A new method for detecting cancer relies on patterns of microbial DNA from bacteria and viruses present in the blood. Looking at more than 18,000 tumor samples, researchers from the University of California San Diego School of Medicine found several distinct microbial signatures associated with cancer types.
In a paper published todayin Nature, the team found that among 10,481 patients with 33 types of cancer, several molecular patterns emerged based on the DNA of microbes associated with these cancers. Some were expected, as in the case of the HPV virus with head/neck cancers. But the researchers found several others, including DNA from Faecalibacterium species in colon cancer but not others.
“Almost all previous cancer research efforts have assumed tumors are sterile environments, and ignored the complex interplay human cancer cells may have with the bacteria, viruses and other microbes that live in and on our bodies,” said author Rob Knight, PhD, principal investigator of UCSD studyand an internationally recognized leader in microbiome research. “The number of microbial genes in our bodies vastly outnumbers the number of human genes, so it shouldn’t be surprising that they give us important clues to our health.”
Microbial signatures differ by cancer type
ReferencingThe Cancer Genome Atlas, the NCI database containing genomic and other information from thousands of patient tumors, the team first noticed distinct microbial DNA patterns among 18,116 tumor samples.
By applying machine learning, they next looked for associations between microbial DNA signatures with specific cancers. After several rounds of modeling, researchers were able to pinpoint a cancer type using only microbial DNA from the patient’s blood.
To determine if the signatures were present and similar between early stage and later-stage cancers, the researchers examined high-grade (stage III and IV) cancers from the dataset and found that many cancer types could be determined at earlier stages when relying solely on blood-derived microbial data.
Real-world microbial DNA testing
The team tested the concept comparing blood-derived plasma samples from 59 patients with prostate cancer, 25 with lung cancer, 16 with melanoma, and 69 healthy control patients.
After applying several machine learning models, they were mostly able to detect patients with cancer from those without. Specifically, they could identify a person with lung cancer with 86 percent sensitivity and a person without lung disease with 100 percent specificity. They could often tell which participants had which of the three cancer types. For example, the models could correctly distinguish between a person with prostate cancer and a person with lung cancer with 81 percent sensitivity.
Several hurdles need to be addressed to advance this technology clinically, including testing in a larger, more diversified patient populations. Just as important, researchers need to look for ‘normal’ blood-based microbial DNA patterns in healthy individuals across many populations.
Going beyond diagnostics, this research opens the door to new theories about the interactions between cancer cells and microbes. Why are microbes specifically associated with certain cancers? What roles, if any, do they have in cancer development, growth and spread? Can they be commandeered to attack cancer? Does anti-microbial therapy have any role in cancer treatment?