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Updated: May 31, 2025
Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
Published on: July 6, 2022
Highly multiplexed spatial transcriptomics in bacteria.
Ari Sarfatis1,2, Yuanyou Wang1,2, Nana Twumasi-Ankrah1,2
1Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
We developed bacterial-MERFISH, a novel imaging technique, to visualize thousands of RNA molecules within single bacteria. This method allows detailed study of bacterial responses and organization in complex environments.
Area of Science:
- Microbiology
- Molecular Biology
- Genomics
Background:
- Bacterial single-cell behaviors are crucial but difficult to study due to dense messenger RNA.
- Existing image-based transcriptomics methods face limitations with high bacterial RNA density.
Purpose of the Study:
- To develop a high-throughput, spatially resolved method for profiling RNA in individual bacteria.
- To overcome the challenge of dense bacterial messenger RNA in imaging approaches.
Main Methods:
- Combined 1000-fold volumetric expansion with multiplexed error-robust fluorescence in situ hybridization (MERFISH).
- Developed bacterial-MERFISH for high-throughput, spatially resolved RNA profiling in single bacteria.
Main Results:
- Successfully profiled thousands of operons within individual bacteria.
- Dissected *Escherichia coli*'s response to carbon starvation.
- Mapped subcellular RNA organization and charted *Bacteroides thetaiotaomicron*'s adaptation to gut niches.
Conclusions:
- Bacterial-MERFISH enables unprecedented insight into bacterial single-cell heterogeneity.
- The method is broadly applicable to studying bacteria in diverse, native, and spatially structured environments.
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