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Biomedical engineers at Duke University have devised an algorithm to remove contaminated microbial genetic information from The Cancer Genome Atlas (TCGA). With a clearer picture of the microbiota living in a variety of organs in both healthy and cancerous states, researchers will now have the ability to find new biomarkers of disease and better understand how numerous cancers affect the human body.
In the first study with the recently decontaminated dataset, the researchers have already discovered that normal and cancerous cells cells have a slightly different microbiota composition, that bacteria from these diseased websites can enter the bloodstream, and that this bacterial data might help diagnose cancer and predict patient outcomes.
TCGA is a landmark cancer genomics program that molecularly characterized over 20,000 main cancer and matched healthy samples spanning 33 cancer types. It has produced more than 2.5 million gigabytes of”omic” data. The atlas includes which DNA is present, what epigenetic markers are on the DNA, which DNA is switched on and which proteins are being generated. It’s freely available for public use.
1 study from the atlas data revealed a wealth of Fusobacterium nucleatum in colorectal cancer, which has since been shown to be indicative of point, survival, metastasis and even drug responses of this sort of cancer. Many more studies have searched for such bacterial biomarkers, however few have been discovered. A big reason for this is pollution.
All microbiota studies are plagued by the notion that if you find a microbe, was it really in the tissue or was it contamination introduced during processing? We’ve invented a method that can extract the microbes that were truly in each sample and used it to build what we’ve called The Cancer Microbiome Atlas, which will be a tremendous resource for the community and allow us to understand how cancer alters an organ’s microbiome.”
Xiling Shen, the Hawkins Family Associate Professor of Biomedical Engineering at Duke
When bacteria become introduced into the samples accidentally by the laboratories, it becomes hard to discern which species were actually in the samples to start with. While similar microbiome studies employing microbe-rich material such as feces can conquer little amounts of contamination, the comparatively miniscule samples taken from live human organs and tumor samples cannot.
When analyzing a subset of TCGA sequencing data, previous analyses found that microbial DNA from a range of species was caused by lab contamination.
The method for removing contamination from TCGA data was devised by Anders Dohlman, a graduate student in Shen’s laboratory. Dohlman first compared the microbiome signatures involving cancer tissues from other organs and blood, and ruled out contaminant species which showed up indiscriminately. Then he compared the microbiome signatures of identical samples which were processed at separate sites, ranging from Harvard to Baylor. Dohlman concluded that the microbial species which can only be discovered from a specific site would be the contaminants, allowing him to assign a special contamination signature for each website.
“A huge challenge in this process was mixed-evidence species, which are bacteria which are both a contaminant and endogenous to the tissue,” said Dohlman. “But because TCGA has so many different types of data, we were able to tease it out. Big data actually helps!”
The effort is already paying dividends in a variety of ways. After using Dohlman’s decontamination algorithm, the researchers took a close look at the microbiota signatures of samples obtained from colorectal cancer patients. They discovered two unique groups of bacteria frequently found together, one of which seems to be related to patient survival.
The researchers also discovered that some cancers do indeed alter the microbiome of their resident organs. It might be, Shen reasons, that tumors alter an organ’s microenvironment, which makes it less conducive to different microbial species. And by looking for microbial signatures within patient blood samples, they also discovered that, despite conventional wisdom to the contrary, some bacteria does find its way into the blood vessels, which could also provide an indication of a cancer’s progress.
“There’s been a sort of crisis in the field about whether high-profile papers can be replicated, because of the challenge of contamination,” said Shen. “For example, while one center would be able to replicate its results, another center wouldn’t. This explains why: Each center has its own quite consistent bias. (Its own resident microbe contaminants.) In the future, new studies may use our method to remove this bias and replicate results, and research centres might be able to use their bias we’ve identified to mitigate their contamination.”
Dohlman, A.B., et al. (2021) The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host & Microbe. doi.org/10.1016/j.chom.2020.12.001.