In the muddy trenches of World War I, thousands of soldiers on both sides fell ill with dysentery, a diarrheal disease often spread by contaminated water. Curiously, one German soldier deployed in the Balkans didn’t become sick when the rest of his comrades did. When scientist Alfred Nissle isolated a strain of E. coli from the soldier’s stool in 1917, he found that it had strong protective effects against Shigella bacteria, a cause of dysentery.
Over the past hundred years, this protective strain—now known as E. coli Nissle—has been used as a probiotic to promote gut health and treat gastrointestinal conditions like inflammatory bowel disease. Now, scientists are genetically engineering E. coli Nissle to perform specific functions in hopes of creating a new class of “living” medicines.
In October, Massachusetts biotech company Synlogic announced results from a small study showing that its engineered version of the bacteria provided some benefit to patients with a rare genetic disease called phenylketonuria, or PKU. People with the disorder can’t break down an amino acid called phenylalanine—or Phe for short—which is found in high-protein foods like meat and eggs. If left unchecked, phenylalanine can build up in the brain and cause intellectual disability, seizures, and behavioral symptoms.
In the Phase 2 trial, the company showed that its engineered bacteria, which 20 volunteers drank mixed into liquid, lowered levels of that amino acid. While the study hasn’t yet been published in a peer-reviewed journal, the results point to a new way of treating disease, says Timothy Lu, an associate professor of biological and electrical engineering at MIT and cofounder of Synlogic: “Similar to how you might program a computer, we can tinker with the DNA of bacteria and have them do things like produce a drug at the right time and the right place, or in this case, break down a toxic metabolite.”
PKU is typically treated with a carefully restricted low-protein diet. Newborns who test positive are placed on a special formula as soon as possible. Children and adults with the disease must avoid meat, fish, eggs, and dairy products, and many continue to drink a medical formula or take supplements to make sure they’re getting enough nutrients. The disease varies in severity, with some patients being able to consume just a few grams of protein a day. (A piece of plain white bread contains 1 or 2 grams of protein.) There are two drugs approved to treat PKU, but one isn’t widely used because it can cause a serious allergic reaction, and the other only helps people with a certain type of PKU.
Aoife Brennan, president and CEO of Synlogic, says the company wants to help patients have more freedom in what they can eat. “They understand the importance of keeping their Phe in control for their brain health. But what they really want is some relief from this incredibly strict diet,” she says.
To that end, scientists at the company genetically engineered E. coli Nissle to produce an enzyme found in plants, yeast, and other bacteria whose job is to gobble up phenylalanine. They also removed a gene from the bacteria so that it wouldn’t replicate in the gut. This was to ensure that the bacteria won’t permanently take up residence and potentially cause gastrointestinal problems later on. The engineered bacteria is cleared from the GI tract in a week, Brennan says.
For the trial, the company enrolled 20 adults with high phenylalanine levels. Three times a day, before every meal, participants drank a powdered version of the engineered bacteria that they mixed with water or juice. The volunteers kept up their usual protein intake during the two-week study so that investigators could accurately gauge the effect of the engineered bacteria. Out of the initial 20 participants, 15 completed all required doses. Of those, 60 percent—or nine people—saw more than 20 percent reduction in their phenylalanine levels at either the one-week or two-week mark, which was measured via blood draws. The average reduction in Phe was 42 percent among the nine participants.
That may seem like a small improvement, but Jessica Kopesky, a clinical dietitian at Children’s Wisconsin who treats PKU patients, says that even a 20 percent reduction can make a big difference. “The types of foods that they are able to eat are extremely limited,” she says. “Any new medical advancement that is able to help bring down Phe levels and potentially allow them to eat even a little bit more protein from food will have a large impact on the types of foods these patients can eat and the flexibility that they have in their day-to-day lives.”
The company chose a 20 percent reduction because that threshold is thought to lower the risk of brain damage due to Phe buildup, according to David Hava, Synlogic’s chief scientific officer. “We were super encouraged by the data. It really showed that we can do something with our platform and with our technology that’s clinically meaningful for patients with a really serious disease,” Brennan says. The company is planning a larger Phase 3 study in the range of 100 to 200 patients that will investigate the effects of the engineered bacteria over a longer period of time.
It’s not yet clear why the engineered bacteria worked better at lowering Phe in some of the participants compared to others. Brennan says the company is exploring what may account for the difference, but one possibility is that people who consumed more protein may have had more limited results.
Amir Zarrinpar, a gastroenterologist at the University of California, San Diego whose lab is engineering therapeutic bacteria, says a major challenge with potential treatments that target the microbiome is that this community of bacteria is heavily influenced by food and medicine and can change in the timespan of just a few days. “Showing that these therapeutics can work consistently over time is going to be a high bar for any microbiome-mediated therapy,” he says. “I think that we will find that they are going to be incredibly effective in some patients, and not so effective in others, and we will have to understand what drives these factors.”
Another challenge will be making sure these engineered bugs don’t cause too many side effects. Of the five patients who didn’t finish the Synlogic study, three discontinued due to gastrointestinal side effects, one withdrew consent, and one stopped after experiencing facial flushing due to a possible allergic reaction to the bacteria.
Still, Zarrinpar is encouraged by the results. “Diseases like PKU are good low-hanging fruit to answer the first question, which is whether the bacteria can do something that benefits the individual,” he says.
Engineered E. coli is already used in the lab to churn out therapeutic proteins, such as insulin and those found in some cancer drugs. But in those cases, patients are treated with the finished product, not the engineered bacteria itself. Delivering it straight to the gut would be a medical first. Zarrinpar says if researchers can improve how they engineer the bug, they could reprogram it to treat diseases that are more prevalent than PKU, such as diabetes, rheumatoid arthritis, skin conditions, and even cancer—which all have links to the microbiome.
Synlogic is genetically engineering E. Coli with the goal of treating gout and inflammatory bowel disease, but those efforts aren’t as far along. Meanwhile, Vedanta Biosciences of Cambridge, Massachusetts, is using bacteria in their natural form to combat infections of dangerous bacteria, such as Clostridium difficile, as well as cancer and food allergies. The company isn’t engineering bacteria, but is looking for groups of bacteria with drug-like properties and carefully cultivating several beneficial types together.
Zarrinpar says if Synlogic’s engineered bacteria continue to show progress, it could open the door to a new way of treating disease. “This is just the first wave of us being able to manipulate bacteria to perform therapeutic actions within the gut,” Zarrinpar says.
