Model-based analysis of spatio-temporal heterogeneity of mouse embryonic stem cells with respect to its functional role in regulating pluripotency
Final Report Abstract
Embryonic stem cells (ESCs) have the remarkable capacity to divide indefinitely in culture (self-renewal) while they retain the potential to differentiate into all cell types of an adult organism (pluripotency). Because of these unique properties, ESCs are a prime system to investigate regulatory and potentially multiscale mechanisms of cell fate decision processes. Notably, ESCs populations display heterogeneous gene expression patterns associated with different cell fate propensity. In particular, it is the expression of pluripotency factors like Nanog and Rex1 that obeys a heterogeneous (i.e. bimodal) distribution of functionally different ESCs, which is reestablished after cell sorting. In our project, we comprehensively studied different types of heterogeneity and their relations in mouse ESCs, and investigate how heterogeneity acts as functional element in the balance between self-renewal and differentiation. Therefore, we first developed an intracellular network model, which consistently describes transcription factor (TF) dynamics under different culture conditions. We explicitly integrated autocrine FGF4/Erk signaling into a network of pluripotency factors (namely Oct4, Sox2, Nanog and Rex1) deriving predictions on the alteration of molecular heterogeneity and transitions between a Nanog-high state, in which ESCs are protected from differentiation, and a Nanog-low state, in which they are susceptible to differentiation cues. Second, we performed cell sorting experiments on a Rex1GFPd2 reporter cell line and analyzed the dynamics of the reestablishment of the original bimodal distribution. Thus, we arrived at a more realistic population model incorporating both intra- and cellular aspects of pluripotency regulation. In particular, ESCs are described as individual objects with typical attributes like lifespans, division rates and cell fates. Applying the model we accessed the effect of differential cell properties on the overall proportion of different subpopulations and found that TF-related cell cycle times facilitate dynamically stabilized cell cultures. However, differences in the state of individual ESCs are not only detectable on a molecular level, but are also reflected in their morphology and their spatial arrangement in colony structures. Thus, in the third part we applied new imaging and analysis techniques to monitor the spatiotemporal development of living Rex1GFPd2 cells. In particular, we established an automated colony-tracking framework to objectively quantify changes in structural properties, like shape and internal motion. Moreover, we designed quantitative measures describing the spatial distribution of functionally different ESCs in and between cell colonies. Finally, we used these analyses to extend the agent-based model by a spatial dimension, incorporate different modes of cellular interaction and compare it to the experimental results. Thus, we found that a coupling of individual ESCs with TF-related adhesions through FGF/Erk signaling is fully consistent with the experimentally observed colony structures evaluated from microscopy images. In this project, we addressed questions on regulatory mechanisms of heterogeneity and on the spatio-temporal pattern formation of ESC cultures by a systems biology approach. Our image-based modeling approach translates new experimental findings with respect to dynamic ESC patterns into a mathematical framework that feeds testable predictions back into refined experimental strategies. The gained systemic understanding of ESC development in terms of a quantitative and mathematical model goes well beyond the descriptive level, thus offering the opportunity to suggest and to experimentally validate new hypotheses about functional mechanisms of ESC cell organization especially with respect to targeted differentiation and reprogramming.
Publications
-
Epigenetic Nanog regulation and the role of functional heterogeneity. Cell cycle (Georgetown, Tex.) 10 (2011) 2252-3
Herberg M, Roeder I
-
Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions. Bioinformatics (Oxford, England) 28 (2012) i556-i561
Scherf N, Herberg M, Thierbach K, Zerjatke T, Kalkan T, Humphreys P, Smith A, Glauche I, Roeder I
-
Beyond Genealogies: Mutual information of causal paths to analyse single cell tracking data IEEE: 10th International Symposium on Biomedical Imaging: From Nano to Macro, San Francisco, CA, USA, April 7-11, 2013. ISBN: 978-1-4673-6454-6/13
Scherf N, Zerjatke T, Klemm K, Glauche I, Roeder I
-
A Model-Based Analysis of Culture-Dependent Phenotypes of mESCs. PloS one 9 (2014) e92496
Herberg M, Kalkan T, Glauche I, Smith A, Roeder I
-
Elucidating functional heterogeneity in haematopoietic progenitor cells: a combined experimental and modelling approach. Experimental hematology (2014)
Bach E, Zerjatke T, Herklotz M, Scherf N, Niederwieser D, Roeder I, Pompe T, Cross M, Glauche I
