379-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Systems medicine, which is based on computational modelling of biological systems, is emerging as an increasingly prominent part of the personalized medicine movement. It is often promoted as 'P4 medicine' (predictive, preventive, personalized, and participatory). In this article, we test promises made by some of its proponents that systems medicine will be able to develop a scientific, quantitative metric for wellness that will eliminate the purported vagueness, ambiguity, and incompleteness-that is, normativity-of previous health definitions. We do so by examining the most concrete and relevant evidence for such a metric available: a patent that describes a systems medicine method for assessing health and disease. We find that although systems medicine is promoted as heralding an era of transformative scientific objectivity, its definition of health seems at present still normatively based. As such, we argue that it will be open to influence from various stakeholders and that its purported objectivity may conceal important scientific, philosophical, and political issues. We also argue that this is an example of a general trend within biomedicine to create overly hopeful visions and expectations for the future.
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Affiliation(s)
- Henrik Vogt
- General Practice Research Unit, Department of Public Health and General Practice, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Bjørn Hofmann
- Section for Health, Technology, and Society, Norwegian University of Science and Technology, Gjøvik, Norway
- Centre for Medical Ethics, University of Oslo, Oslo, Norway
| | - Linn Getz
- General Practice Research Unit, Department of Public Health and General Practice, Norwegian University of Science and Technology, Trondheim, Norway
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Abstract
The cardiovascular research and clinical communities are ideally positioned to address the epidemic of noncommunicable causes of death, as well as advance our understanding of human health and disease, through the development and implementation of precision medicine. New tools will be needed for describing the cardiovascular health status of individuals and populations, including 'omic' data, exposome and social determinants of health, the microbiome, behaviours and motivations, patient-generated data, and the array of data in electronic medical records. Cardiovascular specialists can build on their experience and use precision medicine to facilitate discovery science and improve the efficiency of clinical research, with the goal of providing more precise information to improve the health of individuals and populations. Overcoming the barriers to implementing precision medicine will require addressing a range of technical and sociopolitical issues. Health care under precision medicine will become a more integrated, dynamic system, in which patients are no longer a passive entity on whom measurements are made, but instead are central stakeholders who contribute data and participate actively in shared decision-making. Many traditionally defined diseases have common mechanisms; therefore, elimination of a siloed approach to medicine will ultimately pave the path to the creation of a universal precision medicine environment.
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Affiliation(s)
- Elliott M Antman
- Brigham and Women's Hospital, TIMI Study Group, 350 Longwood Avenue, Office Level One, Boston, Massachusetts 02115, USA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
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Vogt H, Hofmann B, Getz L. The new holism: P4 systems medicine and the medicalization of health and life itself. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2016; 19:307-23. [PMID: 26821201 PMCID: PMC4880637 DOI: 10.1007/s11019-016-9683-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The emerging concept of systems medicine (or 'P4 medicine'-predictive, preventive, personalized and participatory) is at the vanguard of the post-genomic movement towards 'precision medicine'. It is the medical application of systems biology, the biological study of wholes. Of particular interest, P4 systems medicine is currently promised as a revolutionary new biomedical approach that is holistic rather than reductionist. This article analyzes its concept of holism, both with regard to methods and conceptualization of health and disease. Rather than representing a medical holism associated with basic humanistic ideas, we find a technoscientific holism resulting from altered technological and theoretical circumstances in biology. We argue that this holism, which is aimed at disease prevention and health optimization, points towards an expanded form of medicalization, which we call 'holistic medicalization': Each person's whole life process is defined in biomedical, technoscientific terms as quantifiable and controllable and underlain a regime of medical control that is holistic in that it is all-encompassing. It is directed at all levels of functioning, from the molecular to the social, continual throughout life and aimed at managing the whole continuum from cure of disease to optimization of health. We argue that this medicalization is a very concrete materialization of a broader trend in medicine and society, which we call 'the medicalization of health and life itself'. We explicate this holistic medicalization, discuss potential harms and conclude by calling for preventive measures aimed at avoiding eventual harmful effects of overmedicalization in systems medicine (quaternary prevention).
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Affiliation(s)
- Henrik Vogt
- General Practice Research Unit, Department of Public Health and General Practice, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Bjørn Hofmann
- Section for Health, Technology, and Society, Norwegian University of Science end Technology, Gjøvik, Norway
- Centre for Medical Ethics, University of Oslo, Oslo, Norway
| | - Linn Getz
- General Practice Research Unit, Department of Public Health and General Practice, Norwegian University of Science and Technology, Trondheim, Norway
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48
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Sung YK, Yuan K, de Jesus Perez VA. Novel approaches to pulmonary arterial hypertension drug discovery. Expert Opin Drug Discov 2016; 11:407-14. [PMID: 26901465 PMCID: PMC4933595 DOI: 10.1517/17460441.2016.1153625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Pulmonary arterial hypertension (PAH) is a rare disorder associated with abnormally elevated pulmonary pressures that, if untreated, leads to right heart failure and premature death. The goal of drug development for PAH is to develop effective therapies that halt, or ideally, reverse the obliterative vasculopathy that results in vessel loss and obstruction of blood flow to the lungs. AREAS COVERED This review summarizes the current approach to candidate discovery in PAH and discusses the currently available drug discovery methods that should be implemented to prioritize targets and obtain a comprehensive pharmacological profile of promising compounds with well-defined mechanisms. EXPERT OPINION To improve the successful identification of leading drug candidates, it is necessary that traditional pre-clinical studies are combined with drug screening strategies that maximize the characterization of biological activity and identify relevant off-target effects that could hinder the clinical efficacy of the compound when tested in human subjects. A successful drug discovery strategy in PAH will require collaboration of clinician scientists with medicinal chemists and pharmacologists who can identify compounds with an adequate safety profile and biological activity against relevant disease mechanisms.
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Affiliation(s)
- Yon K. Sung
- Division of Pulmonary and Critical Care Medicine, The Vera Moulton Wall Center for Pulmonary Vascular Medicine, Stanford Cardiovascular Institute, Stanford, California
| | - Ke Yuan
- Division of Pulmonary and Critical Care Medicine, The Vera Moulton Wall Center for Pulmonary Vascular Medicine, Stanford Cardiovascular Institute, Stanford, California
| | - Vinicio A. de Jesus Perez
- Division of Pulmonary and Critical Care Medicine, The Vera Moulton Wall Center for Pulmonary Vascular Medicine, Stanford Cardiovascular Institute, Stanford, California
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Staiger H, Schaeffeler E, Schwab M, Häring HU. Pharmacogenetics: Implications for Modern Type 2 Diabetes Therapy. Rev Diabet Stud 2016; 12:363-76. [PMID: 27111121 DOI: 10.1900/rds.2015.12.363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Many clinical treatment studies have reported remarkable interindividual variability in the response to pharmaceutical drugs, and uncovered the existence of inadequate treatment response, non-response, and even adverse drug reactions. Pharmacogenetics addresses the impact of genetic variants on treatment outcome including side-effects. In recent years, it has also entered the field of clinical diabetes research. In modern type 2 diabetes therapy, metformin is established as first-line drug. The latest pharmaceutical developments, including incretin mimetics, dipeptidyl peptidase 4 inhibitors (gliptins), and sodium/glucose cotransporter 2 inhibitors (gliflozins), are currently experiencing a marked increase in clinical use, while the prescriptions of α-glucosidase inhibitors, sulfonylureas, meglitinides (glinides), and thiazolidinediones (glitazones) are declining, predominantly because of reported side-effects. This review summarizes the current knowledge about gene-drug interactions observed in therapy studies with the above drugs. We report drug interactions with candidate genes involved in the pharmacokinetics (e.g., drug transporters) and pharmacodynamics (drug targets and downstream signaling steps) of the drugs, with known type 2 diabetes risk genes and previously unknown genes derived from hypothesis-free approaches such as genome-wide association studies. Moreover, some new and promising candidate genes for future pharmacogenetic assessment are highlighted. Finally, we critically appraise the current state of type 2 diabetes pharmacogenetics in the light of its impact on therapeutic decisions, and we refer to major problems, and make suggestions for future efforts in this field to help improve the clinical relevance of the results, and to establish genetically determined treatment failure.
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Affiliation(s)
- Harald Staiger
- Interfaculty Centre for Pharmacogenomics and Pharma Research at the University of Tübingen, Tübingen, Germany
| | - Elke Schaeffeler
- Interfaculty Centre for Pharmacogenomics and Pharma Research at the University of Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Interfaculty Centre for Pharmacogenomics and Pharma Research at the University of Tübingen, Tübingen, Germany
| | - Hans-Ulrich Häring
- Interfaculty Centre for Pharmacogenomics and Pharma Research at the University of Tübingen, Tübingen, Germany
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50
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Soares MB. Collaborative research in light of the prevailing criteria for promotion and tenure in academia. Genomics 2015; 106:193-5. [PMID: 26232606 DOI: 10.1016/j.ygeno.2015.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 07/22/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Marcelo Bento Soares
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.
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