Seq-Scope-eXpanded: spatial omics beyond optical resolution

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• Sequencing-based spatial transcriptomics (sST) offers transcriptome-wide gene expression mapping.
• Current sST methods lack the optical resolution of imaging techniques (200-300 nm).
• Limitations in resolution hinder the detailed study of subcellular structures and gene expression patterns.

Purpose of the Study:

• To develop an enhanced spatial transcriptomics method with submicrometer resolution.
• To overcome the resolution limitations of existing sST techniques.
• To enable ultra-high-resolution whole-transcriptome and proteome profiling in tissues.

Main Methods:

• Introduction of Seq-Scope-X (Seq-Scope-eXpanded), a technique combining Seq-Scope with tissue expansion.
• Physical enlargement of tissues to minimize transcript diffusion and increase spatial feature density.
• Application in liver, brain, and colon tissues, and adaptation for spatial proteomics.

Main Results:

• Seq-Scope-X achieves submicrometer resolution, surpassing conventional sST limitations.
• Nuclear and cytoplasmic compartments were resolved in nearly all cells in liver tissue.
• Widespread differences in nuclear vs. cytoplasmic transcriptome patterns were identified, suggesting dynamic metabolic switching in hepatocytes.
• Successful application in brain and colon tissues, and adaptation for spatial proteomics in spleen and tonsil.

Conclusions:

• Seq-Scope-X is a powerful platform for ultra-high-resolution whole-transcriptome and proteome profiling.
• The method significantly expands spatial precision for studying cellular architecture and function.
• Findings provide new insights into cellular heterogeneity and disease mechanisms at an unprecedented resolution.