BioGPS has become the valuable resource that it is because of the contributions from our wonderful user community. Thank you for contributing plugins, suggestions, and ideas–all of which have improved BioGPS for everyone. In order to celebrate the contributions of BioGPS users to the scientific research community, this series will feature publications and articles generated by BioGPS users. We sincerely hope you will join us in celebrating the fascinating work that YOU do.
This week, we will feature an article springing from the collaborative efforts of researchers from institutions in South Korea and the US: Anomalies in Network Bridges Involved in Bile Acid Metabolism Predict Outcomes of Colorectal Cancer Patients by Sunjae Lee, KiYoung Lee, Seyeol Yoon, Jae W. Lee, and Doheon Lee.
Dr. Doheon Lee kindly answered our inquiries for this series.
- Who is the team behind the work that was published in Anomalies in Network Bridges Involved in Bile Acid Metabolism Predict Outcomes of Colorectal Cancer Patients?.
Collaborative efforts have gone into this work, with Dr. Doheon Lee’s laboratory from Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, South Korea; Dr. Jae W. Lee’s laboratory from Department of Pediatrics, Oregon Health and Science University, U.S.; and Dr. KiYoung Lee’s laboratory from Department of Medical Informatics, School of Medicine, Ajou University, South Korea.
- What inspired the work published in Anomalies in Network Bridges Involved in Bile Acid Metabolism Predict Outcomes of Colorectal Cancer Patients?
This work was prompted by an idea that the driving force of metabolic diseases, including colorectal cancer, comes from the anomalous regulation of cellular metabolism. Due to the lack of systematic studies that probe genes involved in metabolic regulation, relevant genes were still missed out in discovering novel biomarkers for those metabolic diseases.
- Please provide a brief summary of the findings reported in your article, Anomalies in Network Bridges Involved in Bile Acid Metabolism Predict Outcomes of Colorectal Cancer Patients.
To keep cellular homeostasis of metabolism, cells equipped several machinery genes to regulate metabolism: metabolic sensors, which perceive the metabolic status of a cell, and metabolic enzymes, which actually modulate metabolites by catalysis.
In this work, we present that not only metabolic sensors and metabolic enzymes, but also proteins relaying metabolic information between them play a critical role in metabolic regulation – we called them as bridge proteins, with regarding them as potential prognostic biomarkers of metabolic diseases.
Based on our network-based approach, we identified bridge proteins of bile acid, which is specifically colon-carcinogenic, metabolism and confirmed their significant association with colorectal cancer at the transcriptome-level. Lastly, their prognostic ability in patients with colorectal cancer was identified as being reproducibly high, in comparison to known prognostic markers of colorectal cancer.
- How did the team learn about BioGPS?
We have been looking for comprehensive database of gene expression profile in all human tissues, and BioGPS meets our demand. To identify bridge proteins of bile acid metabolism in colon tissue context, we have integrated all relevant molecular interaction data into a reference network, called a bridge network, and pruned the network according to colon tissue context, based on BioGPS data. From this final bridge network, we eventually identified the bridge proteins, suggesting them as novel prognostic markers for colorectal cancer.
Thanks again to Dr. Doheon Lee for taking the time to answer our questions. Click here to read their fascinating article. Have a look because these awesome researchers have made their compelling research open access–so you can read the whole exciting article for free!
Used BioGPS and cited it in your publication? Let us know! We would love to feature YOUR work, no matter how long ago it was published. BioGPS Featured Article Series only started recently, but we know your contributions to science is ongoing.