Periodic Reporting for period 1 - ORGANIZE (Origins of cell diversity in multicellular tissues)
Reporting period: 2021-11-01 to 2023-10-31
Multicellular tissues, and ultimately complex organisms, are composed of multiple distinct cell types that differ in function and phenotype. Such diversity in cell composition (i.e. phenotypic diversity) arises during development and tissue regeneration, where progenitor cells differentiate along multiple cell fate lineages to form a heterogeneous population. To ensure the proper form and function of the tissue, cell types must achieve the correct equilibrium in cell type proportions and self-organize into higher order structures. Indeed, loss or misregulation of phenotypic diversity can lead to a variety of diseases such as cancer and autoimmune disorders. While the molecular signals (i.e. cell states) that specify individual cell fates are widely studied in the context of development and stem cell engineering, less is known about how multiple cell types can simultaneously emerge from a seemingly homogeneous population and form a complex multicellular system with specified form and function. Though this multitude of cell states and types are present and heterogenous across the cell population, the cause and consequence of this diversity is poorly understood. There is a concomitant lack of tools to quantify cell heterogeneity in a multicellular system and measure its effect on emergence of tissue form and function. The aim of this project is to develop quantitative methods to measure single-cell heterogeneity in a 3D multicellular system and to investigate the role of this heterogeneity in emergence of shape complexity of the tissue. As a result, we developed a workflow for quantitative 3D image-based analysis of single-cell state as well as tissue-level morphology and use it to define measures of heterogeneity and complexity during the self-organization of a model 3D multicellular system, mouse small intestinal organoids. We are using this framework to generate a morphological landscape of organoids under varying growth conditions and correlate phenotypic diversity with emergence of morphological complexity. We also compare the predominantly cell-intrinsic self-organization of organoids to small intestinal development within the in vivo context of the organism. This project answers fundamental unresolved questions in developmental and systems biology on the role of cell diversity in multicellular tissues, how heterogeneous cell processes can ensure robust organization of a tissue, and the maintenance of phenotypic equilibrium in tissue homeostasis and disease.
The self-organization of mouse small intestinal organoids from a single cell into a complex 3D multicellular structure occurs concurrently with the emergence of multiple cell fates. During this project, we have used transcriptomics and 3D imaging to identify the cell states and lineages present during organoid growth and compare their identities to the in vivo small intestine. We find that cell lineage heterogeneity can be predictive of organoid morphological complexity and develop an analysis toolkit for cell state and morphometric analysis of cells and tissues, called scMultiplex. The results from this project have been shared with the scientific community via presentations at multiple conferences, symposia, and workshops, and advance our conceptual understanding of cell heterogeneity and shape emergence in multicellular systems.
The capacity of multicellular systems to self-organize across biological scales, from molecules to cells to entire tissues and organisms that have specific functions and phenotypes, remains one of the most enigmatic processes in biology. Through complex networks of interactions and signaling feedback, cells differentiate along specialized lineages and organize to form larger-scale multicellular structures that themselves possess emergent, specialized properties within an organism. Though crucial for understanding multicellular development, homeostasis, and disease, such multicellular self-organization remains challenging to study as experimental and analysis methods must be suited to the study the large range of length scales and resolutions needed, from molecules, to cells, and to tissues. The approach of this project is to develop an analysis method that is able to bridge the biological scale between cells and tissues, where the 3D shape and structural properties of the multicellular system, e.g. the small intestinal organoid, is quantified along with its single-cell composition and molecular expression patterns at the cellular scale. This novel approach opens new questions and opportunities to analyze the origins of biological organization, patterning, and morphogenesis in 3D. In summary, the results of this project address a need for quantitative methods that bridge biological scales, uncovers a new role for cell heterogeneity during multicellular self-organization, and enables future mechanistic insights into emergence of tissue form and function from single cells within diverse multicellular systems.