Dr. Jeffrey Moffitt, Assistant Professor, Department of Microbiology Harvard Medical School; Investigator, Program in Cellular and Molecular Medicine, Boston Children's Hospital

Imaging the transcriptome: mapping the microbiome-host interface with MERFISH

Image-based approaches to single-cell transcriptomics offer the exciting ability to both define and discover cell types and states while simultaneously mapping their organization within intact tissues.  I will describe a leading image-based spatial transcriptomics technique, multiplexed error robust fluorescence in situ hybridization (MERFISH), which is capable of imaging and identifying thousands of different mRNA molecules within intact tissue slices. In addition, I will describe the recent work of our laboratory to apply MERFISH to questions at the interface between the gut microbiome and the mammalian GI tract. Specifically, I will describe how MERFISH has provided new insights into how the gut senses microbial activity and, in turn, is shaped by the presence of the microbiome; how MERFISH has revealed the cellular and spatial remodeling that happens when the barrier between host and microbe breaks down and the gut is inflamed; and how gut bacteria adapt their gene expression to micron-scale niches within the gut.

Biography

Dr. Moffitt received his PhD in Physics from the University of California, Berkeley where he developed Angstrom-scale-resolution optical tweezers and used them to map the movement of nucleic acid molecular motors with Dr. Carlos Bustamante. Dr. Moffitt received postdoctoral training with Dr. Xiaowei Zhuang at Harvard University where he co-developed MERFISH, a method for image-based transcriptomics, and used this method to create the first molecular, cellular, and functional atlas of a portion of the mammalian brain. Dr. Moffitt started his laboratory at Boston Children's Hospital and Harvard Medical School in 2018, where he continues to develop and extend genomic microscopy methods with a particular focus on the interface between microbe and