Nav: Home

Cracking colibactin's code

February 14, 2019

For more than a decade, scientists have worked to understand the connection between colibactin, a compound produced by certain strains of E. coli, and colorectal cancer, but have been hampered by their inability to isolate the compound.

So Emily Balskus instead decided to focus on the mess it leaves behind.

A Professor of Chemistry and Chemical Biology, Balskus and colleagues are the authors of a new study that seeks to understand how colibactin causes cancer by precisely identifying how the chemical reacts with DNA to create DNA adducts. The study is described in a February 15 paper published in Science.

"It's been known since 2006 that there are a set of genes in certain gut commensal bacteria - mostly in strains of E. coli - that give them the ability to make molecules that can lead to DNA damage," Balskus said. "Over the years, there have been a number of studies that have shown a correlation between the abundance of bacteria carrying this pathway and cancer in humans, and multiple mouse models of colitis-associated colorectal cancer have demonstrated that this specific set of genes...can effect tumor progression and invasiveness."

Unfortunately, the compound created through that pathway - colibactin - has so far eluded efforts to isolate it, leaving researchers in the dark as to how it works.

"My lab started studying this, because we were interested in this problem of how you can understand a molecule you can't isolate," Balskus said. "And the summary of our earlier work to understand colibactin was that, unexpectedly, we and other groups who worked on this pathway found that this natural product has what's called a cyclopropane ring in it."

It's that chemical structure that Balskus and colleagues believe forms the colibactin "warhead" - in part because similar structures are found in other, unrelated molecules capable of causing direct DNA damage by reacting with it.

"When we realized that, we hypothesized that a direct interaction with DNA may be important for colibactin's genotoxic activity," Balskus said. "That illuminated a new strategy for getting information about colibactin's structure - instead of trying to isolate the molecule itself, we could isolate and characterize the DNA adducts, or the products of the reaction with DNA."

Isolating those DNA adducts, however, is no easy feat.

To do it, Balskus and her team turned to Silvia Balbo, a professor at the University of Minnesota School of Public Health, who developed a novel technique to identify DNA adducts based on how they fragment in a high resolution mass spectrometer.

"What we did, which I thought was a very exciting experiment, was to take a strain of E. coli that could produce colibactin and a mutant strain with the same genotype, except it didn't have the gene cluster that makes colibactin," Balskus said. "We incubated those strains with human cell lines...and isolated the DNA from both sets of cells, put it in the mass spectrometer and compared the abundance of different DNA adducts in the samples, so we were able to find DNA adducts that were only generated in the cells that were treated with the genotoxin-producing bacteria."

Armed with that information, Balskus said, their next challenge was to understand the chemical structure of those adducts.

"It looked like they came from colibactin based on the fragmentation in the mass spectrometer, but that's not enough to solve a chemical structure," Balskus said. "What researchers in my lab did, and it was a heroic effort, was to chemically-synthesize a standard...and we then compared it to the adducts produced in the cells, and they were the same."

To demonstrate that the process was also at work in living animals, the team collaborated with Wendy Garrett at the Harvard T.H. Chan School of Public Health, to conduct an experiment in which germ-free mice were colonized with strains of E. coli which could and couldn't produce colibactin.

"We showed that we were able to detect these same DNA adducts in the colonic epithelial tissue of the mice with the colibactin-producing strains," Balskus said. "That tells us that all the chemistry that we and others have been doing ex vivo really might be relevant for what's going on in vivo."

Going forward, Balskus hopes to investigate whether those same adducts can be detected in samples from patients, and to understand the specific types of DNA damage caused by colibactin and whether they influence cancer development.

And now that researchers have a good understanding of the chemical structure of the DNA adducts created by colibactin, Balskus said, they may be able to work backwards toward the molecule itself.

"The adducts we identified are most likely coming from decomposition of a larger species," Balskus said. "So we're still trying to solve this chemical mystery and working toward figuring out what the full structure might be."

In the end, Balskus said, the findings also suggest that DNA adducts could be used as a key biomarker for the activity of compounds like colibactin and other potential carcinogens derived from the activity of gut microbes.

"Up until this point, when people were looking for organisms with the ability to make these DNA-damaging compounds, they were looking for the biosynthetic genes," Balskus said. "That tells you about the genetic potential, but it doesn't tell you that DNA damage has actually occurred, and we know from other areas of toxicology that if you have good biomarkers for predicting carcinogenesis, that can be powerful when thinking about assessing cancer risks.

"It's still very early, but that is one area where our work could potentially lead," she continued. "It's still too early to know if colibactin plays a causal role in tumor development in humans, but we would like to have better ways of monitoring colon cancer susceptibility."
-end-
This research was supported with funding from the Packard Fellowship for Science and Engineering, the Damon Runyon-Rachleff Innovation Award, the National Institutes of Health, the National Institute of Environmental Health Sciences, the Center for Environmental Health Sciences and the U.S. National Institutes of Health and National Cancer Institute.

Harvard University

Related Cancer Articles:

Cancer mortality continues steady decline, driven by progress against lung cancer
The cancer death rate declined by 29% from 1991 to 2017, including a 2.2% drop from 2016 to 2017, the largest single-year drop in cancer mortality ever reported.
Stress in cervical cancer patients associated with higher risk of cancer-specific mortality
Psychological stress was associated with a higher risk of cancer-specific mortality in women diagnosed with cervical cancer.
Cancer-sniffing dogs 97% accurate in identifying lung cancer, according to study in JAOA
The next step will be to further fractionate the samples based on chemical and physical properties, presenting them back to the dogs until the specific biomarkers for each cancer are identified.
Moffitt Cancer Center researchers identify one way T cell function may fail in cancer
Moffitt Cancer Center researchers have discovered a mechanism by which one type of immune cell, CD8+ T cells, can become dysfunctional, impeding its ability to seek and kill cancer cells.
More cancer survivors, fewer cancer specialists point to challenge in meeting care needs
An aging population, a growing number of cancer survivors, and a projected shortage of cancer care providers will result in a challenge in delivering the care for cancer survivors in the United States if systemic changes are not made.
New cancer vaccine platform a potential tool for efficacious targeted cancer therapy
Researchers at the University of Helsinki have discovered a solution in the form of a cancer vaccine platform for improving the efficacy of oncolytic viruses used in cancer treatment.
American Cancer Society outlines blueprint for cancer control in the 21st century
The American Cancer Society is outlining its vision for cancer control in the decades ahead in a series of articles that forms the basis of a national cancer control plan.
Oncotarget: Cancer pioneer employs physics to approach cancer in last research article
In the cover article of Tuesday's issue of Oncotarget, James Frost, MD, PhD, Kenneth Pienta, MD, and the late Donald Coffey, Ph.D., use a theory of physical and biophysical symmetry to derive a new conceptualization of cancer.
Health indicators for newborns of breast cancer survivors may vary by cancer type
In a study published in the International Journal of Cancer, researchers from the UNC Lineberger Comprehensive Cancer Center analyzed health indicators for children born to young breast cancer survivors in North Carolina.
Few women with history of breast cancer and ovarian cancer take a recommended genetic test
More than 80 percent of women living with a history of breast or ovarian cancer at high-risk of having a gene mutation have never taken the test that can detect it.
More Cancer News and Cancer Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Reinvention
Change is hard, but it's also an opportunity to discover and reimagine what you thought you knew. From our economy, to music, to even ourselves–this hour TED speakers explore the power of reinvention. Guests include OK Go lead singer Damian Kulash Jr., former college gymnastics coach Valorie Kondos Field, Stockton Mayor Michael Tubbs, and entrepreneur Nick Hanauer.
Now Playing: Science for the People

#562 Superbug to Bedside
By now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.
Now Playing: Radiolab

Dispatch 6: Strange Times
Covid has disrupted the most basic routines of our days and nights. But in the middle of a conversation about how to fight the virus, we find a place impervious to the stalled plans and frenetic demands of the outside world. It's a very different kind of front line, where urgent work means moving slow, and time is marked out in tiny pre-planned steps. Then, on a walk through the woods, we consider how the tempo of our lives affects our minds and discover how the beats of biology shape our bodies. This episode was produced with help from Molly Webster and Tracie Hunte. Support Radiolab today at Radiolab.org/donate.