Fruit flies will produce the next groundbreaking medical therapy
And, according to a new life cycle assessment, will significantly reduce biotech's environmental footprint
Deep in a lab at the University of Washington, Dr. Cole DeForest and his students meticulously tend to suspensions of E. coli, their masses of growing cells clouding caramel broth. While these benchtop bioreactors look fancy, long plastic tubes snaking out of shining metallic canisters, their contents appear altogether unassuming, if not a little bit like old cappuccino.
Unlike cappuccino though, these humble slurries of E. coli can be used to engineer materials that transform in spectacular ways.
From carriers designed to deliver bioactive proteins to injectable hydrogels for controlled cell delivery, these materials are uniquely powered by photo-responsive proteins made in Dr. DeForest’s E. coli, their photochemistries transforming initially homogeneous materials into high-performance implants.
While biomaterial designers routinely fashion materials that shape shift, aggregating or degrading in response to simple changes in pH or temperature, DeForest told me that photochemistries allow engineers to “selectively modulate or functionalize an initially uniform material,” precisely controlling how they assemble, transform, and/or degrade in real time at fractions of a second and at resolutions that are “subcellular.”
To use a metaphor, the bakers in the DeForest Lab not only seek to control how the cake (ie. the biomaterial) is made—what ingredients sit inside each layer and how the tufts of colorful frosting blend across the surface—but also how it’s served, eaten, and metabolized by the wedding guests (ie. the invading cells).
For example, a photo-responsive therapy made in the DeForest Lab may one day be injected into the knee of a patient with osteoarthritis, filling a hole in the knee’s cartilage. After injection, the joint could be illuminated with a specific wavelength of light chosen to activate the photopolymer network, solidifying the hydrogel in place in a geometry ideally suited for new cartilage development. Additional proteins in this gel could be designed to degrade in response to other stimuli, such as changes in the joint’s pH level or the concentration of enzymes secreted by inflammatory cells, releasing drugs that promote further healing.
Unlike many regenerative biomaterials, which often rely on oil-derived polymers or animal-derived extracellular matrices, Dr. DeForest’s unique 4D materials are fabricated almost exclusively from recombinant proteins (aka proteins made by artificially inserting the DNA sequences that encode them into an organism that may not typically make them—effectively “remixing” or “recombining” that creature’s genome).
But why use E. coli and not some other creature to make these proteins?
Every living organism on Earth makes proteins. The hydrangeas lining the stone walkway at my neighborhood park, their cells bursting with protein in splotches of blush as their petals paint the wind in watercolor. The honeybees dancing across the hydrangeas’ pink faces, their gelatinous pollen-covered abdomens full of protein. The mushrooms springing from the oak stump rotting by the dog park, their hyphae inching between the pores of wet summer soil, protein hugging the hydrangeas’ roots. In theory, Dr. DeForest could have picked any of these organisms to make his photopolymers.
However, the biotech industry typically only uses a select few creatures to manufacture recombinant proteins. Until fairly recently, this collection of organisms, otherwise known as “protein expression systems,” was limited to just four single-cell options: E. coli, yeast, CHO (Chinese Hamster Ovary) cells, or HEK (Human Embryonic Kidney) cells.
So why use E. coli and not one of the other three systems?
For starters, E. coli is easy to grow, fast, and exceptionally modular, meaning Dr. DeForest and his students can easily make as much or as little of these proteins as they need in just a matter of days. Dr. DeForest didn’t hesitate to express his praise for the bacterium: “Working with E. coli is exceptionally cost effective. Protein expression can be readily scaled to large volumes as needed with minimal process optimization. We have several projects in our lab where we’re making intact hydrogels exclusively from recombinant proteins expressed in these systems.”
And if it works well to make the proteins DeForest needs, why would he pick a less efficient, more expensive protein expression system? Working with E. coli doesn’t come without its disadvantages though, the biggest being that “bacterial proteins don’t have the same sort of post-translational modifications,” DeForest described, “that may be needed to interact as intended with human cells.” Because E. coli are less evolutionarily complex than mammalian cells, they can’t make all the complex, often tissue-specific proteins our cells make. They just don’t have all the right machinery to finish the task.
For these more complex proteins, instead of using E. coli, the DeForest Lab uses mammalian cells, either HEK or CHO. “Both of these benefit tremendously by being able to produce proteins with proper post-translational modifications. These proteins are generally more bioactive and can be more complex in structure, but they are also much more expensive to produce,” DeForest said. The need for costly media components to grow mammalian cells limits the subsequent volume of protein that can be practically made. Ultimately, these mammalian protein expression systems just aren’t amenable to scale up in the same way bacterial expression systems are.
That begs the question: Can any protein expression system produce highly complex mammalian proteins efficiently and at low cost?
During his PhD work in cell biology at the University of Edmonton, Dr. Matt Anderson-Baron spent late nights and long weekends trying to answer that question, tinkering with the technology that ultimately led to the founding of Future Fields, the Edmonton-based startup he co-founded with his wife Jalene Anderson-Baron in 2018.
Anderson-Baron (Matt) believes they’ve created a superior protein expression system, one that balances complexity and cost by harnessing a common kitchen nuisance.
Fruit flies to be specific. Drosophila melanogaster to be scientific.
While I wanted to paint a picture detailing just how exactly this all happens, how the humble fruit fly creates incredibly valuable chains of peptides that people like myself can then buy and use in the lab for medical research and drug development, I didn’t actually visit the startup’s laboratory and production facility. This blog doesn’t have that kind of budget for travel. Or really any budget if we’re being honest. So I did the next best thing:
I imagined the larvae of the commonly-loathed fruit fly, small white worms wriggling across a floor of decomposing fruit, peaches and plums transmuting to valuable protein inside their delicate bodies.
I imagined their short lives peacefully and usefully spent eating and pooping, their spent forms piling into haphazard mounds on the chamber’s false bottom, absolutely brimming with gold.
I imagined the heavy drone permeating the room next door, the buzz of adult Drosophila melanogaster wings filling the air, scoring the dance of thousands of multi-faceted eyes across the backdrop of a temperature- and humidity-controlled mating chamber as they birthed the next generation of progeny.
The company’s current small library of products includes Fibroblast Growth Factor 2, Prolactin, and, as of this fall, Interleukin 2 and Interleukin 10, but they’re committed to reaching far beyond growth factor manufacturing. They’ve also been producing a hybrid drug molecule for one of Jenthera Therapeutics’ experimental gene therapy cancer treatments that is currently in preclinical testing.
With that said, are there limits to what proteins fruit flies can produce? Anderson-Baron believes Drosophila can “do more than any of the other [protein expression] systems.”
“Our [protein expression] system is basically 200 expression systems in one,” he said. “The reason for that is that you literally have 200 distinct cell types with distinct cellular machinery, each of which is equipped differently for making proteins. We have the tools to do selective expression in Drosophila. If we do come across proteins that are difficult to express, we can screen multiple cell types in parallel to see which cell type is best suited for making this particular protein. In traditional single cell expression systems, you kind of get one shot or you could try all three.”
Vassie Ware, a molecular biologist at Lehigh University, found that claim to be both reasonable and exciting. Dr. Ware studies how ribosomal heterogeneity in fruit flies impacts subsequent protein expression, and for her, as a molecular biologist, it all came down to proper function.
“For proteins that every cell type makes naturally,” Dr. Ware explained, “having all 200 cell types make that protein is reasonable, even though the protein might be modified differently in some cell types,” as long as you can “separate the functional from non-functional protein that this whole system makes.”
For other proteins that not every cell naturally makes, Dr. Ware stipulated that “it really boils down to whether or not there’s anything specific about how the protein functions that is dictated by one particular cell type.” Future Field’s claim to be able to selectively engineer individual cell types “sounds good” to Ware. “It sounds very good, as long as what [the flies] are making comes out as functional and you can demonstrate that it functions the way you would expect.”
Though fruit flies have great potential for making complex proteins at cost, their biggest selling point may be their low carbon footprint.
In total, the healthcare supply chain emits 3.12% of global emissions, according to the 2023 Carbon Impact Report published by My Green Lab, and those emissions are projected to grow without significant intervention. The report estimates that the global biotech market is expected to increase by 13.9% annually from 2023 to 2030, noting that the industry needs to focus on rapid decarbonization of its supply chain to reach UN climate goals while accommodating the projected growth.
According to a recent third party life cycle assessment, Future Fields claims that their production process is more sustainable than traditional biomanufacturing, requiring 75% less water and generating 86% fewer greenhouse gas emissions than other protein expression systems.
Future Fields’ low environmental impact can undoubtedly be attributed to the fact that they don’t need to rely on stainless steel bioreactors to make product, opting instead for thousands of tiny living bioreactors in the form of flies. Traditional biomanufacturing using single cell organisms grown in stainless steel tanks necessitates a host of energy-intensive inputs, including the agricultural feedstocks that go into bioreactors (the sugars that fuel cellular growth), heating and cooling the bioreactor itself, and steam sterilizing the stainless steel tanks in between production batches.
While single-use bioreactors require less energy to produce and operate by eliminating the need for steam sterilization, they create plastic waste in the form of single-use plastic liners.
By using fruit flies as living bioreactors, Future Fields isn’t bound to the confines or the stringent energy requirements of a bioreactor tank. It doesn’t make their production system energy positive though. The flies still need to be fed. They need to be reared in humidity- and temperature-controlled rooms. The proteins still need to be extracted, purified, and shipped to customers, all of which uses energy and creates emissions.
But fruit flies ultimately leave no waste. No plastic bioreactor liners piling up in landfills. No major infrastructure to be scrapped in 10-15 years. Just biomass. Lots and lots of biomass in the form of fly bodies and rotten fruit. “Our goal is to be completely waste-free,” Anderson-Baron said. “As we scale and start producing meaningful quantities of biomass, we can begin to generate high value products.” Products like fertilizer that will help Future Fields achieve a more circular supply chain.
During my conversation with Dr. Anderson-Baron, it was clear that sustainability is encoded into Future Fields’ DNA. From a technological platform built on a vision of circularity to the simple act of running their -80 freezers at -70 degrees Celsius to save energy and their employee-led initiative to deliver sterilized ice packs for reuse by Meals on Wheels, the motivation to build an environmentally-conscious company obviously runs deeper than a mere market force or industry mandate.
“Being a dad is truly my greatest joy,” Anderson-Baron told me, “and my daughter is the single greatest motivating factor for building this company.” He hopes their startup “can play some small part in solving the world’s biggest problems”—curing debilitating disease, solving food insecurity, and mitigating climate change—so that they don’t exist in his daughter’s future.
At the beginning of November, Future Fields’ announced the opening of their new 6,000 square foot production facility, called Instar 1.0, bringing the production of recombinant proteins in fruit flies at scale and their sustainability promise one step closer to reality.
Perhaps proteins grown in fruit flies at Instar 1.0 could one day be deployed in the DeForest Lab’s photo-responsive biomaterials, ushering in an era of sustainable healing for both patients and planet.