• intermediates in the morphogenesis of intestinal villi.
  • output from a computational model for self-organized tissue origami.
  • 4D printing methods for preparing precise arrays of self-organizing tissues.
  • breast organoid

The human body contains over 10 trillion cells spanning hundreds of morphologically distinct cell types. These cells are arranged into three dimensional structures called tissues that help cells work together. Our goal is to reveal how tissue structure emerges through programs of self-organization and to harness these programs for regenerative medicine and to block the progression of disease.

What is tissue structure?

cellular structures combine progressively larger to result in a human.

Tissue structure—or the number, composition and three dimensional arrangement of cells—helps to coordinate cellular behaviors by organizing the flow of chemical, mechanical, and electrical information. Thus, building tissue structure correctly and maintaining tissue structure over time are prerequisites for engineering functional organs and stopping the progression of diseases like cancer.

However, we have an incomplete understanding of tissue structure and its implications on human physiology. For example, precise measures of tissue structure that capture its intrinsic dynamics and heterogeneity do not exist. Additionally, strategies for controlling the formation of tissue structure by engineering the process of self-organization remain in their infancy. Further, the mechanisms through which the structure of tissues change during the progression of diseases like cancer and aging have not been defined.

We are therefore interested in three general questions about how tissue structure forms and functions:

  1. How does tissue structure form through the process of self-organization?
  2. How does tissue structure help cells to arrive at collective decisions and to organize collective behaviors?
  3. How does tissue structure breakdown during the progression of diseases like cancer?

To answer these questions we take a synthetic approach, studying and engineering tissues from the bottom-up. This approach allows us to measure and perturb the molecular and physical properties of individual cells, reconstitute them into living tissue, then observe their interactions to reveal the underlying "principles" guiding their self-organization and decision making. We study the cells and tissues of the human breast, digestive track, pancreas, and immune system. Our work incorporates experimental principles from the chemical, biological, and engineering sciences.

Building tissues: Controlling the arrangement of cells in three dimensions

Engineering complex human tissues from simpler cellular building blocks remains difficult. One important challenge is defining the initial arrangement of cells and ECM molecules in three dimensions so that the cells’ own program of self-organization can take over. We have developed several tools to facilitate this process.

The first is a chemical approach for patterning tissues that incorporate multiple cell types, arranged with high spatial precision, and assembled from the bottom-up and across three-dimensions. Cells are functionalized with chemical “Velcro”—short DNA oligonucleotides that impart specific adhesive properties between neighboring cells. Hybridization of complementary DNA sequences enables the assembly of multicellular structures with defined cell-cell contacts. We call this approach DNA Programmed Assembly. Our current efforts aim to extend the synthetic capabilities of DNA Programmed Assembly, so as to help more robustly guide tissue self-organization, with the goal of building fully integrated and functional human tissue. For example, we are working to program the assembly of the human mammary gland from purified cellular components in vitro. We are using the assembled structures as models to learn how cell-cell signaling networks regulate the behaviors of cells in vivo, and to reveal how these networks breakdown or are co-opted during the early stages of breast cancer.

We are also developing tools to precisely define the absolute number and composition of cells when placed into culture. In collaboration with Adam Abate’s lab at UCSF, we developed a technique called Printed Droplet Microfluidics. At its core, this technique provides a quantitatively precise means of combining any combination of cells together into a small volume of liquid. Once a combination is prepared it is transferred to physiologically relevant conditions for long-term study.

Representative publications

Building tissues: Understanding and engineering self-organization

cycle diagram: cell-cell signaling arrow points from tissue structure to microenvironment, then gene regulatory networks arrow points from microenvironment to cell state, then active mechanics arrow points from cell state back to tissue structure.

Cells are living materials—their properties are not static but rather change dynamically in response to their surroundings. This property of cells as materials gives them the capacity to self-organize into a wide variety of three dimensional structures. Indeed, the capacity of cells to self-organize is critical to their normal developmental and their ability to self-repair. A better understanding of how tissues self-organize will improve our ability to synthesize tissues and organs in the lab, and suggest new strategies to slow the breakdown of tissue structure that contributes to the initiation and progression of diseases such as cancer.

We are working to understand the physical principles used by cells to self-organize robustly into specific tissue structures. For example, we are characterizing the active mechanical properties of the interfaces between cell types in the human mammary epithelium to reveal the forces that guide their self-organization. We are particularly interested in how these properties contribute to the heterogeneous nature of tissue structure observed both in vitro and in vivo. We are also asking how genes involved in breast cancer alter cell properties, increasing the probability of developing invasive disease.

Video, 10 seconds, no audio. We investigate how the mammary gland maintains a single three-dimensional structure through a robust program of self-organization. Luminal (green) and myoepithelial (red) cells self-organize correctly in extracellular matrix (IrECM, left) but into an inverted structure in non-adhesive microenvironments such as agarose (right).

We are also investigating how tissues regulate the pattern and extent of folding during their self-organization. This project has two components. In the first, we are working to engineer the autonomous folding of tissues using cells that contract in a manner that causes the tissue to fold. In the second, we are collaborating with Ophir Klein’s lab to understand the molecular and physical mechanism through which a pattern of folds form during the morphogenesis of intestinal villi. Our goal is to place this process under engineering control and to improve the regeneration of the gut.

Video, 5 seconds, no audio. Tissue origami: groups of mesenchymal cells dispersed in a loose and fibrous ECM compact to form condensates. We use this fundamental cell behavior to engineer tissues that fold up along specific trajectories, in a manner analogous to self-folding origami. Fibroblasts (green) generate forces that transform a collagen-rich gel (black) into an origami-like four-fold junction.

In a parallel effort, we are developing tools to reveal how cell-cell signaling networks allow cells to couple their state across a tissue or allow cells to change their identity as they move into, or out of, specific microenvironments (niches). Our goal is to combine these measurements with an emerging understanding of cell mechanics during self-organization to provide a more holistic molecular and mechanical view of tissue formation.

Representative publications

Collective behaviors and decision making

Individual cells can behave differently, even when in the same tissue. These behavioral differences can combine in non-intuitive ways to drive new and emergent behaviors at the level of cell communities. For example, many cellular behaviors related to growth, motility, differentiation and adhesion are controlled by signaling pathways downstream of the protein Ras. Ras integrates signals impinging on cells from their extracellular environment, and is also one of the most frequently mutated proteins in cancer. We demonstrated that sustained patterns of heterogeneity (also known as cell-to-cell variability) in signaling downstream of Ras are sufficient to drive several emergent behaviors that are not observed when the pathways are activated homogeneously among all the cells of a tissue. These emergent behaviors include dissemination of single hypermotile cells, basal cell extrusions, as well as collective and motile protrusions (see video below). These phenomena are frequently associated with aggressive tumors, a context where heterogeneity can become exaggerated.

We are also working to understand how different types of cells communicate within tissues to arrive at collective decisions. In order to investigate collective cell decision making, we are integrating human tissue models (organoids) with new multiplexed single cell analysis tools developed in the lab (MULTI-seq). These tools allow us to investigate how groups of interacting cells within a tissue change their collective decisions as we alter tissue composition, snip lines of cell-cell communication, or perturb the gene-regulatory networks that integrate these lines of communication. We are focusing our efforts on immune cell activation (in collaboration with Matt Thomson at Caltech) and hormone signaling in the human breast (in collaboration with Thea Tlsty at UCSF).

Representative publications

Probing the organization of the cell surface

Many cell-surface receptors for extracellular signals can organize into larger, nanoscale structures. How do these nanoscale structures affect the propagation of signals from the outside to the inside of the cell? This has been a difficult question to answer because few tools are available to observe or alter the organization and dynamics of these signaling complexes at the nanoscale. In collaboration with Young wook Jun’s and Natalia Jura’s labs we are developing new tools to image (e.g. monovalent quantum dots) and perturb (e.g. DNA-scaffolded multivalent ligands) the dynamics and organization of these receptors with a focus on the biology of the human Notch and Epidermal Growth Factor Receptors. Our goal is to provide new insight into the spatial organization of these signaling complexes, and how their dynamical organization contributes to cell-cell interactions affecting cell-fate decisions and cancer.

Representative publications