Building a reference manual for how cells connect with each other

Every multicellular organism, from tiny worms to humans, elephants, and whales, needs a way for their cells to connect with each other to form tissues, organs, and organize their overall body plan. Cells have a variety of protein receptors on their surfaces that connect with receptors on other cells to form so called adhesive structures, as well as communicate with other cells and respond to cues from their environment. The sum total of these cell-to-cell interactions is called the cell surface “interactome,” which serves as a reference manual for understanding how cells connect and communicate with each other.

In a recent study published in Cell Genomics, scientists from the University of Chicago published the first extracellular interactome for the nematode worm Caenorhabditis elegans, a classic model organism for studying genetic and cellular development. The data describes extracellular interactions for 374 proteins, including 159 interactions that were previously unknown, revealing numerous unexpected connections involved in neuron development and insulin signaling.

For Engin Özkan, PhD, an Associate Professor of Biochemistry and Molecular Biology at UChicago and senior author of the paper, building this interactome has been a decade-long quest.

“Multicellular life is one complex manual, right? So many parts have to come together. The cells need to get to the right place to perform and have the correct molecules to connect with other molecules from surrounding tissues and other cells,” he said. “We've been missing so much of this blueprint because we lacked the basic data about which molecules interact with which. And that's the gap my lab has been trying to fill for the last 10 years, so that we can understand how the synaptic connections between all neurons form.”

A tiny model animal with relevance for humans

While the tiny (<1 mm long) C. elegans worm couldn’t look more different from complex multicellular animals like humans, it’s a powerful and beloved scientific model. Simplicity helps—an adult worm has about 1,000 cells, with exactly 302 neurons, all carefully mapped and genetically sequenced. They are easily manipulated with modern genetic tools, plus they grow quickly and are easy to maintain, making them ideal experimental animals.

Despite these differences, many molecular pathways—including processes for cell death, aging, metabolism, and development—are highly conserved between the worms and humans. That means many of those cellular processes work the same way in both organisms, so, scientific discoveries in worms are relevant to human biology.

“You would think by 2026, we would know the majority of interactions that hold this animal’s cells together, but we still don't, which is an opportunity for a lab like mine,” Özkan said. As a structural biologist by trade, his lab specializes in building a variety of biochemical tools, imaging techniques, protein engineering strategies and genetic modifications to document and decipher the surface receptors that help cells connect to each other.

Most surface receptors are embedded in cell membranes made from lipids, which pose a lot of technical challenges for researchers trying to study them. Özkan’s team has developed several biochemical tools that allow them to study these receptors at high volume, filling in that hole of up to 80% of their interactions that hadn’t been discovered yet. István Kovács’s group at Northwestern University also contributed novel mathematical analysis methods for the study, which was a collaboration made possible by the National Institute for Theory and Mathematics in Biology, a joint partnership between the two universities.

A full understanding of multicellular function

The new research project uncovered several protein families that interact in unexpected ways, including one group, normally thought to be involved in the growth of neurons, that also participates in insulin signaling. Experiments that increased the expression of these proteins also extended the lifespan of the worms. Other new interactions had unexpected roles in signaling for growth factors.

Since so many of these receptors are similar in humans, understanding how they work is important for understanding what they do—and, more importantly, what happens when something goes wrong and leads to disease. Combining this new set of interaction data (the interactome) with decades of work cataloging C. elegans genes (the genome) and gene expression (the transcriptome) builds a more complete reference manual for understanding basic biology.

“The modern biologist is often after this thing we call mechanism, or how it works,” Özkan said. “Now at least for cell surface molecules, we know what those molecules are supposed to interact with. Now we have good ideas about how to connect that to function, through decades of genetics work by others, and begin to complete the circle into a full understanding of multicellular function.”

The study, “Nematode extracellular protein interactome expands connections between signaling pathways,” was supported by the National Institute for Theory and Mathematics in Biology, National Science Foundation, and the Simons Foundation. Additional authors include Wioletta I. Nawrocka, Shouqiang Cheng, Matthew C. Rosen, Elena Cortés, Elana E. Baltrusaitis, and Zainab Aziz from UChicago; Leo T.H. Tang from the University of Vermont; and Bingjie Hao and István A. Kovács from Northwestern University.