UIC
Dr. Guy Adami.
Dr. Joel Schwartz.
|
College of Dentistr y
Dr. Saurabh Sinha.
.
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, Dr. 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 explained. 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,” said Dr. Adami. “We could clearly see the effects of green tea on the cells lining the mouth.”. Polyphenols are a category of chemicals that naturally occur in many vegetables and fruits. 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 often are 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 four 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.” The cloud-based KnowEnG is an analytical platform
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