1
|
Osmanoglu Ö, Gupta SK, Almasi A, Yagci S, Srivastava M, Araujo GHM, Nagy Z, Balkenhol J, Dandekar T. Signaling network analysis reveals fostamatinib as a potential drug to control platelet hyperactivation during SARS-CoV-2 infection. Front Immunol 2023; 14:1285345. [PMID: 38187394 PMCID: PMC10768010 DOI: 10.3389/fimmu.2023.1285345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Pro-thrombotic events are one of the prevalent causes of intensive care unit (ICU) admissions among COVID-19 patients, although the signaling events in the stimulated platelets are still unclear. Methods We conducted a comparative analysis of platelet transcriptome data from healthy donors, ICU, and non-ICU COVID-19 patients to elucidate these mechanisms. To surpass previous analyses, we constructed models of involved networks and control cascades by integrating a global human signaling network with transcriptome data. We investigated the control of platelet hyperactivation and the specific proteins involved. Results Our study revealed that control of the platelet network in ICU patients is significantly higher than in non-ICU patients. Non-ICU patients require control over fewer proteins for managing platelet hyperactivity compared to ICU patients. Identification of indispensable proteins highlighted key subnetworks, that are targetable for system control in COVID-19-related platelet hyperactivity. We scrutinized FDA-approved drugs targeting indispensable proteins and identified fostamatinib as a potent candidate for preventing thrombosis in COVID-19 patients. Discussion Our findings shed light on how SARS-CoV-2 efficiently affects host platelets by targeting indispensable and critical proteins involved in the control of platelet activity. We evaluated several drugs for specific control of platelet hyperactivity in ICU patients suffering from platelet hyperactivation. The focus of our approach is repurposing existing drugs for optimal control over the signaling network responsible for platelet hyperactivity in COVID-19 patients. Our study offers specific pharmacological recommendations, with drug prioritization tailored to the distinct network states observed in each patient condition. Interactive networks and detailed results can be accessed at https://fostamatinib.bioinfo-wuerz.eu/.
Collapse
Affiliation(s)
- Özge Osmanoglu
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Shishir K. Gupta
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Anna Almasi
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Seray Yagci
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mugdha Srivastava
- Core Unit Systems Medicine, University of Wuerzburg, Wuerzburg, Germany
- Algorithmic Bioinformatics, Department of Computer Science, Heinrich Heine University, Düsseldorf, Germany
| | - Gabriel H. M. Araujo
- University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Zoltan Nagy
- University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Johannes Balkenhol
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- Chair of Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- European Molecular Biology Laboratory (EMBL) Heidelberg, BioComputing Unit, Heidelberg, Germany
| |
Collapse
|
2
|
Gupta SK, Osmanoglu Ö, Minocha R, Bandi SR, Bencurova E, Srivastava M, Dandekar T. Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information. Front Med (Lausanne) 2022; 9:1008527. [PMID: 36405591 PMCID: PMC9669072 DOI: 10.3389/fmed.2022.1008527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2023] Open
Abstract
Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial outbreaks in healthcare associated settings. It is known to cause infection in all age groups and exhibits multi-drug resistance with high potential for horizontal transmission. Because of this reason combined with limited therapeutic choices available, C. auris infection has been acknowledged as a potential risk for causing a future pandemic, and thus seeking a promising strategy for its treatment is imperative. Here, we combined evolutionary information with reverse vaccinology approach to identify novel epitopes for vaccine design that could elicit CD4+ T-cell responses against C. auris. To this end, we extensively scanned the family of proteins encoded by C. auris genome. In addition, a pathogen may acquire substitutions in epitopes over a period of time which could cause its escape from the immune response thus rendering the vaccine ineffective. To lower this possibility in our design, we eliminated all rapidly evolving genes of C. auris with positive selection. We further employed highly conserved regions of multiple C. auris strains and identified two immunogenic and antigenic T-cell epitopes that could generate the most effective immune response against C. auris. The antigenicity scores of our predicted vaccine candidates were calculated as 0.85 and 1.88 where 0.5 is the threshold for prediction of fungal antigenic sequences. Based on our results, we conclude that our vaccine candidates have the potential to be successfully employed for the treatment of C. auris infection. However, in vivo experiments are imperative to further demonstrate the efficacy of our design.
Collapse
Affiliation(s)
- Shishir K. Gupta
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Özge Osmanoglu
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Rashmi Minocha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sourish Reddy Bandi
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- BioComputing Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| |
Collapse
|
3
|
Breitenbach T, Englert N, Osmanoglu Ö, Rukoyatkina N, Wangorsch G, Heinze K, Friebe A, Butt E, Feil R, Dittrich M, Gambaryan S, Dandekar T. A modular systems biological modelling framework studies cyclic nucleotide signaling in platelets. J Theor Biol 2022; 550:111222. [PMID: 35843440 DOI: 10.1016/j.jtbi.2022.111222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND The cyclic nucleotides cAMP and cGMP inhibit platelet activation. Different platelet signaling modules work together. We develop here a modelling framework to integrate different signaling modules and apply it to platelets. RESULTS We introduce a novel standardized bilinear coupling mechanism allowing sub model debugging and standardization of coupling with optimal data driven modelling by methods from optimization. Besides cAMP signaling our model considers specific cGMP effects including external stimuli by drugs. Moreover, the output of the cGMP module serves as input for a modular model of VASP phosphorylation and for the activity of cAMP and cGMP pathways in platelets. Experimental data driven modeling allows us to design models with quantitative output. We use the condensed information about involved regulation and system responses for modeling drug effects and obtaining optimal experimental settings. Stepwise further validation of our model is given by direct experimental data. CONCLUSIONS We present a general framework for model integration using modules and their stimulus responses. We demonstrate it by a multi-modular model for platelet signaling focusing on cGMP and VASP phosphorylation. Moreover, this allows to estimate drug action on any of the inhibitory cyclic nucleotide pathways (cGMP, cAMP) and is supported by experimental data.
Collapse
Affiliation(s)
- Tim Breitenbach
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Nils Englert
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Department of Vegetative Physiology, University of Würzburg, Roentgenring 9, 97070 Würzburg, Germany
| | - Özge Osmanoglu
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Natalia Rukoyatkina
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
| | - Gaby Wangorsch
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Katrin Heinze
- Rudolf Virchow Zentrum, Universität Würzburg, Josef-Schneider-Str. 2, D15, 97080 Würzburg
| | - Andreas Friebe
- Department of Vegetative Physiology, University of Würzburg, Roentgenring 9, 97070 Würzburg, Germany
| | - Elke Butt
- Institute of Experimental Biomedicine II, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Robert Feil
- Interfakultäres Institut für Biochemie (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076 Tübingen, Germany
| | - Marcus Dittrich
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Department of Human Genetics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stepan Gambaryan
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; European Molecular Biology Laboratory (EMBL), Postfach 102209, 69012 Heidelberg, Germany.
| |
Collapse
|
4
|
Osmanoglu Ö, Khaled AlSeiari M, AlKhoori HA, Shams S, Bencurova E, Dandekar T, Naseem M. Topological Analysis of the Carbon-Concentrating CETCH Cycle and a Photorespiratory Bypass Reveals Boosted CO 2-Sequestration by Plants. Front Bioeng Biotechnol 2021; 9:708417. [PMID: 34790651 PMCID: PMC8591258 DOI: 10.3389/fbioe.2021.708417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/25/2021] [Indexed: 01/11/2023] Open
Abstract
Synthetically designed alternative photorespiratory pathways increase the biomass of tobacco and rice plants. Likewise, some in planta-tested synthetic carbon-concentrating cycles (CCCs) hold promise to increase plant biomass while diminishing atmospheric carbon dioxide burden. Taking these individual contributions into account, we hypothesize that the integration of bypasses and CCCs will further increase plant productivity. To test this in silico, we reconstructed a metabolic model by integrating photorespiration and photosynthesis with the synthetically designed alternative pathway 3 (AP3) enzymes and transporters. We calculated fluxes of the native plant system and those of AP3 combined with the inhibition of the glycolate/glycerate transporter by using the YANAsquare package. The activity values corresponding to each enzyme in photosynthesis, photorespiration, and for synthetically designed alternative pathways were estimated. Next, we modeled the effect of the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (CETCH), which is a set of natural and synthetically designed enzymes that fix CO₂ manifold more than the native Calvin-Benson-Bassham (CBB) cycle. We compared estimated fluxes across various pathways in the native model and under an introduced CETCH cycle. Moreover, we combined CETCH and AP3-w/plgg1RNAi, and calculated the fluxes. We anticipate higher carbon dioxide-harvesting potential in plants with an AP3 bypass and CETCH-AP3 combination. We discuss the in vivo implementation of these strategies for the improvement of C3 plants and in natural high carbon harvesters.
Collapse
Affiliation(s)
- Özge Osmanoglu
- Department of Bioinformatics, Functional Genomics and Systems Biology Group, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mariam Khaled AlSeiari
- College of Natural and Health Sciences, Department of Life and Environmental Sciences, Zayed University, Abu Dhabi, UAE
| | - Hasa Abduljaleel AlKhoori
- College of Natural and Health Sciences, Department of Life and Environmental Sciences, Zayed University, Abu Dhabi, UAE
| | - Shabana Shams
- Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Elena Bencurova
- Department of Bioinformatics, Functional Genomics and Systems Biology Group, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Functional Genomics and Systems Biology Group, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Muhammad Naseem
- Department of Bioinformatics, Functional Genomics and Systems Biology Group, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
- College of Natural and Health Sciences, Department of Life and Environmental Sciences, Zayed University, Abu Dhabi, UAE
| |
Collapse
|
5
|
Naseem M, Osmanoglu Ö, Dandekar T. Synthetic Rewiring of Plant CO 2 Sequestration Galvanizes Plant Biomass Production. Trends Biotechnol 2020; 38:354-359. [PMID: 31959363 DOI: 10.1016/j.tibtech.2019.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 11/23/2022]
Abstract
Synthetically designed alternative photorespiratory pathways in tobacco and rice plants have paved the way to enhanced plant biomass production. Likewise, some in vitro- and in vivo-tested carbon-concentrating cycles hold promise to increase plant biomass. We hypothesize a further increase in plant productivity if photorespiratory bypasses are integrated with carbon-concentrating cycles in plants.
Collapse
Affiliation(s)
- Muhammad Naseem
- College of Natural and Health Sciences, Department of Life and Environmental Sciences, Zayed University, Abu Dhabi, UAE.
| | - Özge Osmanoglu
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Thomas Dandekar
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany.
| |
Collapse
|
6
|
Gupta SK, Srivastava M, Osmanoglu Ö, Dandekar T. Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. Sci Rep 2020; 10:2334. [PMID: 32047225 PMCID: PMC7012867 DOI: 10.1038/s41598-020-59344-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 01/22/2020] [Indexed: 12/18/2022] Open
Abstract
Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6% of the entire C. floridanus proteome.
Collapse
Affiliation(s)
- Shishir K Gupta
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, D-97074, Würzburg, Germany.,Department of Microbiology, Biocenter, Am Hubland, D-97074, Würzburg, Germany
| | - Mugdha Srivastava
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, D-97074, Würzburg, Germany
| | - Özge Osmanoglu
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, D-97074, Würzburg, Germany
| | - Thomas Dandekar
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, D-97074, Würzburg, Germany. .,EMBL Heidelberg, BioComputing Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| |
Collapse
|