MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing...

Area of Science:

• Genomics
• Cell Biology
• Biotechnology

Background:

• Spatial transcriptomics technologies are crucial for understanding tissue organization.
• Existing methods face limitations in gene coverage, multimodal analysis, and scalability.
• Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) is a key technology in this field.

Purpose of the Study:

• To present MERFISH+, an advanced version of MERFISH with improved capabilities.
• To demonstrate MERFISH+ for high-resolution 3D spatial multi-omics in complex tissues.
• To reconstruct a comprehensive 3D atlas of the developing human heart.

Main Methods:

• MERFISH+ integrates chemical probe anchoring in hydrogels with microfluidics and microscopy for robust hybridization.
• The platform supports repeated hybridization cycles across centimeter-scale tissue samples.
• A generative integration framework (Spateo-VI) was used to harmonize transcriptomic and chromatin data.

Main Results:

• MERFISH+ enabled simultaneous quantification of over 1,800 genes.
• The 3D organization of chromatin loci and epigenomic marks in developing human hearts was resolved.
• A 3D spatially-resolved multi-omic atlas of the developing human heart, comprising 3.1 million cells across 34 populations, was reconstructed at subcellular resolution.
• The atlas allowed characterization of 3D cellular neighborhoods and transcriptional gradients.

Conclusions:

• MERFISH+ provides a robust, large-format platform for spatial multi-omics.
• This technology enables high-resolution gene expression mapping at the subcellular level.
• MERFISH+ facilitates detailed characterization of cellular organization within 3D organs.