Update: Spatial Transcriptomics in FSHD Skeletal Muscle

Posted by Friends of FSH Research on Dec 19, 2025

Update by Dr. van der Maarel
See also Spatial Transcriptomics in FSHD Skeletal Muscle

Facioscapulohumeral muscular dystrophy (FSHD) is driven by sporadic activation of the transcription factor DUX4. While many disrupted molecular functions and pathways have been identified, their interconnections, dependencies, and timing remain unclear. Both in vitro and in vivo studies show that DUX4 and its signature genes activate in focal patterns. Imaging confirms localized muscle changes—such as inflammation and fat infiltration—while transcriptome studies reveal distinct gene expression signatures.

FSHD affects a complex mix of pathways within muscle tissue composed of diverse cell types. Key questions persist about how these pathways and cell types interact over time and space. Recent advances in single-cell and single-nucleus RNA sequencing have improved our understanding of transcriptional heterogeneity, but these methods lose spatial context—critical for fully explaining disease mechanisms.

This project aims to integrate spatial transcriptomics with existing high-resolution omics approaches to uncover how spatial organization shapes FSHD pathology.

During the first year of this project, we used Spatial Transcriptomics to study muscle tissue from patients with FSHD1 and FSHD2. Our initial analysis revealed small, localized areas where DUX4 and its target genes were active. We also observed that FSHD muscles show highly variable patterns of pathology across different regions.

We are now examining the full dataset to identify all possible signs of DUX4 activation and to better understand how these focal patterns fit into the overall spatial context of FSHD muscle pathology.

In parallel, we developed a single-myofiber RNA sequencing method to confirm the findings from our spatial data (preprint available on ResearchSquare). Using this approach, we validated the high degree of heterogeneity in DUX4 activation within individual muscle fibers. We will continue applying this single-fiber RNA sequencing technique to more precisely determine how often DUX4-related signatures occur at the level of individual fibers.