1
|
Chee FT, Harun S, Mohd Daud K, Sulaiman S, Nor Muhammad NA. Exploring gene regulation and biological processes in insects: Insights from omics data using gene regulatory network models. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 189:1-12. [PMID: 38604435 DOI: 10.1016/j.pbiomolbio.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/18/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Gene regulatory network (GRN) comprises complicated yet intertwined gene-regulator relationships. Understanding the GRN dynamics will unravel the complexity behind the observed gene expressions. Insect gene regulation is often complicated due to their complex life cycles and diverse ecological adaptations. The main interest of this review is to have an update on the current mathematical modelling methods of GRNs to explain insect science. Several popular GRN architecture models are discussed, together with examples of applications in insect science. In the last part of this review, each model is compared from different aspects, including network scalability, computation complexity, robustness to noise and biological relevancy.
Collapse
Affiliation(s)
- Fong Ting Chee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Sarahani Harun
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Kauthar Mohd Daud
- Faculty of Information Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Suhaila Sulaiman
- FGV R&D Sdn Bhd, FGV Innovation Center, PT23417 Lengkuk Teknologi, Bandar Baru Enstek, 71760 Nilai, Negeri Sembilan, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| |
Collapse
|
2
|
Manser CL, Perez-Carrasco R. A mathematical framework for measuring and tuning tempo in developmental gene regulatory networks. Development 2024; 151:dev202950. [PMID: 38780527 PMCID: PMC11234385 DOI: 10.1242/dev.202950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Embryo development is a dynamic process governed by the regulation of timing and sequences of gene expression, which control the proper growth of the organism. Although many genetic programmes coordinating these sequences are common across species, the timescales of gene expression can vary significantly among different organisms. Currently, substantial experimental efforts are focused on identifying molecular mechanisms that control these temporal aspects. In contrast, the capacity of established mathematical models to incorporate tempo control while maintaining the same dynamical landscape remains less understood. Here, we address this gap by developing a mathematical framework that links the functionality of developmental programmes to the corresponding gene expression orbits (or landscapes). This unlocks the ability to find tempo differences as perturbations in the dynamical system that preserve its orbits. We demonstrate that this framework allows for the prediction of molecular mechanisms governing tempo, through both numerical and analytical methods. Our exploration includes two case studies: a generic network featuring coupled production and degradation, with a particular application to neural progenitor differentiation; and the repressilator. In the latter, we illustrate how altering the dimerisation rates of transcription factors can decouple the tempo from the shape of the resulting orbits. We conclude by highlighting how the identification of orthogonal molecular mechanisms for tempo control can inform the design of circuits with specific orbits and tempos.
Collapse
Affiliation(s)
- Charlotte L. Manser
- Department of Life Sciences, Imperial College London, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Ruben Perez-Carrasco
- Department of Life Sciences, Imperial College London, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
3
|
Rafelski SM, Theriot JA. Establishing a conceptual framework for holistic cell states and state transitions. Cell 2024; 187:2633-2651. [PMID: 38788687 DOI: 10.1016/j.cell.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Cell states were traditionally defined by how they looked, where they were located, and what functions they performed. In this post-genomic era, the field is largely focused on a molecular view of cell state. Moving forward, we anticipate that the observables used to define cell states will evolve again as single-cell imaging and analytics are advancing at a breakneck pace via the collection of large-scale, systematic cell image datasets and the application of quantitative image-based data science methods. This is, therefore, a key moment in the arc of cell biological research to develop approaches that integrate the spatiotemporal observables of the physical structure and organization of the cell with molecular observables toward the concept of a holistic cell state. In this perspective, we propose a conceptual framework for holistic cell states and state transitions that is data-driven, practical, and useful to enable integrative analyses and modeling across many data types.
Collapse
Affiliation(s)
- Susanne M Rafelski
- Allen Institute for Cell Science, 615 Westlake Avenue N, Seattle, WA 98125, USA.
| | - Julie A Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
4
|
Uchida Y, Tsutsumi M, Ichii S, Irie N, Furusawa C. Deciphering the origin of developmental stability: The role of intracellular expression variability in evolutionary conservation. Evol Dev 2024; 26:e12473. [PMID: 38414112 DOI: 10.1111/ede.12473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 02/29/2024]
Abstract
Progress in evolutionary developmental biology (evo-devo) has deepened our understanding of how intrinsic properties of embryogenesis, along with natural selection and population genetics, shape phenotypic diversity. A focal point of recent empirical and theoretical research is the idea that highly developmentally stable phenotypes are more conserved in evolution. Previously, we demonstrated that in Japanese medaka (Oryzias latipes), embryonic stages and genes with high stability, estimated through whole-embryo RNA-seq, are highly conserved in subsequent generations. However, the precise origin of the stability of gene expression levels evaluated at the whole-embryo level remained unclear. Such stability could be attributed to two distinct sources: stable intracellular expression levels or spatially stable expression patterns. Here we demonstrate that stability observed in whole-embryo RNA-seq can be attributed to stability at the cellular level (low variability in gene expression at the cellular levels). We quantified the intercellular variations in expression levels and spatial gene expression patterns for seven key genes involved in patterning dorsoventral and rostrocaudal regions during early development in medaka. We evaluated intracellular variability by counting transcripts and found its significant correlation with variation observed in whole-embryo RNA-seq data. Conversely, variation in spatial gene expression patterns, assessed through intraindividual left-right asymmetry, showed no correlation. Given the previously reported correlation between stability and conservation of expression levels throughout embryogenesis, our findings suggest a potential general trend: the stability or instability of developmental systems-and the consequent evolutionary diversity-may be primarily anchored in intrinsic fundamental elements such as the variability of intracellular states.
Collapse
Affiliation(s)
- Yui Uchida
- Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
| | - Masato Tsutsumi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Shunsuke Ichii
- Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoki Irie
- Research Center for Integrative Evolutionary Science, SOKENDAI, Kanagawa, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
5
|
Nadolski EM, Moczek AP. Promises and limits of an agency perspective in evolutionary developmental biology. Evol Dev 2023; 25:371-392. [PMID: 37038309 DOI: 10.1111/ede.12432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/23/2023] [Accepted: 03/02/2023] [Indexed: 04/12/2023]
Abstract
An agent-based perspective in the study of complex systems is well established in diverse disciplines, yet is only beginning to be applied to evolutionary developmental biology. In this essay, we begin by defining agency and associated terminology formally. We then explore the assumptions and predictions of an agency perspective, apply these to select processes and key concept areas relevant to practitioners of evolutionary developmental biology, and consider the potential epistemic roles that an agency perspective might play in evo devo. Throughout, we discuss evidence supportive of agential dynamics in biological systems relevant to evo devo and explore where agency thinking may enrich the explanatory reach of research efforts in evolutionary developmental biology.
Collapse
Affiliation(s)
- Erica M Nadolski
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| |
Collapse
|
6
|
Kumar N, Mukhtar MS. Integrated Systems Biology Pipeline to Compare Co-Expression Networks in Plants and Elucidate Differential Regulators. PLANTS (BASEL, SWITZERLAND) 2023; 12:3618. [PMID: 37896081 PMCID: PMC10610404 DOI: 10.3390/plants12203618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
To identify sets of genes that exhibit similar expression characteristics, co-expression networks were constructed from transcriptome datasets that were obtained from plant samples at various stages of growth and development or treated with diverse biotic, abiotic, and other environmental stresses. In addition, co-expression network analysis can provide deeper insights into gene regulation when combined with transcriptomics. The coordination and integration of all these complex networks to deduce gene regulation are major challenges for plant biologists. Python and R have emerged as major tools for managing complex scientific data over the past decade. In this study, we describe a reproducible protocol POTFUL (pant co-expression transcription factor regulators), implemented in Python 3, for integrating co-expression and transcription factor target protein networks to infer gene regulation.
Collapse
Affiliation(s)
| | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
7
|
Kravtsova N, Chamberlin HM, Dawes AT. Efficient parameter generation for constrained models using MCMC. Sci Rep 2023; 13:16285. [PMID: 37770498 PMCID: PMC10539337 DOI: 10.1038/s41598-023-43433-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/23/2023] [Indexed: 09/30/2023] Open
Abstract
Mathematical models of complex systems rely on parameter values to produce a desired behavior. As mathematical and computational models increase in complexity, it becomes correspondingly difficult to find parameter values that satisfy system constraints. We propose a Markov Chain Monte Carlo (MCMC) approach for the problem of constrained model parameter generation by designing a Markov chain that efficiently explores a model's parameter space. We demonstrate the use of our proposed methodology to analyze responses of a newly constructed bistability-constrained model of protein phosphorylation to perturbations in the underlying protein network. Our results suggest that parameter generation for constrained models using MCMC provides powerful tools for modeling-aided analysis of complex natural processes.
Collapse
Affiliation(s)
- Natalia Kravtsova
- Department of Mathematics, The Ohio State University, Columbus, OH, USA
| | - Helen M Chamberlin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Adriana T Dawes
- Department of Mathematics, The Ohio State University, Columbus, OH, USA.
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
8
|
Zhao J, Perkins ML, Norstad M, Garcia HG. A bistable autoregulatory module in the developing embryo commits cells to binary expression fates. Curr Biol 2023; 33:2851-2864.e11. [PMID: 37453424 PMCID: PMC10428078 DOI: 10.1016/j.cub.2023.06.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/13/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Bistable autoactivation has been proposed as a mechanism for cells to adopt binary fates during embryonic development. However, it is unclear whether the autoactivating modules found within developmental gene regulatory networks are bistable, unless their parameters are quantitatively determined. Here, we combine in vivo live imaging with mathematical modeling to dissect the binary cell fate dynamics of the fruit fly pair-rule gene fushi tarazu (ftz), which is regulated by two known enhancers: the early (non-autoregulating) element and the autoregulatory element. Live imaging of transcription and protein concentration in the blastoderm revealed that binary Ftz fates are achieved as Ftz expression rapidly transitions from being dictated by the early element to the autoregulatory element. Moreover, we discovered that Ftz concentration alone is insufficient to activate the autoregulatory element, and that this element only becomes responsive to Ftz at a prescribed developmental time. Based on these observations, we developed a dynamical systems model and quantitated its kinetic parameters directly from experimental measurements. Our model demonstrated that the ftz autoregulatory module is indeed bistable and that the early element transiently establishes the content of the binary cell fate decision to which the autoregulatory module then commits. Further in silico analysis revealed that the autoregulatory element locks the Ftz fate quickly, within 35 min of exposure to the transient signal of the early element. Overall, our work confirms the widely held hypothesis that autoregulation can establish developmental fates through bistability and, most importantly, provides a framework for the quantitative dissection of cellular decision-making.
Collapse
Affiliation(s)
- Jiaxi Zhao
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mindy Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Matthew Norstad
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hernan G Garcia
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA; Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
9
|
Hari K, Duncan W, Ibrahim MA, Jolly MK, Cummins B, Gedeon T. Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space. NPJ Syst Biol Appl 2023; 9:29. [PMID: 37400474 DOI: 10.1038/s41540-023-00289-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
Mathematical modeling of the emergent dynamics of gene regulatory networks (GRN) faces a double challenge of (a) dependence of model dynamics on parameters, and (b) lack of reliable experimentally determined parameters. In this paper we compare two complementary approaches for describing GRN dynamics across unknown parameters: (1) parameter sampling and resulting ensemble statistics used by RACIPE (RAndom CIrcuit PErturbation), and (2) use of rigorous analysis of combinatorial approximation of the ODE models by DSGRN (Dynamic Signatures Generated by Regulatory Networks). We find a very good agreement between RACIPE simulation and DSGRN predictions for four different 2- and 3-node networks typically observed in cellular decision making. This observation is remarkable since the DSGRN approach assumes that the Hill coefficients of the models are very high while RACIPE assumes the values in the range 1-6. Thus DSGRN parameter domains, explicitly defined by inequalities between systems parameters, are highly predictive of ODE model dynamics within a biologically reasonable range of parameters.
Collapse
Affiliation(s)
- Kishore Hari
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - William Duncan
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Mohammed Adil Ibrahim
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, 502285, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
| | - Breschine Cummins
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717, USA.
| | - Tomas Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717, USA.
| |
Collapse
|
10
|
Mendes P. Reproducibility and FAIR principles: the case of a segment polarity network model. Front Cell Dev Biol 2023; 11:1201673. [PMID: 37346177 PMCID: PMC10279958 DOI: 10.3389/fcell.2023.1201673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023] Open
Abstract
The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. I analyze a computational model of the segment polarity network in Drosophila embryos published in 2000. Despite the high number of citations to this publication, 23 years later the model is barely accessible, and consequently not interoperable. Following the text of the original publication allowed successfully encoding the model for the open source software COPASI. Subsequently saving the model in the SBML format allowed it to be reused in other open source software packages. Submission of this SBML encoding of the model to the BioModels database enables its findability and accessibility. This demonstrates how the FAIR principles can be successfully enabled by using open source software, widely adopted standards, and public repositories, facilitating reproducibility and reuse of computational cell biology models that will outlive the specific software used.
Collapse
Affiliation(s)
- Pedro Mendes
- Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Cell Biology, University of Connecticut School of Medicine, Farmington, CT, United States
| |
Collapse
|
11
|
Sreedharan V, Bhalla US, Ramakrishnan N. Using sensitivity analyses to understand bistable system behavior. BMC Bioinformatics 2023; 24:136. [PMID: 37024783 PMCID: PMC10080961 DOI: 10.1186/s12859-023-05206-2] [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: 12/12/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Bistable systems, i.e., systems that exhibit two stable steady states, are of particular interest in biology. They can implement binary cellular decision making, e.g., in pathways for cellular differentiation and cell cycle regulation. The onset of cancer, prion diseases, and neurodegenerative diseases are known to be associated with malfunctioning bistable systems. Exploring and characterizing parameter spaces in bistable systems, so that they retain or lose bistability, is part of a lot of therapeutic research such as cancer pharmacology. RESULTS We use eigenvalue sensitivity analysis and stable state separation sensitivity analysis to understand bistable system behaviors, and to characterize the most sensitive parameters of a bistable system. While eigenvalue sensitivity analysis is an established technique in engineering disciplines, it has not been frequently used to study biological systems. We demonstrate the utility of these approaches on a published bistable system. We also illustrate scalability and generalizability of these methods to larger bistable systems. CONCLUSIONS Eigenvalue sensitivity analysis and separation sensitivity analysis prove to be promising tools to define parameter design rules to make switching decisions between either stable steady state of a bistable system and a corresponding monostable state after bifurcation. These rules were applied to the smallest two-component bistable system and results were validated analytically. We showed that with multiple parameter settings of the same bistable system, we can design switching to a desirable state to retain or lose bistability when the most sensitive parameter is varied according to our parameter perturbation recommendations. We propose eigenvalue and stable state separation sensitivity analyses as a framework to evaluate large and complex bistable systems.
Collapse
Affiliation(s)
- Vandana Sreedharan
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Upinder S Bhalla
- National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore, 560065, India
| | - Naren Ramakrishnan
- Department of Computer Science, Virginia Tech, Arlington, VA, 22203, USA
| |
Collapse
|
12
|
Uchida Y, Takeda H, Furusawa C, Irie N. Stability in gene expression and body-plan development leads to evolutionary conservation. EvoDevo 2023; 14:4. [PMID: 36918942 PMCID: PMC10015717 DOI: 10.1186/s13227-023-00208-w] [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: 11/06/2022] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Phenotypic evolution is mainly explained by selection for phenotypic variation arising from factors including mutation and environmental noise. Recent theoretical and experimental studies have suggested that phenotypes with greater developmental stability tend to have a constant phenotype and gene expression level within a particular genetic and environmental condition, and this positively correlates with stronger evolutionary conservation, even after the accumulation of genetic changes. This could reflect a novel mechanism that contributes to evolutionary conservation; however, it remains unclear whether developmental stability is the cause, or whether at least it contributes to their evolutionary conservation. Here, using Japanese medaka lines, we tested experimentally whether developmental stages and gene expression levels with greater stability led to their evolutionary conservation. RESULTS We first measured the stability of each gene expression level and developmental stage (defined here as the whole embryonic transcriptome) in the inbred F0 medaka population. We then measured their evolutionary conservation in the F3 generation by crossing the F0 line with the distantly related Japanese medaka line (Teradomori), followed by two rounds of intra-generational crossings. The results indicated that the genes and developmental stages that had smaller variations in the F0 generation showed lower diversity in the hybrid F3 generation, which implies a causal relationship between stability and evolutionary conservation. CONCLUSIONS These findings suggest that the stability in phenotypes, including the developmental stages and gene expression levels, leads to their evolutionary conservation; this most likely occurs due to their low potential to generate phenotypic variation. In addition, since the highly stable developmental stages match with the body-plan-establishment stage, it also implies that the developmental stability potentially contributed to the strict conservation of animal body plan.
Collapse
Affiliation(s)
- Yui Uchida
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.,Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan. .,Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
13
|
Fajiculay E, Hsu CP. Localization of Noise in Biochemical Networks. ACS OMEGA 2023; 8:3043-3056. [PMID: 36713703 PMCID: PMC9878546 DOI: 10.1021/acsomega.2c06113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
Noise, or uncertainty in biochemical networks, has become an important aspect of many biological problems. Noise can arise and propagate from external factors and probabilistic chemical reactions occurring in small cellular compartments. For species survival, it is important to regulate such uncertainties in executing vital cell functions. Regulated noise can improve adaptability, whereas uncontrolled noise can cause diseases. Simulation can provide a detailed analysis of uncertainties, but parameters such as rate constants and initial conditions are usually unknown. A general understanding of noise dynamics from the perspective of network structure is highly desirable. In this study, we extended the previously developed law of localization for characterizing noise in terms of (co)variances and developed noise localization theory. With linear noise approximation, we can expand a biochemical network into an extended set of differential equations representing a fictitious network for pseudo-components consisting of variances and covariances, together with chemical species. Through localization analysis, perturbation responses at the steady state of pseudo-components can be summarized into a sensitivity matrix that only requires knowledge of network topology. Our work allows identification of buffering structures at the level of species, variances, and covariances and can provide insights into noise flow under non-steady-state conditions in the form of a pseudo-chemical reaction. We tested noise localization in various systems, and here we discuss its implications and potential applications. Results show that this theory is potentially applicable in discriminating models, scanning network topologies with interesting noise behavior, and designing and perturbing networks with the desired response.
Collapse
Affiliation(s)
- Erickson Fajiculay
- Institute
of Chemistry, Academia Sinica, Taipei115201, Taiwan
- Bioinformatics
Program, Institute of Information Science, Taiwan International Graduate
Program, Academia Sinica, Taipei115201, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Chao-Ping Hsu
- Institute
of Chemistry, Academia Sinica, Taipei115201, Taiwan
- Bioinformatics
Program, Institute of Information Science, Taiwan International Graduate
Program, Academia Sinica, Taipei115201, Taiwan
- Physics
Division, National Center for Theoretical
Sciences, Taipei106319, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University, Taipei106319, Taiwan
| |
Collapse
|
14
|
Posadas-García YS, Espinosa-Soto C. Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks. BMC Bioinformatics 2022; 23:509. [DOI: 10.1186/s12859-022-05067-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
Background
Research on gene duplication is abundant and comes from a wide range of approaches, from high-throughput analyses and experimental evolution to bioinformatics and theoretical models. Notwithstanding, a consensus is still lacking regarding evolutionary mechanisms involved in evolution through gene duplication as well as the conditions that affect them. We argue that a better understanding of evolution through gene duplication requires considering explicitly that genes do not act in isolation. It demands studying how the perturbation that gene duplication implies percolates through the web of gene interactions. Due to evolution’s contingent nature, the paths that lead to the final fate of duplicates must depend strongly on the early stages of gene duplication, before gene copies have accumulated distinctive changes.
Methods
Here we use a widely-known model of gene regulatory networks to study how gene duplication affects network behavior in early stages. Such networks comprise sets of genes that cross-regulate. They organize gene activity creating the gene expression patterns that give cells their phenotypic properties. We focus on how duplication affects two evolutionarily relevant properties of gene regulatory networks: mitigation of the effect of new mutations and access to new phenotypic variants through mutation.
Results
Among other observations, we find that those networks that are better at maintaining the original phenotype after duplication are usually also better at buffering the effect of single interaction mutations and that duplication tends to enhance further this ability. Moreover, the effect of mutations after duplication depends on both the kind of mutation and genes involved in it. We also found that those phenotypes that had easier access through mutation before duplication had higher chances of remaining accessible through new mutations after duplication.
Conclusion
Our results support that gene duplication often mitigates the impact of new mutations and that this effect is not merely due to changes in the number of genes. The work that we put forward helps to identify conditions under which gene duplication may enhance evolvability and robustness to mutations.
Collapse
|
15
|
Hebbar A, Moger A, Hari K, Jolly MK. Robustness in phenotypic plasticity and heterogeneity patterns enabled by EMT networks. Biophys J 2022; 121:3600-3615. [PMID: 35859419 PMCID: PMC9617164 DOI: 10.1016/j.bpj.2022.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022] Open
Abstract
Epithelial-mesenchymal plasticity (EMP) is a key arm of cancer metastasis and is observed across many contexts. Cells undergoing EMP can reversibly switch between three classes of phenotypes: epithelial (E), mesenchymal (M), and hybrid E/M. While a large number of multistable regulatory networks have been identified to be driving EMP in various contexts, the exact mechanisms and design principles that enable robustness in driving EMP across contexts are not yet fully understood. Here, we investigated dynamic and structural robustness in EMP networks with regard to phenotypic heterogeneity and plasticity. We use two different approaches to simulate these networks: a computationally inexpensive, parameter-independent continuous state space Boolean model, and an ODE-based parameter-agnostic framework (RACIPE), both of which yielded similar phenotypic distributions. While the latter approach is useful for measurements of plasticity, the former model enabled us to extensively investigate robustness in phenotypic heterogeneity. Using perturbations to network topology and by varying network parameters, we show that multistable EMP networks are structurally and dynamically more robust compared with their randomized counterparts, thereby highlighting their topological hallmarks. These features of robustness are governed by a balance of positive and negative feedback loops embedded in these networks. Using a combination of the number of negative and positive feedback loops weighted by their lengths, we identified a metric that can explain the structural and dynamical robustness of these networks. This metric enabled us to compare networks across multiple sizes, and the network principles thus obtained can be used to identify fragilities in large networks without simulating their dynamics. Our analysis highlights a network topology-based approach to quantify robustness in the phenotypic heterogeneity and plasticity emergent from EMP networks.
Collapse
Affiliation(s)
- Anish Hebbar
- Undergraduate Programme, Indian Institute of Science, Bengaluru, India
| | - Ankush Moger
- Undergraduate Programme, Indian Institute of Science, Bengaluru, India
| | - Kishore Hari
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
| |
Collapse
|
16
|
Rozum J, Albert R. Leveraging network structure in nonlinear control. NPJ Syst Biol Appl 2022; 8:36. [PMID: 36182954 PMCID: PMC9526710 DOI: 10.1038/s41540-022-00249-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Over the last twenty years, dynamic modeling of biomolecular networks has exploded in popularity. Many of the classical tools for understanding dynamical systems are unwieldy in the highly nonlinear, poorly constrained, high-dimensional systems that often arise from these modeling efforts. Understanding complex biological systems is greatly facilitated by purpose-built methods that leverage common features of such models, such as local monotonicity, interaction graph sparsity, and sigmoidal kinetics. Here, we review methods for controlling the systems of ordinary differential equations used to model biomolecular networks. We focus on methods that make use of the structure of the network of interactions to help inform, which variables to target for control, and highlight the computational and experimental advantages of such approaches. We also discuss the importance of nonperturbative methods in biomedical and experimental molecular biology applications, where finely tuned interventions can be difficult to implement. It is well known that feedback loops, and positive feedback loops in particular, play a major determining role in the dynamics of biomolecular networks. In many of the methods we cover here, control over system trajectories is realized by overriding the behavior of key feedback loops.
Collapse
Affiliation(s)
- Jordan Rozum
- Department of Physics, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Réka Albert
- Department of Physics, Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
17
|
Shan D, Ali M, Shahid M, Arif A, Waheed MQ, Xia X, Trethowan R, Tester M, Poland J, Ogbonnaya FC, Rasheed A, He Z, Li H. Genetic networks underlying salinity tolerance in wheat uncovered with genome-wide analyses and selective sweeps. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2925-2941. [PMID: 35915266 DOI: 10.1007/s00122-022-04153-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r2) ranged between 0.57 and 0.74. The r2 values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4 Mb on chromosome (chr)1B, 7.1 Mb on chr2A, 11.2 Mb on chr2D, 200 Mb on chr3D, 600 Mb on chr6B, and 700.9 Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575 Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat.
Collapse
Affiliation(s)
- Danting Shan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China
| | - Mohsin Ali
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China
| | - Mohammed Shahid
- International Center for Biosaline Agriculture (ICBA), Al Ruwayyah 2, Academic City, Dubai, UAE
| | - Anjuman Arif
- National Institute of Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | | | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Richard Trethowan
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006, Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KASUT), Thuwal, 23955-6900, Saudi Arabia
| | - Jesse Poland
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KASUT), Thuwal, 23955-6900, Saudi Arabia
- Kansas State University, Manhattan, KS, USA
| | | | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China.
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China.
| |
Collapse
|
18
|
Thermodynamic Modelling of Transcriptional Control: A Sensitivity Analysis. MATHEMATICS 2022. [DOI: 10.3390/math10132169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Modelling is a tool used to decipher the biochemical mechanisms involved in transcriptional control. Experimental evidence in genetics is usually supported by theoretical models in order to evaluate the effects of all the possible interactions that can occur in these complicated processes. Models derived from the thermodynamic method are critical in this labour because they are able to take into account multiple mechanisms operating simultaneously at the molecular micro-scale and relate them to transcriptional initiation at the tissular macro-scale. This work is devoted to adapting computational techniques to this context in order to theoretically evaluate the role played by several biochemical mechanisms. The interest of this theoretical analysis relies on the fact that it can be contrasted against those biological experiments where the response to perturbations in the transcriptional machinery environment is evaluated in terms of genetically activated/repressed regions. The theoretical reproduction of these experiments leads to a sensitivity analysis whose results are expressed in terms of the elasticity of a threshold function determining those activated/repressed regions. The study of this elasticity function in thermodynamic models already proposed in the literature reveals that certain modelling approaches can alter the balance between the biochemical mechanisms considered, and this can cause false/misleading outcomes. The reevaluation of classical thermodynamic models gives us a more accurate and complete picture of the interactions involved in gene regulation and transcriptional control, which enables more specific predictions. This sensitivity approach provides a definite advantage in the interpretation of a wide range of genetic experimental results.
Collapse
|
19
|
Marazzi L, Shah M, Balakrishnan S, Patil A, Vera-Licona P. NETISCE: a network-based tool for cell fate reprogramming. NPJ Syst Biol Appl 2022; 8:21. [PMID: 35725577 PMCID: PMC9209484 DOI: 10.1038/s41540-022-00231-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
The search for effective therapeutic targets in fields like regenerative medicine and cancer research has generated interest in cell fate reprogramming. This cellular reprogramming paradigm can drive cells to a desired target state from any initial state. However, methods for identifying reprogramming targets remain limited for biological systems that lack large sets of experimental data or a dynamical characterization. We present NETISCE, a novel computational tool for identifying cell fate reprogramming targets in static networks. In combination with machine learning algorithms, NETISCE estimates the attractor landscape and predicts reprogramming targets using signal flow analysis and feedback vertex set control, respectively. Through validations in studies of cell fate reprogramming from developmental, stem cell, and cancer biology, we show that NETISCE can predict previously identified cell fate reprogramming targets and identify potentially novel combinations of targets. NETISCE extends cell fate reprogramming studies to larger-scale biological networks without the need for full model parameterization and can be implemented by experimental and computational biologists to identify parts of a biological system relevant to the desired reprogramming task.
Collapse
Affiliation(s)
- Lauren Marazzi
- Center for Quantitative Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Milan Shah
- Center for Quantitative Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Shreedula Balakrishnan
- Center for Quantitative Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Ananya Patil
- Center for Quantitative Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Paola Vera-Licona
- Center for Quantitative Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA. .,Department of Cell Biology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA. .,Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT, 06030, USA. .,Institute for Systems Genomics, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
| |
Collapse
|
20
|
Lev O, Edgecombe GD, Chipman AD. Serial Homology and Segment Identity in the Arthropod Head. Integr Org Biol 2022; 4:obac015. [PMID: 35620450 PMCID: PMC9128542 DOI: 10.1093/iob/obac015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The anterior-most unit of the crown-group arthropod body plan includes three segments, the pre-gnathal segments, that contain three neuromeres that together comprise the brain. Recent work on the development of this anterior region has shown that its three units exhibit many developmental differences to the more posterior segments, to the extent that they should not be considered serial homologs. Building on this revised understanding of the development of the pre-gnathal segments, we suggest a novel scenario for arthropod head evolution. We posit an expansion of an ancestral single-segmented head at the transition from Radiodonta to Deuteropoda in the arthropod stem group. The expanded head subdivided into three segmental units, each maintaining some of the structures of the ancestral head. This scenario is consistent with what we know of head evolution from the fossil record and helps reconcile some of the debates about early arthropod evolution.
Collapse
Affiliation(s)
- Oren Lev
- The Dept. of Ecology, Evolution & Behavior, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Ariel D Chipman
- The Dept. of Ecology, Evolution & Behavior, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem
| |
Collapse
|
21
|
Amar A, Hubbard EJA, Kugler H. Modeling the C. elegans germline stem cell genetic network using automated reasoning. Biosystems 2022; 217:104672. [PMID: 35469833 PMCID: PMC9142837 DOI: 10.1016/j.biosystems.2022.104672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/18/2022]
Abstract
Computational methods and tools are a powerful complementary approach to experimental work for studying regulatory interactions in living cells and systems. We demonstrate the use of formal reasoning methods as applied to the Caenorhabditis elegans germ line, which is an accessible system for stem cell research. The dynamics of the underlying genetic networks and their potential regulatory interactions are key for understanding mechanisms that control cellular decision-making between stem cells and differentiation. We model the “stem cell fate” versus entry into the “meiotic development” pathway decision circuit in the young adult germ line based on an extensive study of published experimental data and known/hypothesized genetic interactions. We apply a formal reasoning framework to derive predictive networks for control of differentiation. Using this approach we simultaneously specify many possible scenarios and experiments together with potential genetic interactions, and synthesize genetic networks consistent with all encoded experimental observations. In silico analysis of knock-down and overexpression experiments within our model recapitulate published phenotypes of mutant animals and can be applied to make predictions on cellular decision-making. A methodological contribution of this work is demonstrating how to effectively model within a formal reasoning framework a complex genetic network with a wealth of known experimental data and constraints. We provide a summary of the steps we have found useful for the development and analysis of this model and can potentially be applicable to other genetic networks. This work also lays a foundation for developing realistic whole tissue models of the C. elegans germ line where each cell in the model will execute a synthesized genetic network.
Collapse
Affiliation(s)
- Ani Amar
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel.
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Department of Pathology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, United States of America.
| | - Hillel Kugler
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel.
| |
Collapse
|
22
|
|
23
|
Arboleda-Rivera JC, Machado-Rodríguez G, Rodríguez BA, Gutiérrez J. Elucidating multi-input processing 3-node gene regulatory network topologies capable of generating striped gene expression patterns. PLoS Comput Biol 2022; 18:e1009704. [PMID: 35157698 PMCID: PMC8880922 DOI: 10.1371/journal.pcbi.1009704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 02/25/2022] [Accepted: 11/30/2021] [Indexed: 11/18/2022] Open
Abstract
A central problem in developmental and synthetic biology is understanding the mechanisms by which cells in a tissue or a Petri dish process external cues and transform such information into a coherent response, e.g., a terminal differentiation state. It was long believed that this type of positional information could be entirely attributed to a gradient of concentration of a specific signaling molecule (i.e., a morphogen). However, advances in experimental methodologies and computer modeling have demonstrated the crucial role of the dynamics of a cell’s gene regulatory network (GRN) in decoding the information carried by the morphogen, which is eventually translated into a spatial pattern. This morphogen interpretation mechanism has gained much attention in systems biology as a tractable system to investigate the emergent properties of complex genotype-phenotype maps. In this study, we apply a Markov chain Monte Carlo (MCMC)-like algorithm to probe the design space of three-node GRNs with the ability to generate a band-like expression pattern (target phenotype) in the middle of an arrangement of 30 cells, which resemble a simple (1-D) morphogenetic field in a developing embryo. Unlike most modeling studies published so far, here we explore the space of GRN topologies with nodes having the potential to perceive the same input signal differently. This allows for a lot more flexibility during the search space process, and thus enables us to identify a larger set of potentially interesting and realizable morphogen interpretation mechanisms. Out of 2061 GRNs selected using the search space algorithm, we found 714 classes of network topologies that could correctly interpret the morphogen. Notably, the main network motif that generated the target phenotype in response to the input signal was the type 3 Incoherent Feed-Forward Loop (I3-FFL), which agrees with previous theoretical expectations and experimental observations. Particularly, compared to a previously reported pattern forming GRN topologies, we have uncovered a great variety of novel network designs, some of which might be worth inquiring through synthetic biology methodologies to test for the ability of network design with minimal regulatory complexity to interpret a developmental cue robustly. Systems biology is a fast growing field largely powered by advances in high-performance computing and sophisticated mathematical modeling of biological systems. Based on these advances, we are now in a position to mechanistically understand and accurately predict the behavior of complex biological processes, including cell differentiation and spatial pattern formation during embryogenesis. In this article, we use an in silico approach to probe the design space of multi-input, three-node Gene Regulatory Networks (GRNs) capable of generating a striped gene expression pattern in the context of a simplified 1-D morphogenetic field.
Collapse
Affiliation(s)
- Juan Camilo Arboleda-Rivera
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Medellín, Colombia
- * E-mail:
| | - Gloria Machado-Rodríguez
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Boris A. Rodríguez
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Medellín, Colombia
| | | |
Collapse
|
24
|
Abstract
Even if a species' phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical phenotypes. Here we use linear system theory to explore the consequences of this idea, describing how a gene network underlying a conserved phenotype evolves, as the genetic drift of small changes to these molecular pathways causes a population to explore the set of mechanisms with identical phenotypes. To do this, we model an organism's internal state as a linear system of differential equations for which the environment provides input and the phenotype is the output, in which context there exists an exact characterization of the set of all mechanisms that give the same input-output relationship. This characterization implies that selectively neutral directions in genotype space should be common and that the evolutionary exploration of these distinct but equivalent mechanisms can lead to the reproductive incompatibility of independently evolving populations. This evolutionary exploration, or system drift, is expected to proceed at a rate proportional to the amount of intrapopulation genetic variation divided by the effective population size ( Ne$N_e$ ). At biologically reasonable parameter values this could lead to substantial interpopulation incompatibility, and thus speciation, on a time scale of Ne$N_e$ generations. This model also naturally predicts Haldane's rule, thus providing a concrete explanation of why heterogametic hybrids tend to be disrupted more often than homogametes during the early stages of speciation.
Collapse
Affiliation(s)
- Joshua S. Schiffman
- New York Genome CenterNew YorkNew York 10013,Weill Cornell MedicineNew YorkNew York 10065,Department of Molecular and Computational BiologyUniversity of Southern CaliforniaLos AngelesCalifornia 90089
| | - Peter L. Ralph
- Department of Molecular and Computational BiologyUniversity of Southern CaliforniaLos AngelesCalifornia 90089,Department of Mathematics, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon 97403,Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon 97403
| |
Collapse
|
25
|
Veerman F, Mercker M, Marciniak-Czochra A. Beyond Turing: far-from-equilibrium patterns and mechano-chemical feedback. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200278. [PMID: 34743599 DOI: 10.1098/rsta.2020.0278] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Turing patterns are commonly understood as specific instabilities of a spatially homogeneous steady state, resulting from activator-inhibitor interaction destabilized by diffusion. We argue that this view is restrictive and its agreement with biological observations is problematic. We present two alternatives to the classical Turing analysis of patterns. First, we employ the abstract framework of evolution equations to enable the study of far-from-equilibrium patterns. Second, we introduce a mechano-chemical model, with the surface on which the pattern forms being dynamic and playing an active role in the pattern formation, effectively replacing the inhibitor. We highlight the advantages of these two alternatives vis-à-vis the classical Turing analysis, and give an overview of recent results and future challenges for both approaches. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
Collapse
Affiliation(s)
- Frits Veerman
- University of Leiden, Mathematical Institute, Niels Bohrweg 1, Leiden 2333 CA, The Netherlands
| | - Moritz Mercker
- Institute for Applied Mathematics and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
| | - Anna Marciniak-Czochra
- Institute for Applied Mathematics and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
| |
Collapse
|
26
|
Gaiewski MJ, Drewell RA, Dresch JM. Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm. Math Biosci 2021; 342:108716. [PMID: 34687735 DOI: 10.1016/j.mbs.2021.108716] [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: 02/03/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
A detailed comprehension of transcriptional regulation is critical to understanding the genetic control of development and disease across many different organisms. To more fully investigate the complex molecular interactions controlling the precise expression of genes, many groups have constructed mathematical models to complement their experimental approaches. A critical step in such studies is choosing the most appropriate parameter estimation algorithm to enable detailed analysis of the parameters that contribute to the models. In this study, we develop a novel set of evolutionary algorithms that use a pseudo-random Sobol Set to construct the initial population and incorporate parameter sensitivities into the adaptation of mutation rates, using local, global, and hybrid strategies. Comparison of the performance of these new algorithms to a number of current state-of-the-art global parameter estimation algorithms on a range of continuous test functions, as well as synthetic biological data representing models of gene regulatory systems, reveals improved performance of the new algorithms in terms of runtime, error and reproducibility. In addition, by analyzing the ability of these algorithms to fit datasets of varying quality, we provide the experimentalist with a guide to how the algorithms perform across a range of noisy data. These results demonstrate the improved performance of the new set of parameter estimation algorithms and facilitate meaningful integration of model parameters and predictions in our understanding of the molecular mechanisms of gene regulation.
Collapse
Affiliation(s)
- Michael J Gaiewski
- Department of Mathematics and Computer Science, Clark University, Worcester, MA, USA; Department of Mathematics, University of Connecticut, Storrs, CT, USA.
| | | | | |
Collapse
|
27
|
Hong J, Palme J, Hua B, Springer M. Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation. PLoS Comput Biol 2021; 17:e1008691. [PMID: 34570755 PMCID: PMC8496860 DOI: 10.1371/journal.pcbi.1008691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 10/07/2021] [Accepted: 08/17/2021] [Indexed: 11/19/2022] Open
Abstract
Quantitative traits are measurable phenotypes that show continuous variation over a wide phenotypic range. Enormous effort has recently been put into determining the genetic influences on a variety of quantitative traits with mixed success. We identified a quantitative trait in a tractable model system, the GAL pathway in yeast, which controls the uptake and metabolism of the sugar galactose. GAL pathway activation depends both on galactose concentration and on the concentrations of competing, preferred sugars such as glucose. Natural yeast isolates show substantial variation in the behavior of the pathway. All studied yeast strains exhibit bimodal responses relative to external galactose concentration, i.e. a set of galactose concentrations existed at which both GAL-induced and GAL-repressed subpopulations were observed. However, these concentrations differed in different strains. We built a mechanistic model of the GAL pathway and identified parameters that are plausible candidates for capturing the phenotypic features of a set of strains including standard lab strains, natural variants, and mutants. In silico perturbation of these parameters identified variation in the intracellular galactose sensor, Gal3p, the negative feedback node within the GAL regulatory network, Gal80p, and the hexose transporters, HXT, as the main sources of the bimodal range variation. We were able to switch the phenotype of individual yeast strains in silico by tuning parameters related to these three elements. Determining the basis for these behavioral differences may give insight into how the GAL pathway processes information, and into the evolution of nutrient metabolism preferences in different strains. More generally, our method of identifying the key parameters that explain phenotypic variation in this system should be generally applicable to other quantitative traits. Microbes adopt elaborate strategies for the preferred uptake and use of nutrients to cope with complex and fluctuating environments. As a result, yeast strains originating from different ecological niches show significant variation in the way they induce genes in the galactose metabolism (GAL) pathway in response to nutrient signals. To identify the mechanistic sources of this variation, we built a mathematical model to simulate the dynamics of the galactose metabolic regulation network, and studied how parameters with different biological implications contributed to the natural variation. We found that variations in the behavior of the galactose sensor Gal3p, the negative feedback node Gal80p, and the hexose transporters HXT were critical elements in the GAL pathway response. Tuning single parameters in silico was sufficient to achieve phenotype switching between different yeast strains. Our computational approach should be generally useful to help pinpoint the genetic and molecular bases of natural variation in other systems.
Collapse
Affiliation(s)
- Jiayin Hong
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Julius Palme
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bo Hua
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
28
|
Mukaigasa K, Sakuma C, Yaginuma H. The developmental hourglass model is applicable to the spinal cord based on single-cell transcriptomes and non-conserved cis-regulatory elements. Dev Growth Differ 2021; 63:372-391. [PMID: 34473348 PMCID: PMC9293469 DOI: 10.1111/dgd.12750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 11/27/2022]
Abstract
The developmental hourglass model predicts that embryonic morphology is most conserved at the mid‐embryonic stage and diverges at the early and late stages. To date, this model has been verified by examining the anatomical features or gene expression profiles at the whole embryonic level. Here, by data mining approach utilizing multiple genomic and transcriptomic datasets from different species in combination, and by experimental validation, we demonstrate that the hourglass model is also applicable to a reduced element, the spinal cord. In the middle of spinal cord development, dorsoventrally arrayed neuronal progenitor domains are established, which are conserved among vertebrates. By comparing the publicly available single‐cell transcriptome datasets of mice and zebrafish, we found that ventral subpopulations of post‐mitotic spinal neurons display divergent molecular profiles. We also detected the non‐conservation of cis‐regulatory elements located around the progenitor fate determinants, indicating that the cis‐regulatory elements contributing to the progenitor specification are evolvable. These results demonstrate that, despite the conservation of the progenitor domains, the processes before and after the progenitor domain specification diverged. This study will be helpful to understand the molecular basis of the developmental hourglass model.
Collapse
Affiliation(s)
- Katsuki Mukaigasa
- Department of Neuroanatomy and Embryology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Chie Sakuma
- Department of Neuroanatomy and Embryology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hiroyuki Yaginuma
- Department of Neuroanatomy and Embryology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| |
Collapse
|
29
|
Chipman AD. The evolution of the gene regulatory networks patterning the Drosophila Blastoderm. Curr Top Dev Biol 2021; 139:297-324. [PMID: 32450964 DOI: 10.1016/bs.ctdb.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Drosophila blastoderm gene regulatory network is one of the best studied networks in biology. It is composed of a series of tiered sub-networks that act sequentially to generate a primary segmental pattern. Many of these sub-networks have been studied in other arthropods, allowing us to reconstruct how each of them evolved over the transition from the arthropod ancestor to the situation seen in Drosophila today. I trace the evolution of each of these networks, showing how some of them have been modified significantly in Drosophila relative to the ancestral state while others are largely conserved across evolutionary timescales. I compare the putative ancestral arthropod segmentation network with that found in Drosophila and discuss how and why it has been modified throughout evolution, and to what extent this modification is unusual.
Collapse
Affiliation(s)
- Ariel D Chipman
- The Department of Ecology, Evolution & Behavior, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel.
| |
Collapse
|
30
|
Lev O, Chipman AD. Development of the Pre-gnathal Segments in the Milkweed Bug Oncopeltus fasciatus Suggests They Are Not Serial Homologs of Trunk Segments. Front Cell Dev Biol 2021; 9:695135. [PMID: 34422818 PMCID: PMC8378449 DOI: 10.3389/fcell.2021.695135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022] Open
Abstract
The three anterior-most segments in arthropods contain the ganglia that make up the arthropod brain. These segments, the pre-gnathal segments (PGS), are known to exhibit many developmental differences to other segments, believed to reflect their divergent morphology. We have analyzed the expression and function of the genes involved in the conserved segment-polarity network, including genes from the Wnt and Hedgehog pathways, in the PGS, compared with the trunk segments, in the hemimetabolous insect Oncopeltus fasciatus. Gene function was tested by manipulating expression through RNA interference against components of the two pathways. We show that there are fundamental differences in the expression patterns of the segment polarity genes, in the timing of their expression and in the interactions among them in the process of pre-gnathal segment generation, relative to all other segments. We argue that given these differences, the PGS should not be considered serially homologous to trunk segments. This realization raises important questions about the differing evolutionary ancestry of different regions of the arthropod head.
Collapse
Affiliation(s)
| | - Ariel D. Chipman
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
31
|
Lyu Y, Promislow DEL, Pletcher SD. Serotonin signaling modulates aging-associated metabolic network integrity in response to nutrient choice in Drosophila melanogaster. Commun Biol 2021; 4:740. [PMID: 34131274 PMCID: PMC8206115 DOI: 10.1038/s42003-021-02260-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/14/2021] [Indexed: 11/21/2022] Open
Abstract
Aging arises from complex interactions among multiple biochemical products. Systems-level analyses of biological networks may provide insights into the causes and consequences of aging that evade single-gene studies. We have previously found that dietary choice is sufficient to modulate aging in the vinegar fly, Drosophila melanogaster. Here we show that nutrient choice influenced several measures of metabolic network integrity, including connectivity, community structure, and robustness. Importantly, these effects are mediated by serotonin signaling, as a mutation in serotonin receptor 2A (5-HT2A) eliminated the effects of nutrient choice. Changes in network structure were associated with organism resilience and increased susceptibility to genetic perturbation. Our data suggest that the behavioral or perceptual consequences of exposure to individual macronutrients, involving serotonin signaling through 5-HT2A, qualitatively change the state of metabolic networks throughout the organism from one that is highly connected and robust to one that is fragmented, fragile, and vulnerable to perturbations.
Collapse
Affiliation(s)
- Yang Lyu
- Department of Molecular and Integrative Physiology and Geriatrics Center, Biomedical Sciences and Research Building, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel E L Promislow
- Department of Lab Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Scott D Pletcher
- Department of Molecular and Integrative Physiology and Geriatrics Center, Biomedical Sciences and Research Building, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
32
|
Hayford CE, Tyson DR, Robbins CJ, Frick PL, Quaranta V, Harris LA. An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PLoS Biol 2021; 19:e3000797. [PMID: 34061819 PMCID: PMC8195356 DOI: 10.1371/journal.pbio.3000797] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/11/2021] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Tumor heterogeneity is a primary cause of treatment failure and acquired resistance in cancer patients. Even in cancers driven by a single mutated oncogene, variability in response to targeted therapies is well known. The existence of additional genomic alterations among tumor cells can only partially explain this variability. As such, nongenetic factors are increasingly seen as critical contributors to tumor relapse and acquired resistance in cancer. Here, we show that both genetic and nongenetic factors contribute to targeted drug response variability in an experimental model of tumor heterogeneity. We observe significant variability to epidermal growth factor receptor (EGFR) inhibition among and within multiple versions and clonal sublines of PC9, a commonly used EGFR mutant nonsmall cell lung cancer (NSCLC) cell line. We resolve genetic, epigenetic, and stochastic components of this variability using a theoretical framework in which distinct genetic states give rise to multiple epigenetic "basins of attraction," across which cells can transition driven by stochastic noise. Using mutational impact analysis, single-cell differential gene expression, and correlations among Gene Ontology (GO) terms to connect genomics to transcriptomics, we establish a baseline for genetic differences driving drug response variability among PC9 cell line versions. Applying the same approach to clonal sublines, we conclude that drug response variability in all but one of the sublines is due to epigenetic differences; in the other, it is due to genetic alterations. Finally, using a clonal drug response assay together with stochastic simulations, we attribute subclonal drug response variability within sublines to stochastic cell fate decisions and confirm that one subline likely contains genetic resistance mutations that emerged in the absence of drug treatment.
Collapse
Affiliation(s)
- Corey E. Hayford
- Chemical and Physical Biology Graduate Program, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Darren R. Tyson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - C. Jack Robbins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Peter L. Frick
- Chemical and Physical Biology Graduate Program, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Leonard A. Harris
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, United States of America
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Cancer Biology Program, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| |
Collapse
|
33
|
Mani S, Tlusty T. A comprehensive survey of developmental programs reveals a dearth of tree-like lineage graphs and ubiquitous regeneration. BMC Biol 2021; 19:111. [PMID: 34020630 PMCID: PMC8140435 DOI: 10.1186/s12915-021-01013-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
Background Multicellular organisms are characterized by a wide diversity of forms and complexity despite a restricted set of key molecules and mechanisms at the base of organismal development. Development combines three basic processes—asymmetric cell division, signaling, and gene regulation—in a multitude of ways to create this overwhelming diversity of multicellular life forms. Here, we use a generative model to test the limits to which such processes can be combined to generate multiple differentiation paths during development, and attempt to chart the diversity of multicellular organisms generated. Results We sample millions of biologically feasible developmental schemes, allowing us to comment on the statistical properties of cell differentiation trajectories they produce. We characterize model-generated “organisms” using the graph topology of their cell type lineage maps. Remarkably, tree-type lineage differentiation maps are the rarest in our data. Additionally, a majority of the “organisms” generated by our model appear to be endowed with the ability to regenerate using pluripotent cells. Conclusions Our results indicate that, in contrast to common views, cell type lineage graphs are unlikely to be tree-like. Instead, they are more likely to be directed acyclic graphs, with multiple lineages converging on the same terminal cell type. Furthermore, the high incidence of pluripotent cells in model-generated organisms stands in line with the long-standing hypothesis that whole body regeneration is an epiphenomenon of development. We discuss experimentally testable predictions of our model and some ways to adapt the generative framework to test additional hypotheses about general features of development. Supplementary Information The online version contains supplementary material available at (10.1186/s12915-021-01013-4).
Collapse
Affiliation(s)
- Somya Mani
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, South Korea.
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, South Korea. .,Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
| |
Collapse
|
34
|
Kohsokabe T, Kaneko K. Dynamical systems approach to evolution-development congruence: Revisiting Haeckel's recapitulation theory. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 338:62-75. [PMID: 33600605 PMCID: PMC9291011 DOI: 10.1002/jez.b.23031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 11/16/2022]
Abstract
It is acknowledged that embryonic development has a tendency to proceed from common toward specific. Ernst Haeckel raised the question of why that tendency prevailed through evolution, and the question remains unsolved. Here, we revisit Haeckel's recapitulation theory, that is, the parallelism between evolution and development through numerical evolution and dynamical systems theory. By using intracellular gene expression dynamics with cell‐to‐cell interaction over spatially aligned cells to represent the developmental process, gene regulation networks (GRN) that govern these dynamics evolve under the selection pressure to achieve a prescribed spatial gene expression pattern. For most numerical evolutionary experiments, the evolutionary pattern changes over generations, as well as the developmental pattern changes governed by the evolved GRN exhibit remarkable similarity. Changes in both patterns consisted of several epochs where stripes are formed in a short time, whereas for other temporal regimes, the pattern hardly changes. In evolution, these quasi‐stationary generations are needed to achieve relevant mutations, whereas, in development, they are due to some gene expressions that vary slowly and control the pattern change. These successive epochal changes in development and evolution are represented as common bifurcations in dynamical systems theory, regulating working network structure from feedforward subnetwork to those containing feedback loops. The congruence is the correspondence between successive acquisitions of subnetworks through evolution and changes in working subnetworks in development. Consistency of the theory with the segmentation gene‐expression dynamics is discussed. Novel outlook on recapitulation and heterochrony are provided, testable experimentally by the transcriptome and network analysis. We confirmed recapitulation, parallelism between evolution and development, by evolutionary simulation of pattern formation. Its origin is analyzed in terms of bifurcation in dynamical systems theory, slow‐mode control, and network structures.
Collapse
Affiliation(s)
- Takahiro Kohsokabe
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, RIKEN, Kobe, Hyogo, Japan
| | - Kunihiko Kaneko
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
35
|
Deciphering the Role of Wnt and Rho Signaling Pathway in iPSC-Derived ARVC Cardiomyocytes by In Silico Mathematical Modeling. Int J Mol Sci 2021; 22:ijms22042004. [PMID: 33670616 PMCID: PMC7923182 DOI: 10.3390/ijms22042004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/16/2021] [Indexed: 02/07/2023] Open
Abstract
Arrhythmogenic Right Ventricular cardiomyopathy (ARVC) is an inherited cardiac muscle disease linked to genetic deficiency in components of the desmosomes. The disease is characterized by progressive fibro-fatty replacement of the right ventricle, which acts as a substrate for arrhythmias and sudden cardiac death. The molecular mechanisms underpinning ARVC are largely unknown. Here we propose a mathematical model for investigating the molecular dynamics underlying heart remodeling and the loss of cardiac myocytes identity during ARVC. Our methodology is based on three computational models: firstly, in the context of the Wnt pathway, we examined two different competition mechanisms between β-catenin and Plakoglobin (PG) and their role in the expression of adipogenic program. Secondly, we investigated the role of RhoA-ROCK pathway in ARVC pathogenesis, and thirdly we analyzed the interplay between Wnt and RhoA-ROCK pathways in the context of the ARVC phenotype. We conclude with the following remark: both Wnt/β-catenin and RhoA-ROCK pathways must be inactive for a significant increase of PPARγ expression, suggesting that a crosstalk mechanism might be responsible for mediating ARVC pathogenesis.
Collapse
|
36
|
Johnson ME, Chen A, Faeder JR, Henning P, Moraru II, Meier-Schellersheim M, Murphy RF, Prüstel T, Theriot JA, Uhrmacher AM. Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry. Mol Biol Cell 2021; 32:186-210. [PMID: 33237849 PMCID: PMC8120688 DOI: 10.1091/mbc.e20-08-0530] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/13/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022] Open
Abstract
Most of the fascinating phenomena studied in cell biology emerge from interactions among highly organized multimolecular structures embedded into complex and frequently dynamic cellular morphologies. For the exploration of such systems, computer simulation has proved to be an invaluable tool, and many researchers in this field have developed sophisticated computational models for application to specific cell biological questions. However, it is often difficult to reconcile conflicting computational results that use different approaches to describe the same phenomenon. To address this issue systematically, we have defined a series of computational test cases ranging from very simple to moderately complex, varying key features of dimensionality, reaction type, reaction speed, crowding, and cell size. We then quantified how explicit spatial and/or stochastic implementations alter outcomes, even when all methods use the same reaction network, rates, and concentrations. For simple cases, we generally find minor differences in solutions of the same problem. However, we observe increasing discordance as the effects of localization, dimensionality reduction, and irreversible enzymatic reactions are combined. We discuss the strengths and limitations of commonly used computational approaches for exploring cell biological questions and provide a framework for decision making by researchers developing new models. As computational power and speed continue to increase at a remarkable rate, the dream of a fully comprehensive computational model of a living cell may be drawing closer to reality, but our analysis demonstrates that it will be crucial to evaluate the accuracy of such models critically and systematically.
Collapse
Affiliation(s)
- M. E. Johnson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218
| | - A. Chen
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218
| | - J. R. Faeder
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260
| | - P. Henning
- Institute for Visual and Analytic Computing, University of Rostock, 18055 Rostock, Germany
| | - I. I. Moraru
- Department of Cell Biology, Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030
| | - M. Meier-Schellersheim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - R. F. Murphy
- Computational Biology Department, Department of Biological Sciences, Department of Biomedical Engineering, Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15289
| | - T. Prüstel
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - J. A. Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| | - A. M. Uhrmacher
- Institute for Visual and Analytic Computing, University of Rostock, 18055 Rostock, Germany
| |
Collapse
|
37
|
Monteiro A. Distinguishing serial homologs from novel traits: Experimental limitations and ideas for improvements. Bioessays 2020; 43:e2000162. [PMID: 33118632 DOI: 10.1002/bies.202000162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022]
Abstract
One of the central but yet unresolved problems in evolutionary biology concerns the origin of novel complex traits. One hypothesis is that complex traits derive from pre-existing gene regulatory networks (GRNs) reused and modified to specify a novel trait somewhere else in the body. This simple explanation encounters problems when the novel trait that emerges in a body is in a region that is known to harbor a latent or repressed trait that has been silent for millions of years. Is the novel trait merely a re-emerged de-repressed trait or a truly novel trait that emerged via a novel deployment of an old GRN? A couple of new studies sided on opposite sides of this question when investigating the origin of horns in dung beetles and helmets in treehoppers that develop in the first thoracic segment (T1) of their bodies, a segment known to harbor a pair of repressed/modified wings in close relatives. Here, I point to some key limitations of the experimental approaches used and highlight additional experiments that could be done in future to resolve the developmental origin of these and other traits.
Collapse
Affiliation(s)
- Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Science Division, Yale-NUS College, Singapore, Singapore
| |
Collapse
|
38
|
Groves I, Placzek M, Fletcher AG. Of mitogens and morphogens: modelling Sonic Hedgehog mechanisms in vertebrate development. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190660. [PMID: 32829689 PMCID: PMC7482217 DOI: 10.1098/rstb.2019.0660] [Citation(s) in RCA: 13] [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] [Accepted: 02/10/2020] [Indexed: 12/22/2022] Open
Abstract
Sonic Hedgehog (Shh) Is a critical protein in vertebrate development, orchestrating patterning and growth in many developing systems. First described as a classic morphogen that patterns tissues through a spatial concentration gradient, subsequent studies have revealed a more complex mechanism, in which Shh can also regulate proliferation and differentiation. While the mechanism of action of Shh as a morphogen is well understood, it remains less clear how Shh might integrate patterning, proliferation and differentiation in a given tissue, to ultimately direct its morphogenesis. In tandem with experimental studies, mathematical modelling can help gain mechanistic insights into these processes and bridge the gap between Shh-regulated patterning and growth, by integrating these processes into a common theoretical framework. Here, we briefly review the roles of Shh in vertebrate development, focusing on its functions as a morphogen, mitogen and regulator of differentiation. We then discuss the contributions that modelling has made to our understanding of the action of Shh and highlight current challenges in using mathematical models in a quantitative and predictive way. This article is part of a discussion meeting issue 'Contemporary morphogenesis'.
Collapse
Affiliation(s)
- Ian Groves
- School of Mathematics and Statistics, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH, UK
- Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Marysia Placzek
- Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Alexander G. Fletcher
- School of Mathematics and Statistics, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH, UK
- Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| |
Collapse
|
39
|
Espah Borujeni A, Zhang J, Doosthosseini H, Nielsen AAK, Voigt CA. Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage. Nat Commun 2020; 11:5001. [PMID: 33020480 PMCID: PMC7536230 DOI: 10.1038/s41467-020-18630-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
To perform their computational function, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to characterize parts in the context of the circuit and identify the origins of failures. Here, we take snapshots of a large genetic circuit in different states: RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts (promoters, ribozymes, RBSs, terminators) are parameterized and used to inform a mathematical model that can predict circuit performance, dynamics, and robustness. The circuit behaves as designed; however, it is riddled with genetic errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons, and a failed gate. While not impacting the expected Boolean logic, they reduce the prediction accuracy and could lead to failures when the parts are used in other designs. Finally, the cellular power (RNAP and ribosome usage) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host.
Collapse
Affiliation(s)
- Amin Espah Borujeni
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jing Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hamid Doosthosseini
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alec A K Nielsen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
40
|
Abstract
Canalization refers to the evolution of populations such that the number of individuals who deviate from the optimum trait, or experience disease, is minimized. In the presence of rapid cultural, environmental, or genetic change, the reverse process of decanalization may contribute to observed increases in disease prevalence. This review starts by defining relevant concepts, drawing distinctions between the canalization of populations and robustness of individuals. It then considers evidence pertaining to three continuous traits and six domains of disease. In each case, existing genetic evidence for genotype-by-environment interactions is insufficient to support a strong inference of decanalization, but we argue that the advent of genome-wide polygenic risk assessment now makes an empirical evaluation of the role of canalization in preventing disease possible. Finally, the contributions of both rare and common variants to congenital abnormality and adult onset disease are considered in light of a new kerplunk model of genetic effects.
Collapse
Affiliation(s)
- Greg Gibson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Kristine A Lacek
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| |
Collapse
|
41
|
Lewis JJ, Van Belleghem SM. Mechanisms of Change: A Population-Based Perspective on the Roles of Modularity and Pleiotropy in Diversification. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
42
|
Enhancement of gene expression noise from transcription factor binding to genomic decoy sites. Sci Rep 2020; 10:9126. [PMID: 32499583 PMCID: PMC7272470 DOI: 10.1038/s41598-020-65750-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/08/2020] [Indexed: 12/29/2022] Open
Abstract
The genome contains several high-affinity non-functional binding sites for transcription factors (TFs) creating a hidden and unexplored layer of gene regulation. We investigate the role of such “decoy sites” in controlling noise (random fluctuations) in the level of a TF that is synthesized in stochastic bursts. Prior studies have assumed that decoy-bound TFs are protected from degradation, and in this case decoys function to buffer noise. Relaxing this assumption to consider arbitrary degradation rates for both bound/unbound TF states, we find rich noise behaviors. For low-affinity decoys, noise in the level of unbound TF always monotonically decreases to the Poisson limit with increasing decoy numbers. In contrast, for high-affinity decoys, noise levels first increase with increasing decoy numbers, before decreasing back to the Poisson limit. Interestingly, while protection of bound TFs from degradation slows the time-scale of fluctuations in the unbound TF levels, the decay of bound TFs leads to faster fluctuations and smaller noise propagation to downstream target proteins. In summary, our analysis reveals stochastic dynamics emerging from nonspecific binding of TFs and highlights the dual role of decoys as attenuators or amplifiers of gene expression noise depending on their binding affinity and stability of the bound TF.
Collapse
|
43
|
On the problem of biological form. Theory Biosci 2020; 139:299-308. [PMID: 32418121 DOI: 10.1007/s12064-020-00317-3] [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: 02/23/2019] [Accepted: 05/05/2020] [Indexed: 10/24/2022]
Abstract
Embryonic development, which inspired the first theories of biological form, was eventually excluded from the conceptual framework of the Modern Synthesis as irrelevant. A major question during the last decades has centred on understanding whether new advances in developmental biology are compatible with the standard view or whether they compel a new theory. Here, I argue that the answer to this question depends on which concept of morphogenesis is held. Morphogenesis can be conceived as (1) a chemically driven or (2) a mechanically driven process. According to the first option, genetic regulatory networks drive morphogenesis. According to the second, morphogenesis results from an invariant tendency of embryonic tissues to restore changes in mechanical stress. While chemically driven morphogenesis allows an extension of the standard view, mechanically driven morphogenesis would deeply transform it. Which of these hypotheses has wider explanatory power is unknown. At present, the problem of biological form remains unsolved.
Collapse
|
44
|
Sokac AM. Mechanical Networks Have Robustness Built into Their Topology, Too. Dev Cell 2020; 50:527-528. [PMID: 31505172 DOI: 10.1016/j.devcel.2019.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Network topology ensures robust outcomes for information-transferring networks in biology (e.g., signaling and gene regulatory networks). In this issue of Developmental Cell, Yevick et al. (2019) demonstrate that a similar principle holds for the mechanical networks that drive morphogenesis.
Collapse
Affiliation(s)
- Anna Marie Sokac
- Chemical & Life Sciences Laboratory, Department of Cell & Molecular Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, IL 60801, USA.
| |
Collapse
|
45
|
Nam KM, Gyori BM, Amethyst SV, Bates DJ, Gunawardena J. Robustness and parameter geography in post-translational modification systems. PLoS Comput Biol 2020; 16:e1007573. [PMID: 32365103 PMCID: PMC7224580 DOI: 10.1371/journal.pcbi.1007573] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/14/2020] [Accepted: 04/02/2020] [Indexed: 11/23/2022] Open
Abstract
Biological systems are acknowledged to be robust to perturbations but a rigorous understanding of this has been elusive. In a mathematical model, perturbations often exert their effect through parameters, so sizes and shapes of parametric regions offer an integrated global estimate of robustness. Here, we explore this “parameter geography” for bistability in post-translational modification (PTM) systems. We use the previously developed “linear framework” for timescale separation to describe the steady-states of a two-site PTM system as the solutions of two polynomial equations in two variables, with eight non-dimensional parameters. Importantly, this approach allows us to accommodate enzyme mechanisms of arbitrary complexity beyond the conventional Michaelis-Menten scheme, which unrealistically forbids product rebinding. We further use the numerical algebraic geometry tools Bertini, Paramotopy, and alphaCertified to statistically assess the solutions to these equations at ∼109 parameter points in total. Subject to sampling limitations, we find no bistability when substrate amount is below a threshold relative to enzyme amounts. As substrate increases, the bistable region acquires 8-dimensional volume which increases in an apparently monotonic and sigmoidal manner towards saturation. The region remains connected but not convex, albeit with a high visibility ratio. Surprisingly, the saturating bistable region occupies a much smaller proportion of the sampling domain under mechanistic assumptions more realistic than the Michaelis-Menten scheme. We find that bistability is compromised by product rebinding and that unrealistic assumptions on enzyme mechanisms have obscured its parametric rarity. The apparent monotonic increase in volume of the bistable region remains perplexing because the region itself does not grow monotonically: parameter points can move back and forth between monostability and bistability. We suggest mathematical conjectures and questions arising from these findings. Advances in theory and software now permit insights into parameter geography to be uncovered by high-dimensional, data-centric analysis. Biological organisms are often said to have robust properties but it is difficult to understand how such robustness arises from molecular interactions. Here, we use a mathematical model to study how the molecular mechanism of protein modification exhibits the property of multiple internal states, which has been suggested to underlie memory and decision making. The robustness of this property is revealed by the size and shape, or “geography,” of the parametric region in which the property holds. We use advances in reducing model complexity and in rapidly solving the underlying equations, to extensively sample parameter points in an 8-dimensional space. We find that under realistic molecular assumptions the size of the region is surprisingly small, suggesting that generating multiple internal states with such a mechanism is much harder than expected. While the shape of the region appears straightforward, we find surprising complexity in how the region grows with increasing amounts of the modified substrate. Our approach uses statistical analysis of data generated from a model, rather than from experiments, but leads to precise mathematical conjectures about parameter geography and biological robustness.
Collapse
Affiliation(s)
- Kee-Myoung Nam
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Benjamin M. Gyori
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Silviana V. Amethyst
- Department of Mathematics, University of Wisconsin–Eau Claire, Eau Claire, Wisconsin, United States of America
| | - Daniel J. Bates
- Department of Mathematics, United States Naval Academy, Annapolis, Maryland, United States of America
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
46
|
Lander AD, Nie Q, Sanchez-Tapia C, Simonyan A, Wan FYM. Regulatory feedback on receptor and non-receptor synthesis for robust signaling. Dev Dyn 2020; 249:383-409. [PMID: 32034817 DOI: 10.1002/dvdy.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022] Open
Abstract
Elaborate regulatory feedback processes are thought to make biological development robust, that is, resistant to changes induced by genetic or environmental perturbations. How this might be done is still not completely understood. Previous numerical simulations on reaction-diffusion models of Dpp gradients in Drosophila wing imaginal disc have showed that feedback (of the Hill function type) on (signaling) receptors and/or non-(signaling) receptors are of limited effectiveness in promoting robustness. Spatial nonuniformity of the feedback processes has also been shown theoretically to lead to serious shape distortion and a principal cause for ineffectiveness. Through mathematical modeling and analysis, the present article shows that spatially uniform nonlocal feedback mechanisms typically modify gradient shape through a shape parameter (that does not change with location). This in turn enables us to uncover new multi-feedback instrument for effective promotion of robust signaling gradients.
Collapse
Affiliation(s)
- Arthur D Lander
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California.,Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, California
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California.,Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, California.,Department of Mathematics, University of California Irvine, Irvine, California.,NSF-Simon Center for Multiscale Cell Fate (CMCF), University of California Irvine, Irvine, California
| | | | - Aghavni Simonyan
- Department of Mathematics, University of California Irvine, Irvine, California.,Geffen Academy, UCLA, Los Angeles, California
| | - Frederic Y M Wan
- Department of Mathematics, University of California Irvine, Irvine, California
| |
Collapse
|
47
|
Ali Al-Radhawi M, Angeli D, Sontag ED. A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks. PLoS Comput Biol 2020; 16:e1007681. [PMID: 32092050 PMCID: PMC7058358 DOI: 10.1371/journal.pcbi.1007681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 03/05/2020] [Accepted: 01/23/2020] [Indexed: 01/26/2023] Open
Abstract
Complex molecular biological processes such as transcription and translation, signal transduction, post-translational modification cascades, and metabolic pathways can be described in principle by biochemical reactions that explicitly take into account the sophisticated network of chemical interactions regulating cell life. The ability to deduce the possible qualitative behaviors of such networks from a set of reactions is a central objective and an ongoing challenge in the field of systems biology. Unfortunately, the construction of complete mathematical models is often hindered by a pervasive problem: despite the wealth of qualitative graphical knowledge about network interactions, the form of the governing nonlinearities and/or the values of kinetic constants are hard to uncover experimentally. The kinetics can also change with environmental variations. This work addresses the following question: given a set of reactions and without assuming a particular form for the kinetics, what can we say about the asymptotic behavior of the network? Specifically, it introduces a class of networks that are "structurally (mono) attractive" meaning that they are incapable of exhibiting multiple steady states, oscillation, or chaos by virtue of their reaction graphs. These networks are characterized by the existence of a universal energy-like function called a Robust Lyapunov function (RLF). To find such functions, a finite set of rank-one linear systems is introduced, which form the extremals of a linear convex cone. The problem is then reduced to that of finding a common Lyapunov function for this set of extremals. Based on this characterization, a computational package, Lyapunov-Enabled Analysis of Reaction Networks (LEARN), is provided that constructs such functions or rules out their existence. An extensive study of biochemical networks demonstrates that LEARN offers a new unified framework. Basic motifs, three-body binding, and genetic networks are studied first. The work then focuses on cellular signalling networks including various post-translational modification cascades, phosphotransfer and phosphorelay networks, T-cell kinetic proofreading, and ERK signalling. The Ribosome Flow Model is also studied.
Collapse
Affiliation(s)
- M. Ali Al-Radhawi
- Departments of Electrical and Computer Engineering and of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
| | - David Angeli
- Department of Electrical & Electronic Engineering, Imperial College London, London, United Kingdom
- Dipartimento di Ingegneria dell’Informazione, University of Florence, Florence, Italy
| | - Eduardo D. Sontag
- Departments of Electrical and Computer Engineering and of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, United States of America
| |
Collapse
|
48
|
Garcia HG, Berrocal A, Kim YJ, Martini G, Zhao J. Lighting up the central dogma for predictive developmental biology. Curr Top Dev Biol 2019; 137:1-35. [PMID: 32143740 DOI: 10.1016/bs.ctdb.2019.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the last 30years have witnessed the mapping of the wiring diagrams of the gene regulatory networks that dictate cell fate and animal body plans, specific understanding building on such network diagrams that shows how DNA regulatory regions control gene expression lags far behind. These networks have yet to yield the predictive power necessary to, for example, calculate how the concentration dynamics of input transcription factors and DNA regulatory sequence prescribes output patterns of gene expression that, in turn, determine body plans themselves. Here, we argue that reaching a predictive understanding of developmental decision-making calls for an interplay between theory and experiment aimed at revealing how the regulation of the processes of the central dogma dictate network connections and how network topology guides cells toward their ultimate developmental fate. To make this possible, it is crucial to break free from the snapshot-based understanding of embryonic development facilitated by fixed-tissue approaches and embrace new technologies that capture the dynamics of developmental decision-making at the single cell level, in living embryos.
Collapse
Affiliation(s)
- Hernan G Garcia
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States; Department of Physics, University of California at Berkeley, Berkeley, CA, United States; Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States; Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, United States.
| | - Augusto Berrocal
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States
| | - Gabriella Martini
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, United States
| |
Collapse
|
49
|
Barr K, Reinitz J, Radulescu O. An in silico analysis of robust but fragile gene regulation links enhancer length to robustness. PLoS Comput Biol 2019; 15:e1007497. [PMID: 31730659 PMCID: PMC6881076 DOI: 10.1371/journal.pcbi.1007497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/27/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Organisms must ensure that expression of genes is directed to the appropriate tissues at the correct times, while simultaneously ensuring that these gene regulatory systems are robust to perturbation. This idea is captured by a mathematical concept called r-robustness, which says that a system is robust to a perturbation in up to r - 1 randomly chosen parameters. r-robustness implies that the biological system has a small number of sensitive parameters and that this number can be used as a robustness measure. In this work we use this idea to investigate the robustness of gene regulation using a sequence level model of the Drosophila melanogaster gene even-skipped. We consider robustness with respect to mutations of the enhancer sequence and with respect to changes of the transcription factor concentrations. We find that gene regulation is r-robust with respect to mutations in the enhancer sequence and identify a number of sensitive nucleotides. In both natural and in silico predicted enhancers, the number of nucleotides that are sensitive to mutation correlates negatively with the length of the sequence, meaning that longer sequences are more robust. The exact degree of robustness obtained is dependent not only on DNA sequence, but also on the local concentration of regulatory factors. We find that gene regulation can be remarkably sensitive to changes in transcription factor concentrations at the boundaries of expression features, while it is robust to perturbation elsewhere.
Collapse
Affiliation(s)
- Kenneth Barr
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - John Reinitz
- Departments of Statistics, Ecology & Evolution, Molecular Genetics & Cell Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Ovidiu Radulescu
- LPHI UMR CNRS 5235, University of Montpellier, Montpellier, France
| |
Collapse
|
50
|
Gerardin J, Reddy NR, Lim WA. The Design Principles of Biochemical Timers: Circuits that Discriminate between Transient and Sustained Stimulation. Cell Syst 2019; 9:297-308.e2. [PMID: 31521602 DOI: 10.1016/j.cels.2019.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/17/2019] [Accepted: 07/23/2019] [Indexed: 10/26/2022]
Abstract
Many cellular responses for which timing is critical display temporal filtering-the ability to suppress response until stimulated for longer than a given minimal time. To identify biochemical circuits capable of kinetic filtering, we comprehensively searched the space of three-node enzymatic networks. We define a metric of "temporal ultrasensitivity," the steepness of activation as a function of stimulus duration. We identified five classes of core network motifs capable of temporal filtering, each with distinct functional properties such as rejecting high-frequency noise, committing to response (bistability), and distinguishing between long stimuli. Combinations of the two most robust motifs, double inhibition (DI) and positive feedback with AND logic (PFAND), underlie several natural timer circuits involved in processes such as cell cycle transitions, T cell activation, and departure from the pluripotent state. The biochemical network motifs described in this study form a basis for understanding common ways cells make dynamic decisions.
Collapse
Affiliation(s)
- Jaline Gerardin
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nishith R Reddy
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Cell Design Initiative, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|