Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

• Published in: bioRxiv
• Main Authors: Johnson, Jeanette A I, Stein-O'Brien, Genevieve L, Booth, Max, Heiland, Randy, Kurtoglu, Furkan, Bergman, Daniel R, Bucher, Elmar, Deshpande, Atul, Forjaz, André, Getz, Michael, Godet, Ines, Lyman, Melissa, Metzcar, John, Mitchell, Jacob, Raddatz, Andrew, Rocha, Heber, Solorzano, Jacobo, Sundus, Aneequa, Wang, Yafei, Gilkes, Danielle, Kagohara, Luciane T, Kiemen, Ashley L, Thompson, Elizabeth D, Wirtz, Denis, Wu, Pei-Hsun, Zaidi, Neeha, Zheng, Lei, Zimmerman, Jacquelyn W, Jaffee, Elizabeth M, Hwan Chang, Young, Coussens, Lisa M, Gray, Joe W, Heiser, Laura M, Fertig, Elana J, Macklin, Paul
• Format: Journal Article Paper
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 05.11.2023
• Subjects: Biology; Immunotherapy; Language; Mathematical models
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2023.09.17.557982

Cells are fundamental units of life, constantly interacting and evolving as dynamical systems. While recent spatial multi-omics can quantitate individual cells' characteristics and regulatory programs, forecasting their evolution ultimately requires mathematical modeling. We develop a conceptual framework-a cell behavior hypothesis grammar-that uses natural language statements (cell rules) to create mathematical models. This allows us to systematically integrate biological knowledge and multi-omics data to make them computable. We can then perform virtual "thought experiments" that challenge and extend our understanding of multicellular systems, and ultimately generate new testable hypotheses. In this paper, we motivate and describe the grammar, provide a reference implementation, and demonstrate its potential through a series of examples in tumor biology and immunotherapy. Altogether, this approach provides a bridge between biological, clinical, and systems biology researchers for mathematical modeling of biological systems at scale, allowing the community to extrapolate from single-cell characterization to emergent multicellular behavior.