Facioscapulohumeral dystrophy transcriptome signatures correlate with different stages of disease and are marked by different MRI biomarkers

Abstract

With several therapeutic strategies for facioscapulohumeral muscular dystrophy (FSHD) entering clinical testing, outcome measures are becoming increasingly important. Considering the spatiotemporal nature of FSHD disease activity, clinical trials would benefit from non-invasive imaging-based biomarkers that can predict FSHD-associated transcriptome changes. This study investigated two FSHD-associated transcriptome signatures (DUX4 and PAX7 signatures) in FSHD skeletal muscle biopsies, and tested their correlation with a variety of disease-associated factors, including Ricci clinical severity score, disease duration, D4Z4 repeat size, muscle pathology scorings and functional outcome measures. It establishes that DUX4 and PAX7 signatures both show a sporadic expression pattern in FSHD-affected biopsies, possibly marking different stages of disease. This study analyzed two imaging-based biomarkers—Turbo Inversion Recovery Magnitude (TIRM) hyperintensity and fat fraction—and provides insights into their predictive power as non-invasive biomarkers for FSHD signature detection in clinical trials. Further insights in the heterogeneity of—and correlation between—imaging biomarkers and molecular biomarkers, as provided in this study, will provide important guidance to clinical trial design in FSHD. Finally, this study investigated the role of infiltrating non-muscle cell types in FSHD signature expression and detected potential distinct roles for two fibro-adipogenic progenitor subtypes in FSHD.

A circulating biomarker of facioscapulohumeral muscular dystrophy clinical severity, valid in skeletal muscle and blood

“…By contrast, DUX4 target genes have discriminatory power limited to separating FSHD muscle from control. Van den Heuvel et al, highlighted importance of minimally invasive biomarkers for FSHD severity, focusing on use of MRI 12 . We propose a complementary approach, based on gene expression in minimally invasive blood samples.…”

“…Recently, van den Heuvel et al, 2022 12 performed RNA-sequencing of FSHD and control muscle biopsies from different muscle groups. The authors identified non-overlapping roles for PAX7 and DUX4 target genes, with both biomarkers independently associated with fatty replacement of muscle but only DUX4 target gene expression associated with inflammation 12 , consistent with our prior findings 9,11 . This emphasises importance of studying biomarkers in inflamed and non-inflamed muscle separately.…”

“…Mis-expression of DUX4 is believed to underlie FSHD pathogenesis, but is extremely difficult to detect in FSHD muscle, with protein found in ~1/1000 FSHD myoblasts ex vivo 2,8 . Despite this, DUX4 target gene biomarkers associate with FSHD status, particularly in the context of active inflammation (e.g., STIR/TIRM positivity on MRI) [9][10][11][12][13][14] . The two DNA-binding homeodomains of DUX4…”

Validation of the association between MRI and gene signatures in facioscapulohumeral dystrophy muscle: implications for clinical trial design

“…Specifically, using an arbitrary cut-off of DUX4 target gene expression based on RNA sequencing to assign a biopsy as DUX4+ or DUX4-showed a high correlation of STIR+ signal with DUX4+ biopsies (22, 23). A similar study also showed an association between a higher expression of DUX4-target genes and STIR+ muscle and that fat fraction measures increased the sensitivity of identifying muscles with higher levels of DUX4-target gene expression (24).…”

A Targeted Approach for Evaluating DUX4-Regulated Proteins as Potential Serum Biomarkers for Facioscapulohumeral Muscular Dystrophy Using Immunoassay Proteomics

“…Indeed, biomarker identification and validation has been a major goal of recent FSHD clinical trial workshops [16, 17]. To date, several studies have examined DUX4 target gene expression as a proxy for DUX4 activity from invasive muscle biopsies guided by MRI imaging [18-20]. However, circulating blood-based molecular biomarkers are of particular interest as they have the potential to provide rapid, objective, minimally invasive, and quantitative measurements that can be assayed repeatedly over time using typically inexpensive methods, in contrast to tissue biomarkers that require repeated muscle biopsies.…”