MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

Scientists have developed an improved technique for reading gene activity directly inside tissue samples, preserving crucial information about where each cell sits in relation to its neighbors. The method, called MERFISH 2.0, builds on an earlier technology that uses fluorescent chemical probes to detect RNA molecules (the molecular messengers that carry instructions from genes) within intact tissue slices. The key challenge it tackles involves archival tissue samples, particularly those preserved in a chemical fixative called formalin and embedded in paraffin wax, a standard hospital storage method known as FFPE. In these samples, RNA becomes fragmented and chemically tangled, making it notoriously difficult to detect. MERFISH 2.0 uses an optimized chemistry that works around these obstacles, detecting up to eight times more RNA transcripts than the original version while still producing accurate, consistent measurements.

The researchers tested the new approach across a range of tissue types from both humans and mice, preserved using several different methods including fresh-frozen and FFPE storage. In archived human brain samples and low-quality FFPE breast cancer specimens, the improvements were striking. The upgraded method uncovered cell populations and clusters that the earlier version missed entirely, painted a clearer picture of how immune cells and tumor cells are arranged in space, and revealed more connections between genes and between neighboring cells. These spatial relationships are increasingly understood to be critical clues in understanding how diseases like cancer develop and resist treatment.