Whole-organism spatial transcriptomics at single-cell resolution in C. elegans.

Area of Science:

• Molecular Biology
• Genomics
• Neuroscience

Background:

• Spatial transcriptomics advances tissue organization studies by mapping gene expression in situ.
• Applying spatial transcriptomics to whole organisms like C. elegans is challenging due to resolution and multiplexing limitations.

Purpose of the Study:

• To develop a high-resolution, multiplexed spatial transcriptomics method for whole C. elegans.
• To enable comprehensive gene expression profiling across intact worms while preserving spatial context.

Main Methods:

• Single-molecule fluorescence in situ hybridization (smFISH) workflow.
• Sequential imaging across 20 hybridization rounds using two fluorescent channels for up to 40 genes.
• Curated marker-gene panel for neuron identification and probabilistic transcript assignment to nuclei.

Main Results:

• Achieved single-cell resolution gene expression profiling across the entire C. elegans.
• Enabled quantitative measurement of gene expression levels and identification of up to 86 neuronal classes.
• Revealed sex- and neuron-specific expression patterns at single-cell resolution.

Conclusions:

• Established a scalable framework for spatial gene expression analysis in intact C. elegans.
• The method facilitates linking molecular data to cellular function and behavior within the worm.
• Provides a powerful tool for understanding whole-organism biology at unprecedented molecular resolution.