[Researcher of the Month] Using Proteogenomic Research to Look into Early Onset Gastric Cancer
Professor Paek Eun-ok (Department of Computer Science)
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Through the proteogenomic research of 80 early onset gastric cancer patients, Professor Paek Eun-ok (Department of Computer Science) and her team have provided a better understanding of cancer biology and patient stratification in diffuse type gastric cancers (GCs). The Research team which professor Paek was mostly responsible for in the interpretation of the collected data using software was recognized by publishing ‘Proteogenomic Characterization of Human Early-Onset Gastric Cancer’ in one of the most significant academic journals in the field of cancer named, Cancer Cell.
15 percent of our country’s gastric cancer patients are young, being 45 years old or younger. This is called Early Onset Gastric Cancer (EOGC). However, many of these types of cancers are diffuse types meaning that they are easy to spread and have shaky prognoses, often resulting in death. The research team collected paired tumors and adjacent normal tissues from 80 Early Onset Gastric Cancer patients under 45. They predicted that the research result, through genes and proteins, would be complementary, which is why they decided to go on with the proteogenomics research, combining both genomic and proteomic analysis.
Through integrated analysis of mRNA and proteins, it has shown that the 80 gastric cancer patients can be sorted into four different subtypes, and that each subtype is engaged in different cell signaling pathways. It is becoming more and more possible to precisely sort out the cause of disease in early onset gastric cancer patients through proteogenomics research. Amongst 7,000 somatic variations, they found rogue genes (CDH1, ARID1A, RHOA) which were related to the occurrence of early onset gastric cancer, and they discovered the high interrelationship in their variations and the state of Phosphorylation, proving that these genes are engaged in very important cell signaling pathways related to occurrences of EOGCs.
While the research was highly successful in that it brought out the importance of personalized therapy in the future by categorizing patients into four different subtypes and allowing the team to look at a patient with more refinement, there were some difficulties that the team had faced during research. They had to take cancer tissues directly from patients which needs to be frozen within minutes out in the air before any proteomic changes happen. Also, professor Paek construed proteogenomics through an algorithm that she created, but she emphasized the need for advancement in technologies to better interpret proteome data, comparing the lack of available software to research around the genome.
When asked what professor Paek considers the most important trait in a researcher, she recalled objectivity. “Researchers must always try to be as objective as possible because it is easy to look only at what you want to see,” she advised to her students. She is currently working closely with researchers participating in the CPTAC (Clinical Proteome Tumor Analysis Consortium) program at NIH (National Institute of Health), USA. They are also actively sharing research methods and data with one another to find yet another discovery that could increase understanding of the once unknown diseases in our society.
Kim Hyun-soo email@example.com
Photo by Park Geun-hyung
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