Q&A: Whitehead Institute Member Pulin Li on recreating development in the lab

As an embryo matures from a cluster of cells, it undergoes a remarkable transformation, arranging itself into distinct, three-dimensional tissues and organs. This complex process is guided by blueprints called gene regulatory networks that dictate which genes are turned on and off and when. Meanwhile, morphogen gradients, groups of signaling molecules that act as compasses, offer cells spatial cues, directing the cells’ behavior and organization.

While studying multicellular organisms in the lab can offer a glimpse into what early development looks like, so much about embryonic development is still shrouded in mystery. In order for scientists to fully understand this process, they need ways to not only observe but manipulate it on a molecular level using approaches from synthetic biology, which offers tools for dismantling and redesigning biological systems.

In this Q&A, Whitehead Institute Member Pulin Li discusses how her lab ventures beyond mere observation to actually engineer developmental events in the Petri dish, and why this approach is vital for understanding health and disease more broadly. This interview is edited for length and clarity.

What are the different areas of focus in your lab?

Our lab is focused on understanding the rules of cell-to-cell communication in spatially organized tissues. We’re asking questions like, “how does communication help different cell types know where they are, and what they should become to pattern a tissue or to change the shape of the tissue?” Our lab uses reconstitution approaches to tackle these questions — the process of recreating cell communication in a culture dish.

What prompted you to investigate cell communication through engineered circuits that mimic natural signaling pathways?

In a developing embryo, there's a whirlwind of activity happening simultaneously. It's like trying to unravel a mystery with multiple suspects — when you see a particular trait, it's tough to pinpoint exactly what's causing it.

When I worked with animal models as a student, I found myself fascinated by the richness of phenotypes and behaviors, but dissatisfied by the level of understanding. The inherent complexity of animal systems is undeniably beautiful, but it also presents a significant challenge in terms of understanding developmental processes as dynamic systems — just altering one gene can lead to a cascade of outcomes, but the constant discovery of new genes raises an important question: how do you put these genetic interactions together to explain how many cells coordinate with another in space and time?

When I was reflecting on this question and thinking of a different way to describe developmental processes, I came across early studies describing gene regulatory networks. Think of them as instruction manuals that cells use to decide which genes to turn on or off and when to do it. This meant that I was no longer going to be confined to considering genes in isolation; instead, I could explore their interactions in time and space, and even model these dynamic behaviors.

We're approaching development from an engineering perspective. We think of building blocks like genes as versatile tools that are reused in different scenarios, but with tweaks and adjustments to create new outcomes. We want to break down development into these modular components to figure out how they come together to create fascinating traits in an organism.

What are the challenges of recreating developmental events in the lab?

We engineer cells by modifying their DNA sequence, and deleting or introducing new genes in order to understand what specific functions these genes might be playing in cell communication. This, however, isn't a simple task — we painstakingly insert these genes into cells one by one. This process pushes the boundaries of synthetic biology. Some of the behaviors we’re programming — like morphogen gradients — may require just a few modifications. But others could demand a lot more genes, which means we’re more likely to run into challenges.  To overcome these technical limitations, we need innovative technologies that can precisely add genes to cells without causing disruptions.  

A class of molecules called signaling proteins can also coordinate cell behavior. To understand how these signaling proteins achieve this, why is it important to study their movement through tissues at various timescales?

Proteins like Hedgehog, which transmit information between cells, are crucial for communication in a multicellular system. By studying how far and how fast these proteins travel, we can determine the communication dynamic between different cell types. However, signaling molecules move in a highly heterogenous way. This is why we’ve been doing miniature scale measurements — from milliseconds to seconds — to track the movement of individual proteins, such as signaling protein Hedgehog, in a Petri dish.

The behavior of individual molecules doesn't just occur in isolation. Instead, it's influenced by the collective actions of many molecules interacting with each other and with surrounding cells and structures. These behaviors combine to create patterns over long distances, which helps us connect characteristics of signaling proteins to bigger biological processes.

Can you offer a glimpse into a current project your lab is particularly excited about?

We're trying to understand how a type of tissues, called stromal tissues, control organ development and physiology. Building an organ of a certain identity and shape is a complex process that requires interaction between different cell types. Both in embryonic and adult organs, stromal tissues communicate with epithelial tissues. This close interaction is critical for guiding proper organ development, and for regulating tissue homeostasis (the maintenance of a balanced internal environment), immune response, and injury repair.

Yet, how different types of stromal cells come together, where they come from, and how they team up is a mystery. In fact, stromal tissues are missing in most engineered organ models in a dish. Our goal is to better understand the development and function of stromal tissues, and ultimately to reconstitute the communication between epithelial and stromal tissues to create better organ models. Currently, we are focusing on the stromal tissues of the lung, an organ with fascinating shapes, function and evolutionary history.

How do you envision your research extending beyond embryonic development and tissue engineering?

It's well-known that the stromal tissues helps with the shaping of organs during development. But recently we’re also discovering that in adult organs, the tissues also help modulate immune response of the organ during viral infection. It turns out, when viruses attack, epithelial tissues are the first line of defense. But these cells have a pretty low sensitivity to influenza virus infection — only about 5% can spot the virus and sound the alarm. When the virus sneaks past them, it goes after the stromal tissue. The stromal cells, however, are way better at spotting infections than the epithelial cells. We call it "tiered innate immunity." Basically, stromal cells are like the backup plan, kicking into action to protect organs before an infection enters the bloodstream. This means the role of stromal tissues goes well beyond development — they keep organs safe from infections.