Crohn’s disease patients with certain gene mutations may not benefit from normally helpful bacteria in their guts, new research published in the journal Science revealed. The new insights may alter how clinical trials are performed and lead to more effective probiotic treatments for patients with Crohn’s disease.
Researchers have known for some time that the gut microbiome — the bacterial flora of our intestines — impacts the immune responses, and much effort has been put into exploring the effects of beneficial bacteria through added probiotics for patients with gut problems.
Patients with Crohn’s disease have an altered composition of the gut microbiome, a condition called dysbiosis. Additionally, people with Crohn’s have gene mutations that disrupt parts of the immune system geared to sense disease-causing gut bacteria and normally trigger the immune response against the bad bacteria. Without defense, Crohn’s patients are overly exposed to the harmful effects of bad microbes.
Researchers at the California Institute of Technology examined the interactions between genes and gut immune responses in mice through the study “Gene-Microbiota Interactions Contribute to the Pathogenesis of Inflammatory Bowel Disease.”
“In this study we were curious to see if some of the genes that are important in sensing pathogenic bacteria may also be important in sensing beneficial bacteria to promote immune health,” said the study’s first author Hiutung Chu, in a press release. “Typically, the signals from these beneficial commensal microbes promote anti-inflammatory responses that dampen inflammation in the gut. However, mutations in genes that sense and respond to pathogenic bacteria would also impair the response to the beneficial ones. So it’s kind of a new spin on the existing dogma.”
Chu, a postdoctoral scholar in biology and biological engineering who works in the laboratory of Sarkis Mazmanian, a professor of Microbiology at Caltech, honed in on the bacterial species B.fragilis to study the interactions between the bacteria and two genes long known to be defective in Crohn’s disease patients.
The genes, ATG16L1 and NOD2, are mutated in a way that renders them dysfunctional. Researchers found that in mice lacking either one of the genes, the addition of B. fragilis did not have beneficial effects on Crohn’s symptoms. This lack of response could be attributed to an inability to produce regulatory T-cells that are crucial for responding to inflammatory symptoms.
To confirm that the findings had relevance also for humans, the research team analyzed blood samples, collected at Cedars-Sinai Medical Center in Los Angeles, from both Crohn’s patients and healthy volunteers.
“We could see that certain patients’ immune cells responded to Bacteroides fragilis, while immune cells from other patients didn’t respond at all,” said Chu. “Because the cells from Cedars had already been genotyped, we were able to match up our results with the patients’ genotypes: immune cells from individuals with the protective version of ATG16L1 responded to the treatment, but cells from patients who had the mutated version of the gene showed no anti-inflammatory response to B. fragilis.”
The study showed that Crohn’s disease might arise by the dual consequences of the faulty genes — the inability to attack harmful bacteria and to trigger protective immune responses elicited by typically beneficial bacteria. Findings underscore the intricate relationship between the genome and the microbiome.
“What (Chu) has shown is that there are specific bacteria in the human microbiome that appear to utilize the pathways that are encoded by these genes, genes normally involved in killing bacteria, to send beneficial signals to the host,” said Mazmanian.
Mazmanian said the new study suggests that, while previous work led to using B. fragilis as a probiotic treatment for certain disorders, some patients would never benefit from the treatment because of their personal genetic predisposition.
“Right now, clinical trials don’t do a good job of identifying which patients might respond best to treatment, but our experiments in mouse models suggest that, conceptually, you could design clinical trials that are more effective.” Mazmanian said.