NOV 07, 2019 10:31 AM PST

A Way to Predict Which Microbes Can Cause Cancer

WRITTEN BY: Carmen Leitch

Researchers at the University of East Anglia (UEA) have created a technique that can identify bacteria and viruses that are linked to cancer. We're already aware of several, like Epstein-Barr virus, which can raise the risk of several cancers including stomach cancer and Burkitt lymphoma. This study, reported in Genome Biology, indicates that genetic data obtained from tumors can help reveal other microbes that are connected to cancer development.

Image credit: Pixabay

"We already know of some strong associations between infections and cancer. For example, the presence of Helicobacter pylori in the digestive tract can lead to stomach ulcers and is associated with stomach cancer," said lead researcher Dr. Dan Brewer of UEA's Norwich Medical School and a Visiting Worker at the Earlham Institute (EI). "Meanwhile some types of the HPV virus can cause cervical cancer."

The scientists are hopeful that this research will not only aid in the detection of microbes that might cause cancer, it may also aid in the development of vaccines, like the HPV vaccine, that can prevent cancer.

"Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine," Brewer added. "When tumor samples are whole genome sequenced, DNA from any pathogens present will also be sequenced, making it possible to detect and quantify pathogens. This gives us a fantastic opportunity to collect data that will help us find new associations between bacteria and viruses and different types of cancer."

In this study, the researchers used computer simulations that could test different approaches before they applied them to actual cancer sequence data. Then they were able to identify a variety of different pathogens.

"There are already a wealth of scientific tools to classify organisms from their genome sequence data. This new research looks at each of the key computational steps involved in conducting this on human tissue sequencing data," noted postdoctoral researcher Abraham Gihawi of UEA's Norwich Medical School.

"We collected computer scripts that stitch together the highest performing tools to apply to large collections of sequencing data. We used computer simulations and then tested our approaches on some real cancer sequence data," Gihawi explained.

"For the simulations, we produced mock genomes containing mostly human sequences and spiked them with very small numbers of pathogenic sequences which is what we expect to see in cancer sequences. Since we knew exactly what pathogens, and how much of them, are in each simulated genome, we could test how well each approach performs," continued Gihawi.

"We then tested our method out on some real cancer sequencing data where we know what we expect to see. As well as finding pathogens that are known to be associated with cancer, we also detected many more. We are only just beginning to scratch the surface on the role that these other pathogens may play in the development of cancer."

Brewer added that "there is already an HPV vaccine which is thought to prevent around 70 percent of cervical cancer cases. We hope that by identifying bacteria and viruses associated with other cancers, new vaccines could be developed in the future."

Sources: AAAS/Eurekalert! via University of East Anglia, Genome Biology

About the Author
  • Experienced research scientist and technical expert with authorships on 28 peer-reviewed publications, traveler to over 60 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
JAN 02, 2020
Genetics & Genomics
JAN 02, 2020
Mysterious Extrachromosomal DNA is Linked to Childhood Cancer
Scientists are learning more about an unusual kind of DNA that's separate from a cell's genomic DNA....
JAN 04, 2020
Genetics & Genomics
JAN 04, 2020
Testing Gene Therapy as a Potential Treatment for CTE
Chronic traumatic encephalopathy (CTE) is caused by repeated trauma to the head, like a boxer, football player, or soldier might experience....
JAN 19, 2020
Genetics & Genomics
JAN 19, 2020
Engineering Mosquitoes to Stop Dengue Virus Transmission
The dengue virus is transmitted by mosquitoes. It is found in over one hundred countries and threatens three billion people with a serious illness....
JAN 19, 2020
Immunology
JAN 19, 2020
Overactive Immune Gene May Cause Schizophrenia
A windy road links excessive activity of the “C4” gene to the development of schizophrenia. Researchers begin to study C4 activity as part of n...
JAN 11, 2020
Neuroscience
JAN 11, 2020
Molecular Therapy to Self-Repair Nerve Cells
Neurodegenerative diseases such as Multiple Sclerosis (MS), Alzheimer's, and Huntington's Disease are predicated on damage to myelin on nerve cells...
MAR 23, 2020
Genetics & Genomics
MAR 23, 2020
Diagnosing Cancer by Looking for Microbial DNA in the Blood
Liquid biopsies aim to diagnose a disease with only a bit of biological fluid, usually blood....
Loading Comments...