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Groß A, Kracher B, Kraus JM, Kühlwein SD, Pfister AS, Wiese S, Luckert K, Pötz O, Joos T, Van Daele D, De Raedt L, Kühl M, Kestler HA. Representing dynamic biological networks with multi-scale probabilistic models. Commun Biol 2019; 2:21. [PMID: 30675519 PMCID: PMC6336720 DOI: 10.1038/s42003-018-0268-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 12/07/2018] [Indexed: 12/26/2022] Open
Abstract
Dynamic models analyzing gene regulation and metabolism face challenges when adapted to modeling signal transduction networks. During signal transduction, molecular reactions and mechanisms occur in different spatial and temporal frames and involve feedbacks. This impedes the straight-forward use of methods based on Boolean networks, Bayesian approaches, and differential equations. We propose a new approach, ProbRules, that combines probabilities and logical rules to represent the dynamics of a system across multiple scales. We demonstrate that ProbRules models can represent various network motifs of biological systems. As an example of a comprehensive model of signal transduction, we provide a Wnt network that shows remarkable robustness under a range of phenotypical and pathological conditions. Its simulation allows the clarification of controversially discussed molecular mechanisms of Wnt signaling by predicting wet-lab measurements. ProbRules provides an avenue in current computational modeling by enabling systems biologists to integrate vast amounts of available data on different scales.
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Affiliation(s)
- Alexander Groß
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Barbara Kracher
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Silke D. Kühlwein
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Astrid S. Pfister
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Katrin Luckert
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Oliver Pötz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Thomas Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Dries Van Daele
- Department of Computer Science, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Luc De Raedt
- Department of Computer Science, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
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Yang L, Yu Y, Ma C, Wang H, Dai J, Duan H, Fu Z, Wu P, Wang D, Yu X. Development of RBC Membrane Antigen Arrays for Validating Blood Grouping Reagents. J Proteome Res 2018; 17:3237-3245. [PMID: 30114910 DOI: 10.1021/acs.jproteome.8b00370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibody reagents have been remained as a standard approach to characterize blood group (BG) antigens in clinic. The specificity and cross-reactivity of these BG antibodies are routine detected using the gel microcolumn assay (GMA). However, the GMA is neither specific nor sensitive, thus increasing the risk of improperly matched RBC transfusions. In this work, we describe a bead-based RBC membrane antigen array to detect BG antibody-antigen binding with ∼700-fold higher sensitivity and dynamic range than the GMA. RBC membrane antigen arrays were fabricated using fragmented RBC membranes highly enriched in BG panel antigens. The arrays were then used to screen the interactions of 15 BG reagents to three antigen panels. The majority of the antibody reactions (i.e., 86.7%; 39/45) aligned with those obtained with the GMA. The six cross-reactive, nonspecific antibody reactions identified only by our arrays (i.e., 13.3%; 6/45) were confirmed by agglutination inhibition and genotyping assays. These results demonstrate that our RBC membrane antigen array has great potential in screening BG antibodies and improving the safety of RBC transfusions.
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Affiliation(s)
- Lu Yang
- Department of Blood Transfusion , Chinese PLA General Hospital , Beijing , 100853 , China
| | - Yang Yu
- Department of Blood Transfusion , Chinese PLA General Hospital , Beijing , 100853 , China
| | - Chunya Ma
- Department of Blood Transfusion , Chinese PLA General Hospital , Beijing , 100853 , China
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Jiayu Dai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Hu Duan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Zhonglin Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Ping Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Deqing Wang
- Department of Blood Transfusion , Chinese PLA General Hospital , Beijing , 100853 , China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
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