Yu-Ju Chen

Distinguished Research Fellow
Institute of Chemistry, Academia Sinic

Yu-Ju Chen obtained her B.S. in chemistry from National Taiwan University and Ph.D. degree in physical chemistry from Iowa State University. After postdoctoral research work at the Ames Laboratory, Department of Energy, USA, and National Tsing Hua University, she joined the Institute of Chemistry of Academia Sinica in 1999, served as the Director (2013-2021) and is currently a Distinguished Research Fellow.
Since her early career, she has actively promoted proteomics research and networking in Taiwan and international community, serving as the current President of the Chemical Society located in Taipei (CSLT, since 2023), President of Human Proteome Organization (HUPO)-largest international society in proteomics (2021-2022), Vice President of Asia Oceana Human Proteome Organization (AOHUPO, 2017-2019), President of Taiwan Society for Mass Spectrometry (2012-2015), President of the Taiwan Proteomics Society (2008-2011),. She is currently the Associate Editor of “Analytical Chemistry”, American Chemical Society (since 2020).
With great passion to reveal disease network, she is one of the pioneering scientists in establishing mass spectrometry-based proteomics in Taiwan. In particular, she is interested in applying these tools for in-depth exploration of the proteome network in biology and diseases. Dr. Chen has published more than 170 articles including Cell, Nat. Commun., Cancer Cell, Mol. & Cell. Proteom., Anal. Chem., J. Am. Chem. Soc., and Proc. Natl. Acad. Sci., and 5 patents. Her technology of nanoprobe-based mass spectrometry was also translated into a start-up company for cancer diagnosis with recognition of National Innovation Award in 2021.
She had assembled a multi-organization and multi-disciplinary team to launch the Taiwan Cancer Moonshot program in 2016 under the collaboration framework of the International Cancer Proteogenome Consortium (ICPC) led by National Cancer Institute, USA. The project aims to establish and translate deep proteogenomics data into precision oncology for emerging cancers in Taiwan, including lung cancer, breast cancer, gastric cancer, and pancreatic cancer. The first study has revealed the pathogenesis and progression of non-smoking lung cancer patients in Taiwan (Cell, Cover Story).

Speech title & Synopsis

Opportunity of Proteomics-guided Precision Oncology

Advances in mass spectrometry-based proteomic technologies have opened the new avenue to identify and quantify thousands of proteins, post-translational modification (PTM) and their system network regulating various biological and physiological functions. Personalized proteomics starts to impact the development of precision medicine by facilitating discovery of protein biomarkers, molecular signature of disease subtype and response to treatment of individual patients. Combing proteomics with the long standing success of genomics, proteogenomics has been rapidly advanced as an emerging tool for full delineation of genomic-to-proteomic network associated with disease. Since the launch of Taiwan Cancer Moonshot, the proteogenomics characterization provides new insight on the molecular signature and pathogenesis of early stage lung adenocarcinomas and breast cancer in Taiwan. We delineated endogenous and exogenesis mutational signatures as well as the proteogenomic hallmarks of tumor progression. Most excitingly, proteomics-informed classification demonstrated differentiation of the diverse clinical trajectories of patients within early stages. Our integrative analysis reveals the molecular architecture of the early-stage lung and breast cancer in East Asia and enables the path for pursuing precision oncology. Following this prospective study, this multi-omic molecular architecture inspired development a few strategies toward precision oncology for management of early stage non-smoking lung adenocarcinoma. Advancement in robust proteomics technology are also under development to facilitate its translation into a next-generation clinical assays. Nevertheless, the translation of proteomic discovery faces multiple challenges in both technical robustness and sensitivity, as well as large-scale validation and assay validation. To implement its practical utility for the most accessible specimen such as needle biopsy and blood, I will introduce our recent development nanoscale-to-single cell proteomics and their application.