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Bioinformatics, Computational and Systems Biology

Multiscale Modeling of BMP Signaling Pathway during Zebrafish Embryogenesis

(A-5) Multiscale Modeling of BMP Signaling Pathway during Zebrafish Embryogenesis

Thursday, October 12, 2023

9:30 AM – 10:30 AM PDT

Location: Exhibit Hall - Row A - Poster # 5

Presenting Author(s)

NL

Nissa J. Larson (she/her/hers)

Graduate Research Assistant
Purdue University
West Lafayette, Indiana, United States

Co-Author(s)

Linlin Li, PhD

Senior Research Scientist
Purdue University, United States
BM

Bobby Madamanchi

Lecturer
University of Michigan, United States

Primary Investigator(s)

DU

David Umulis

Senior Vice Provost for Purdue in Indianapolis, Acting Dane A. Miller Head of Biomedical Engineering
Purdue University, United States

Introduction: In developing tissues, signal transduction from morphogen gradients conveys positional information to cells, resulting in cell specification and differentiation. One such morphogen is bone morphogenetic protein (BMP), of the TGF-β superfamily, whose network is highly conserved across many species. In zebrafish species Danio rerio, this signaling pathway directs dorsoventral axis formation during early embryogenesis. Many of the molecules that play a role in this network are known; however, the mechanisms through which they achieve noise attenuation and gradient robustness have not been defined. Specifically, one tetrameric complex has been shown to be required for signal transduction. Deterministic modeling of the BMP membrane receptors at this stage, however, has not given any insight into evolutionary drivers of this requirement. Building and developing a stochastic, multiscale model of this process will allow us to mechanistically assess zebrafish phenotype variability related to the distributions of noise and stochasticity. To further probe this system, we are working to develop an experimental optogenetics protocol to genetically manipulate dorsoventral signal transduction in vivo and collect and analyze fluorescence intensity of the downstream pSmad gradient.

Materials and Methods:

The stochastic receptor model has been deployed in a ‘virtual embryo’ and was constructed using the open-source python wrapper GillesPy and the framework StochKit2. This framework employs tau-leaping and Gillespie’s stochastic simulation algorithm to rapidly simulate stochastic trajectories in biochemical systems with facilitated cluster-implementation. As these networks are inherently stochastic, this approach takes into consideration the basic random chance of molecular interactions that leads to noise and variability. Stochastic projections over time from this model provide information on the amounts and ratios of certain complexes that form, which can be analyzed for the amount of positional information provided by these complexes under a changing gradient.

The extracellular finite element model has been constructed based on the diffusion-reaction system of the extracellular regulatory BMP network, simulating the spatial-temporal profile formation of BMP dimers during early embryogenesis. Integrating the two model scales will provide a more complete view of the network.

Optogenetics experimentation will provide a light-exposure-dependent, reversible profile that can be quantitatively analyzed. Precise manual adjustment of the signaling gradient will allow us to measure the input and output fluctuations of the network. The correlation of this data between noise and signal processing will provide new insights into the system.

Results, Conclusions, and Discussion: Current results include R code processing of stochastic receptor model data. Our working hypothesis for the stochastic model is that while the heterodimer-heterotetramer complex does not occur at the most abundant levels, it outperforms other complexes in sensitivity and time-response to extracellular BMP gradient progression. Preliminary results support this idea. At the EC50 dimer level for each common complex tested, the required heterodimer-heterotetramer complex expresses the highest sensitivity to an extracellular gradient.

The sensitivity and positional information provided by the required heterodimer-heterotetramer complex exceeds the performance of other common complexes examined. These metrics cannot be analyzed using traditional deterministic modeling efforts. We therefore report that established metrics of noise and information transduction may overlook important temporal effects that may be particularly relevant during development.

Integrating the extracellular and intracellular levels to a multiscale model will allow us to further probe the origins of noise and noise attenuation in the system. We hypothesize that noise arises especially from the membrane receptor level and is attenuated through the following intracellular pSmad network.

As the BMP signaling pathway is highly conserved and has been implicated in human bone growth and regenerative medicine, its study in simpler systems such as zebrafish stands to accelerate our comprehension of BMP network structure and molecular mechanisms and application in regenerative medical studies.

Acknowledgements (Optional): :

References (Optional): :

Agnew, C., Ayaz, P., Kashima, R., Loving, H. S., Ghatpande, P., Kung, J. E., . . . Jura, N. (2021). Structural basis for alk2/bmpr2 receptor complex signaling through kinase domain oligomerization. Nat. Commun., 12 , 4950.

Antebi, Y. E., Linton, J. M., Klumpe, H., Bintu, B., Gong, M., Su, C., . . . Elowitz, M. B. (2017). Combinatorial signal perception in the bmp pathway. Cell, 170(6). (https://doi.org/10.1016/j.cell.2017.08.015)

Carreira, A. C. O., Zambuzzi, W. F., Rossi, M. C., Filho, R. A., Sogayar, M. C., & Granjeiro, J. M. (2015). Bone morphogenetic proteins: Promising molecules for bone healing, bioengineering, and regenerative medicine. Elsevier: Vitamins and Hormones, 99 , 293-322. (https://doi.org/10.1016/bs.vh.2015.06.002)

Karim, M. S., Buzzard, G. T., & Umulis, D. M. (2011). Secreted, receptor-associated bone morphogenetic protein regulators reduce stochastic noise intrinsic to many extracellular morphogen distributions. The Royal Society Interface, 9(70), 1073-1083. (https://doi.org/10.1098/rsif.2011.0547)

Li, L. (2021). Combined physics and bmp signaling network dynamics to model early embryonic development in zebrafish. Doctoral Thesis, Purdue University.

Madamanchi, A., Mullins, M. C., & Umulis, D. M. (2021). Diversity and robustness of bone morphogenetic protein pattern formation. Development, 147(8). (https://doi.org/10.1242/dev.192344)

Mueller, T. D., & Nickel, J. (2012). Promiscuity and specificity in bmp receptor activation. FEBS Lett., 586 , 1846-1859. (https://doi.org/10.1016/j.febslet.2012.02.043)

Rogers, K. W., ElGamacy, M., Jordan, B. M., & Müller, P. (2020). Optogenetic investigation of bmp target gene expression diversity. ELife, 9 . (https://doi.org/10.7554/elife.58641)

Tajer, B., Dutko, J. A., Little, S. C., & Mullins, M. C. (2021). Bmp heterodimers signal via distinct type i receptor class functions. Proceedings of the National Academy of Sciences, 118(15). (https://doi.org/10.1073/pnas.2017952118)

Umulis, D. M., O’Connor, M. B., & Blair, S. S. (2009). The extracellular regulation of bone morphogenetic protein signaling. development. Development, 136(22), 3715-3728. (https://doi.org/10.1242/dev.031534)

Wu, L., Chen, A., Salama, P., Dunn, K. W., & Delp, E. J. (2022, June). Nisnet3d: Three-dimensional nuclear synthesis and instance segmentation for fluorescence microscopy images. bioRxiv. (https://doi.org/10.1101/2022.06.10.495713)

Zinski, J., Bu, Y., Wang, X., Dou, W., Umulis, D. M., & Mullins, M. C. (2017). Systems biology derived source-sink mechanism of bmp gradient formation. ELife, 6 . (https://doi.org/10.7554/elife.22199)