No oxygen? No problem for these cancer-aiding bacteria

Humans can’t survive a lack of oxygen, but Fusobacterium nucleatum thrive without it. These anaerobic bacteria typically live peacefully in the mouth, but a little over a decade ago, scientists found that F. nucleatum can invade colorectal cancer tumors where they drive chemotherapy resistance, enhance the risk of relapse, and increase mortality rates (1,2).

In a new study, researchers at Virginia Tech used live cell imaging and multi-omics approaches to probe how oxygen affects this bacteria-tumor interaction (3). They discovered that not only do hypoxic conditions increase the rate of F. nucleatum infection in colorectal cancer cells, but that both low oxygen and the presence of bacteria together alter cancer gene expression, informing future drug development studies.

“As tumors just keep growing larger, they grow too fast, so the blood vessels can't really form at the same pace. You end up with a hypoxic core, which is a nice environment for [these] bacteria,” said coauthor Barath Udayasuryan, a bioengineer who was a graduate student at Virginia Tech-Wake Forest University at the time of the study. Udayasuryan is now a postdoctoral researcher at Genentech.

First, the team allowed F. nucleatum to invade colorectal cancer cells conditioned to either low or normal oxygen levels. Using flow cytometry and live confocal microscopy, they found that more bacteria invaded the cells in hypoxic conditions.

“It was very interesting to see how the bacterium went intracellular,” said Udayasuryan. “These were giving us some clues into okay, maybe oxygen does play a role in this interaction.”

The researchers then assessed the transcriptomic and epigenomic changes in colorectal cancer cells cultured under normal oxygen levels or hypoxic conditions, both in the presence or absence of F. nucleatum. While they expected to find different gene expression and pathway changes in the various conditions, they were surprised to see that two of the experimental conditions actually looked very much alike.

“When I first looked at the raw data, it wasn't organized as you see in the paper. They were all over the place,” said Udayasuryan. “You can see the red and blue — up and down regulation — and I'm like, ‘Wait a minute. This is very similar to this thing over here. What's happening there?’”

Udayasuryan reached out to his fellow coauthor Zirui Zhou, who was then a graduate student at Virginia Tech and who is now a clinical genomics scientist at the Children's Hospital of Philadelphia. Zhou performed a gene set variation analysis to identify pathways that clustered in the different groups. This revealed that cancer cells in low oxygen conditions without F. nucleatum  modulated similar pathways as cancer cells in normal oxygen conditions with the bacteria. The researchers reasoned that F. nucleatum  could be causing these changes to promote hypoxic conditions in the tumor, which might create a more favorable niche for themselves.

As tumors just keep growing larger, they grow too fast, so the blood vessels can't really form at the same pace. You end up with a hypoxic core, which is a nice environment for [these] bacteria. 
-Barath Udayasuryan, Virginia Tech-Wake Forest University

“Now that we understand that this phenomenon occurs and that it's quite common, how do we utilize this knowledge to develop therapies?” Udayasuryan asked. One step, he suggested, would be to take oxygen levels into account when investigating the bacteria-cancer relationship in in vitro cancer models.

“There are several challenges in trying to measure oxygen as well as live bacteria in the cancer in a patient,” he added. “So just trying to recreate those specific environmental parameters in your system will be useful.”

Udayasuryan hopes that researchers will begin investigating the molecular pathways F. nucleatum alter in cancer cells as well as performing similar experiments in other colorectal cancer cell lines. Scientists have also found F. nucleatum in pancreatic, gastric, esophageal, and breast cancer. Revealing these bacteria-cancer interactions will likely lead to new ways to treat these conditions.

“We used to study infectious diseases separately and cancer biology separately,” Udayasuryan said. “A lot of the field is moving towards understanding the roles of these microbes, and it's not just Fusobacterium but other microbes as well. So, I think it's a really exciting phase to be in.”

References

1. Kostic, A.D. et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res  22, 292-298 (2012).
2. Castellarin, M. et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res  22, 299-306 (2012).
3. Udayasuryan, B. et al. Fusobacterium nucleatum infection modulates the transcriptome and epigenome of HCT116 colorectal cancer cells in an oxygen-dependent manner. Commun Biol  7, 551 (2024).