Spatial Transcriptomics Reveals New Cell Types in Flies

Knowing the location of a gene within intact tissue or a single cell allows scientists to unlock unknown cellular functions. This information is often lost in most genetic sequencing techniques, but spatial transcriptomics, a spatial biology method, offers a way to overcome this limitation.^1,2

“If you have a machine—for example, a bike—all the different components of the bike would need to be fit in the right places for them to function,” said Lambda Moses, a computational biologist at Columbia University. “Spatial transcriptomics allows you to get the location of these components.”

In a study published in eLife, scientists used spatial transcriptomic analysis and a targeted gene panel to capture the positions of 150 mRNAs across the entire body, including the brain, of an adult Drosophila melanogaster.³ In doing so, they were able to map the locations of unique, previously uncharacterized cell types and clusters. The findings add more depth to the single-cell atlas of the fly, setting the stage for future mechanistic studies.

Spatial Transcriptomic Analysis Helped Annotate Genes in Flies

“Drosophila is like a Swiss Army Knife,” said Pierre Mangeol, a biophysicist at Aix-Marseille University and coauthor of the study. Because of their well-defined genes and neurons that function like those in mammals, Drosophila are valuable proxies for studying human brain functions.^4,5

Jasper Janssens, a developmental biologist at ETH Zurich and coauthor on the study, previously sequenced more than 570,000 cells in the adult fly when he was a graduate student at KU Leuven.⁶ Using single-cell sequencing, he and his team annotated 250 unknown Drosophila cell types. Despite this effort, thousands of cells remained uncharacterized because of the lack of information linking gene transcription to fly morphology, Janssens said.

To address this limitation, the researchers turned to molecular cartography—an imaging-based spatial biology technique that allows scientists to visualize single RNA molecules in intact tissue.⁷ The method uses fluorescently-labelled gene probes that bind to specific ribonucleic acid segments. The scientists froze a fruit fly and sliced it into 10-micrometer-thick sections along the middle portion of the body, allowing them to visualize most of its organs. For their proof-of-concept study, Janssens and his team used a 150-gene panel—100 targeted mRNAs expressed in the brain, while the remaining 50 targeted mRNAs in the body.

Locating mRNA Positions Using Spatial Transcriptomic Analysis

“It's a really cool study,” said Moses, who was not involved in the study. “With something like molecular cartography, we can see where the transcripts or mRNA molecules are located within cells. And often that can be very interesting because transcripts can be transported to different locations in the cell to perform biological functions.” For example, in neurons, mRNA moves from the nucleus to the dendritic spines, where they are involved in synaptic activity. This mRNA localization indicates distinct cell types, developmental stages, and tissue phenotypes.⁸

In this study, the scientists observed varied localization of the mRNA encoding Titin—a giant protein abundant in muscle. “We now found that the terminal nuclei that are at the end of the [flight] muscle express more of [these genes],” said study coauthor Frank Schnorrer, an expert in muscle dynamics at Aix-Marseille University. “It was completely unexpected,” he added, because the Titin protein is needed throughout the muscle, not only at the edges. The result of the spatial transcriptomic analysis showed that the mRNA localization and transcriptional activities within these flight muscle cells are more diverse than scientists previously thought and may point to distinct mechanisms that will spark future investigations.

The team is now looking into ways to create a 3D map to identify genes in overlapping cells that are hard to resolve in 2D.