Modelling cell lineage using a meta-Boolean tree model with a relation to gene regulatory networks

Abstract

. Modelling cell lineage using a meta-Boolean tree model with a relation to Gene Regulatory Networks. Journal of Theoretical Biology, Elsevier, 2010, 268 (1) This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.Modelling cell lineage using a meta-Boolean tree model with a relation to Gene Regulatory Networks AbstractA cell lineage is the ancestral relationship between a group of cells that originate from a single founder cell. For example, in the embryo of the nematode Caenorhabditis elegans an invariant cell lineage has been traced, and with this information at hand it is possible to theoretically model the emergence of different cell types in the lineage, starting from the single fertilized egg. In this report we outline a modelling technique for cell lineage trees, which can be used for the C. elegans embryonic cell lineage but also extended to other lineages. The model takes into account both cell-intrinsic (transcription factor-based) and -extrinsic (extracellular) factors as well as synergies within and between these two types of factors. The model can faithfully recapitulate the entire C. elegans cell lineage, but is also general, i.e. it can be applied to describe any cell lineage. We show that synergy between factors, as well as the use of extrinsic factors, drastically reduce the number of regulatory factors needed for recapitulating the lineage. The model gives indications regarding co-variation of factors, number of involved genes and where in the cell lineage tree that asymmetry might be controlled by external influence. Furthermore, the model is able to emulate other (Boolean, discrete and differential-equation-based) models. As an example, we show that the model can be translated to the language of a previous linear sigmoid-limited concentration-based model (Geard and Wiles, 2005). This means that this latter model also can exhibit synergy effects, and also that the cumbersome iterative technique for parameter estimation previously used is no longer needed. In conclusion, the proposed model is general and simple to use, can be mapped onto other models to extend and simplify their use, and can also be used to indicate where synergy and external influence would reduce the complexity of the regulatory process.

Systems Biology of Cancer: A Challenging Expedition for Clinical and Quantitative Biologists

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Meta-Boolean models of asymmetric division patterns in theC. elegansintestinal lineage

“…The regulator g(I|H,–A) describes the production of factor I when factor H is present given that factor A is not. From Larsson et al 20 …”

“…We have recently presented a rule-based low-complexity meta-Boolean model designed for large cell lineage trees 20 . In short, the model utilizes a factor framework to describe the properties of a given cell in the tree.…”

“…The low complexity allows for larger systems such as complete embryonic lineage trees to be modeled, and the model is intended to enable investigation of the general patterns that arise in such large systems. For example, it has been used to indicate where in lineage trees asymmetry breaking may be controlled by external influences 20 . In our previous work, we have shown that the meta-Boolean model is able to faithfully describe the embryonic cell lineage of the nematode C. elegans 20 .…”

“…For example, it has been used to indicate where in lineage trees asymmetry breaking may be controlled by external influences 20 . In our previous work, we have shown that the meta-Boolean model is able to faithfully describe the embryonic cell lineage of the nematode C. elegans 20 . We now focus on a more limited part of this model organism, the intestine or endoderm (reviewed in ref.…”