Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for...

Area of Science:

• Dermatology
• Immunology
• Genomics

Background:

• Skin immune microenvironment organization is crucial for function, with spatial and temporal arrangements.
• Imbalances in the skin immune milieu are linked to disease pathogenesis.
• Spatial transcriptomics provides insights into aberrant inflammation missed by traditional single-cell RNA sequencing.

Purpose of the Study:

• To provide a technical and user experience overview of NanoString's GeoMx Digital Spatial Profiler for spatial transcriptome analysis.
• To identify potential pitfalls and optimization strategies for RNA capture in inflammatory skin diseases.
• To demonstrate the utility of digital spatial profiling in understanding skin disease pathogenesis.

Main Methods:

• Utilized NanoString's GeoMx Digital Spatial Profiler for spatial transcriptome analysis.
• Applied strategies to optimize RNA capture, addressing limitations in manufacturer guidelines.
• Examined inflammatory skin diseases including psoriasis, lichen planus, and discoid lupus erythematosus.

Main Results:

• Demonstrated practical strategies for enhancing RNA capture in spatial transcriptomic analysis of skin.
• Provided concrete experimental examples from psoriasis, lichen planus, and discoid lupus erythematosus.
• Illustrated the potential of digital spatial profiling for spatially resolved dissection of skin disease.

Conclusions:

• Digital spatial profiling is a powerful tool for dissecting skin disease pathogenesis in a spatially resolved manner.
• Optimization strategies enhance RNA capture, improving the depth of spatial transcriptome analysis.
• This work provides a framework for investigators using digital spatial profiling in skin biology research.