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Research

As one of the pioneers of the expansion microscopy technology, Dr. Fei Chen continues to utilize ExM in super resolution approaches. His lab is currently working on new tools for in situ transcriptomics and epigenomics.

 

Research

 
 
The Chen lab - Expansion microscopy 

Expansion microscopy

Expansion microscopy (ExM) represents a novel super-resolution microscopy technique which enables observation of biological structures at nanoscale resolutions across millimeter length scales. ExM physically expands tissues so that the resolution of ordinary microscopes is increased ~5 times by leveraging the swelling properties of polyelectrolyte hydrogels. ExM enables nanoscale imaging over large volumes of intact tissue on conventional fluorescent microscopes, allowing for comparable performance to super-resolution microscopes (~60 nm) on cheaper, more accessible, and faster optical hardware. Furthermore, expanded tissues are transparent, allowing for super-resolution imaging of intact 3D volumes of biological tissue.

We are working towards applying ExM based super-resolution approaches to diverse tissues and systems in collaboration with other members of the Institute. As embedding cells and tissues in an inert hydrogel environment makes it easy to combine many different biochemical assays on the same specimen, we are utilizing the ExM hydrogel as a platform for in situ transcriptomics and epigenomics.

 

In situ transcriptomics

Current approaches for transcriptomic analysis involve grinding up or dissociating the tissue, while in situ hybridization (ISH) approaches are often limited to profiling one transcript at a time. However, to map the spatial heterogeneity of complex tissues requires us to bridge the divide between spatial and molecular resolution.

By leveraging ExM as a platform, we are developing new tools which allow us to directly sequence and profile mRNA within intact tissue samples. We are working on applying these tools to understand the organization of cell types within the brain, as well as the diversity and heterogeneity of cell types in disease states such as cancer. 

 
The Chen lab - in situ epigenomics

In situ epigenomics

The establishment and maintenance of a cell’s identity is largely driven by chromatin structure. We are working on novel tools and techniques which will allow us to profile the structural organization of accessible chromatin directly within cells and tissues with sub-cellular resolution. We hope to use these tools to understand how the structural architecture of the genome is related to regulation and function in health and disease.