Cancer and microorganisms
Scientists have developed a new way to detect oncogenic bacteria and viruses
Polina Gershberg, Naked Science
The study, published in the journal Genome Biology, shows how the study of tumors can identify viruses and bacteria associated with these neoplasms. This work will help determine the pathogenesis of many types of tumors and, quite possibly, create vaccines against certain types of cancer.
Genome sequencing is a research method that has a huge potential for detecting microbial agents. If a complete genome sequencing is carried out in a sample of tumor tissue, then the DNA of pathogenic microorganisms associated with the development of cancer will also be sequenced. This will allow scientists to collect data on the relationship of various viruses and bacteria with certain types of neoplasms.
Scientists from the University of East Anglia conducted a comparative analysis of more than 70 combinations of various tools and settings on 100 fictitious genomes. They consisted of real data on the sequencing of tumor tissues, which were supplemented in various proportions with information obtained during the sequencing of bacterial genomes. In the process, scientists have identified two computer programs that are best suited for processing genomic sequences and detecting DNA pathogenic agents.
These programs turned out to be mOTUs2 and Kraken. The F-measure of classification quality using these programs was 0.9 and 0.91, respectively (the F-measure is called the harmonic mean between completeness and accuracy of classification; ideally, this indicator should tend to unity). Based on these tools, scientists have developed a combined algorithm called SEPATH, which allows us to efficiently and accurately establish the relationship between metagenomics (the diversity of genetic material in a sample) and the disease itself.
SEPATH was tested on several real data sets obtained by sequencing samples of gastric and cervical cancer. It is reliably known that these diseases are often caused by the pathogenic influence of bacteria of the genus Helicobacter and viruses of the genus Alphapapillomavirus, respectively. Upon detailed examination, many other potentially dangerous microorganisms were found in these kits. So, in several data sets on cervical cancer, the algorithm showed the presence of treponema, the causative agent of syphilis. In the case of stomach cancer, except for Helicobacter, genes of viruses of the genus were found in most samples Lymphocryptovirus – for example, the Epstein-Barr virus belongs to them.
"We are just beginning to uncover the role that these and other pathogens may play in the development of cancer," says the study's lead author Dan Brewer. "There is already an HPV vaccine that is believed to prevent about 70 percent of cases of cervical cancer. We hope that by identifying bacteria and viruses associated with other cancers, new vaccines may be developed in the future."
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