Gene “Decorations” Can Serve as Blood Biomarkers To Detect Cancer Interview with:

Kun Zhang, PhD Professor UCSD Department of Bioengineering La Jolla, CA 92093-0412

Dr. Kun Zhang

Kun Zhang, PhD
UCSD Department of Bioengineering
La Jolla, CA 92093-0412 What is the background for this study? What are the main findings?

Response: We have been interested in a type of chemical modification on the DNA, called CpG methylation, for years. This is like a decoration of DNA molecules that is specific to the cell type or tissue type. We were particularly interested in studying how such decoration spread along the DNA molecules. In this study, we did a very comprehensive search of the entire human genome for various human cell types and tissue types, and found close to 150,000 regions (called MHB in this study) in which adjacent CpG share the same decoration. We then went on to find out how many of such regions are unique to each normal cell/tissue type, and how many are specific to cancers. Then we took some of these highly informative regions as “biomarkers”, and showed that we can detect the absence or presence of cancer, and, in the latter case, where the tumor grow, in a patient’s blood. What should readers take away from your report?

Response: There is a great deal of molecular information on the well-being of each human organ in the blood. With the right approaches, we can potentially monitor the health status of the entire body by running molecular assays on the blood. What recommendations do you have for future research as a result of this study?

Response: This study would not have been accomplished without a highly open and cross-disciplinary environment at UCSD. We are a research group working in an engineering school. Yet at the time that we felt that we had an interesting idea to test on real clinical samples, we were able to quickly get access to cancer patients tumor biopsies and bloods with well documented clinical information, without the need to establishing a clinical collaboration, which is a lot of work and a barrier for people like us working in a different field. Having an open and highly collaborative infrastructure is absolutely essential for new innovations. Is there anything else you would like to add?

Response: Patents related to this method have been filed and licensed to a start-up company (Singlera Genomics) that I co-founded. This is a direction we are taking to fully validate the clinical utility of the method. Thank you for your contribution to the community.


Shicheng Guo, Dinh Diep, Nongluk Plongthongkum, Ho-Lim Fung, Kang Zhang, Kun Zhang. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nature Genetics, 2017; DOI: 10.1038/ng.3805

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Last Updated on March 7, 2017 by Marie Benz MD FAAD