北京大学定量生物学中心

学术报告 

题    目: Reconstruct cellular dynamics from single cell data

报告人: Weikang Wang, Ph.D.

Postdoctoral research fellow in Dept. of Computational and Systems Biology, University of Pittsburgh

时    间: 3月21日（周一）13:00-14:00

地    点: 吕志和楼B101

主持人: 林杰 研究员

摘 要:

Recent advances of single cell techniques catalyzed quantitative studies on the dynamics of cell phenotype transition (CPT) emerging as a new field. However, fixed cell-based approaches have fundamental limits on revealing temporal information, and fluorescence-based live cell imaging approaches are technically challenging for multiplex long-term imaging. To tackle the challenges, we developed an integrated experimental/computational platform for reconstructing single cell phenotype transition dynamics. Experimentally, we developed a live-cell imaging platform to record the epithelial-to-mesenchymal transition (EMT) trajectories of A549 VIM-RFP cell line and unveil parallel paths of EMT. Computationally, we modified a finite temperature string method to reconstruct the reaction coordinate and the corresponding quasi-potentials from the EMT trajectories. The potentials revealed a plausible mechanism for the emergence of the two paths where the original stable epithelial attractor collides with two saddle points sequentially with increased TGF-β concentration (induction of EMT), and relaxes to a new one.

Through analyzing single cell RNA sequencing data in the framework of transition path theory, we reconstructed reaction coordinates describing the transition progression in five CPT processes including EMT, and inferred the gene regulation network (GRN) along the reaction coordinates. In all processes we observed common pattern that GRN frustration, effective number of inter-community gene regulation and network heterogeneity increase first and then decrease.

报告人简介：

 Dr. Weikang Wang is currently a postdoctoral research fellow in Dept. of Computational and Systems Biology, University of Pittsburgh, working with Dr. Jianhua Xing. Dr. Wang’s research is focusing on the dynamics of cell phenotype transition (epithelial-mesenchymal transition as example system) by using live cell imaging, machine learning and modeling. Dr. Wang receive his bachelor’s degree and doctor’s degree from school of physics, Peking University. During his Ph.D., his research was studying cancer stem cell via methods of radiation biology and microfabrication. As a visiting scholar, Dr. Wang worked on microfluidic devices in Dr. Yong Chen’s lab, Ecole Normale Superieure (ENS) in Paris when he was a PhD student.