Fighting Oral Cancer with the Power of Machine Learning
Dr. Guy Adami and Dr. Joel Schwartz with the University of Illinois at Chicago College of Dentistry are harnessing the power of big data to change the landscape of oral cancer prevention. To do this, they are combining the latest advances in machine learning with one of the oldest functional food products in the world: green tea.
With a team of oral science experts and computer scientists, Dr. Adami and Dr. Schwartz, Professors in the Department of Oral Medicine and Diagnostic Sciences, aim to gain insight into how different people respond to the polyphenols found in green tea through the genomic analysis of molecules called RNAs. These polyphenols, also present in many other common foods and drinks, have been shown in animal studies to reduce the risk of cancer development and progression.
“If we knew which people show the greatest response to drinking green tea and could apply it to cancer prevention, we could develop more effective treatments, or even personalized medicines," said Dr. Adami.
Using samples from the mouth, the team knew they were on to something because of noticeable changes in the kinds of bacteria found in the tea drinkers’ mouths. From these samples taken using a tool similar to a toothbrush, they analyzed RNA changes in cells from the tongue and gums. “With standard analysis methods, we couldn’t be sure the tea was doing anything to the cells because the variability in the data made it inconclusive,” said Dr. Adami.
To solve this, Dr. Adami brought in a computational genomics expert, Saurabh Sinha, Co-Director of the Knowledge Engine for Genomics (KnowEnG) Center at the University of Illinois Urbana-Champaign and Associate Professor in the Department of Computer Science.
“What our KnowEnG center and platform does is turn big data into knowledge using a combination of data science and machine learning to enhance the analysis of genomics studies,” Dr. Sinha explains.
Using the new cloud-based platform, the team was able to perform a much deeper analysis into how the polyphenols were interacting with human cells. They further enhanced those insights using the power of machine learning by integrating their small sample data with a much larger knowledge base about gene relationships and other bioinformatics developed over decades from a vast genomics research community.
“After running the data through the KnowEng platform, it was like a light bulb turned on. We could clearly see the effects of green tea on the cells lining the mouth,” said Dr. Adami.
Why Green Tea?
Polyphenols are a category of chemicals that naturally occur in many of the vegetables and fruits we eat. They offer several health benefits, including their role as antioxidants, which can combat cell damage, as well as their effects on reducing inflammation and helping to fight cancer. Green tea is rich in polyphenols and offers a number of other health benefits. However, its association with fighting cancer is yet to be well understood.
Drs. Adami and Schwartz’s team analyzed the effects of green tea polyphenols on cells in the mouth and the genes they express for a better understanding of how they might prevent oral cancer. The study included 11 subjects and analyzed 360 microRNAs. Specifically, they wanted to know whether there were any microRNA differences between one group that had been drinking green tea for four weeks and another that did not.
MicroRNAs are often selected for analysis in modern cancer research as potential diagnostic biomarkers and therapeutic targets. They influence multiple processes that are relevant to cancer, such as cell proliferation, metabolism, differentiation, and migration.
With traditional analysis methods, it was unclear if the green tea was doing anything to the cells because of data variability. Through a deeper level of genomics analysis, the team was able to clearly see how RNAs change in sync after drinking green tea, and how some people’s cells were more sensitive to green tea polyphenols than others.
“The biggest ‘a-ha’ moment was when we saw the changes in the bacteria in the tea drinkers after just 4 weeks,” said Dr. Adami. “The deep genomics analysis let us detect changes in the RNA, while also ensuring we weren't just seeing things that happened by chance.”
Applying Machine Learning To Improve Oral Health
The cloud-based KnowEnG is an analytical platform that takes advantage of algorithms used successfully in other data mining endeavors, including Google’s search functions, but have not been previously applied to interpretation of genomic data. By placing their new results into the context of the Knowledge Network, biomedical researchers can produce a high-powered analysis of new genomic and transcriptomic datasets.
“These studies were a great match for our computational genomics capabilities because our deep analysis methods could help answer questions that have eluded researchers for some time, and those answers may one day lead to improvements in how cancers, particularly cancers of the head and neck, are diagnosed and treated,“ said Dr. Sinha, who leads the KnowEnG platform.
KnowEnG’s Knowledge Network combines a vast volume of prior data from multiple high quality public genomic information sources and integrates the information with new research data. This helps researchers better understand and identify the connection between genes and cells, how RNAs and miRNAs regulate cell activity, and disease progression in the context of a genomic study.
Changing The Future of Oral Cancer
The team is planning further research to better understand the significance of the RNA changes. “While the computational biological methods led us to identify changes in human oral cell RNA with green tea consumption, we do not know what these changes mean yet,” Adami says.
There is certainly a need for such research that holds the promise of one day saving millions from a cancer diagnosis.
In the United States, over 43 thousand people will be diagnosed this year and over 9 thousand will die from head and neck cancers (cancers in the mouth and throat). The disease is the sixth most common cancer type worldwide and remains a major cause of death and disability.
Ask the Expert: What is Oral Cancer?
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Researchers at UIC continue to work on discoveries that may one day move us closer to cures and effective preventative measures. From tailored chemotherapy treatments to improved screening and preventative diets, there is significant promise for unlocking unprecedented medical precision.
“In our center (KnowEnG) we are using similar genomics analysis to determine the right drug treatment for particular types of cancer, where there isn’t a clear answer as to which drug or dosage is best,” says Dr. Sinha.
One day a quick mouth swab during a routine physical check-up may be able to generate a genetic data sample that could quickly lead to diagnosis and preventive treatment. From tailored chemotherapy treatments to improved screening and preventative diets, big data holds significant promise for unlocking unprecedented medical precision.
“Every person is different, and we hope to one day use those differences to help the ones who are suffering from cancers and other oral diseases,” said Dr. Adami.
This is good news for the over one million people diagnosed with cancer this year in the US.
Oral Medicine Specialists Serving Chicago
The Oral Medicine Clinic at University of Illinois at Chicago provides a broad range of diagnosis and non-surgical treatment for the treatment of oral mucosal diseases including oral complications of medical therapy including cancer treatment (i.e. chemotherapy and radiation therapy); oral changes associated with systemic diseases; salivary gland dysfunction and dry mouth; Inflammatory conditions including mucosal auto-immune diseases; viral, bacterial and fungal infections; benign growths; diagnosis of oral cancer and pre-cancerous lesions; canker sores; bad breath; taste changes; oral manifestations of HIV. We use a multidisciplinary approach to expertly diagnose and treat these oral mucosal diseases.
The Oral Medicine clinic is staffed by faculty members who have extensive professional expertise and experience in all aspects of Oral Medicine and Clinical Oral Pathology. We are the only academic center of this kind in Chicago.
Services
Conditions routinely treated
- Oral complications of medical therapy including cancer treatment (i.e. chemotherapy and radiation therapy)
- Oral changes associated with systemic diseases
- Salivary gland dysfunction and dry mouth
- Inflammatory conditions including mucosal auto-immune diseases
- Viral, bacterial and fungal infections
- Benign growths
- Diagnosis of oral cancer and pre-cancerous lesions
- Canker sores
- Bad breath
- Taste changes
- Oral manifestations of HIV
Our approach
We use a multidisciplinary approach to expertly diagnose and treat these oral mucosal diseases. The Oral Medicine team collaborates with all dental disciplines, including Periodontics, Endodontics, and Oral Surgery as well as a number of medical disciplines, including ENT, Dermatology, Oncology, Neurology, Hematology, Radiology, Surgery, and Psychiatry.
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(National Institute of Dental and Craniofacial Research)