A Workflow for Spatial Transcriptomic Analysis from Intra-operative Human Skeletal Muscle Biopsies

Area of Science:

• Molecular biology
• Neuroscience
• Skeletal muscle physiology

Background:

• Peripheral nerve injury outcomes are variable, with poorly understood molecular mechanisms of human muscle degeneration and recovery.
• High-resolution, spatially resolved gene expression data from human skeletal muscle in clinical settings is critically needed.

Purpose of the Study:

• To establish the feasibility of spatial transcriptomics for intraoperative human muscle biopsies.
• To create a framework for identifying gene expression signatures linked to reinnervation outcomes.

Main Methods:

• Intraoperative upper-extremity muscle biopsies were collected 5 months post-traumatic brachial plexus injury.
• Biopsies were flash-frozen and processed using the 10x Genomics Visium HD platform for high-resolution spatial transcriptomics.
• Quality control confirmed high RNA integrity and transcript detection at 8 µm resolution.

Main Results:

• Genes crucial for neuromuscular junction formation, degeneration, and regeneration were identified.
• These genes exhibited fiber-type-specific expression patterns at subcellular resolution.
• Analysis utilized complementary approaches in Seurat and Loupe Browser.

Conclusions:

• Spatial transcriptomics is feasible in human muscle tissue.
• Baseline gene-expression signatures associated with nerve injury and recovery were established.
• This study provides a foundation for identifying biomarkers for successful reinnervation and enhanced nerve-repair strategies.