Longitudinal measures of RNA expression and disease activity in FSHD muscle biopsies

Abstract

Advances in understanding the pathophysiology of facioscapulohumeral dystrophy (FSHD) have led to the discovery of candidate therapeutics, and it is important to identify markers of disease activity to inform clinical trial design. For drugs that inhibit DUX4 expression, measuring DUX4 or DUX4-target gene expression might be an interim measure of drug activity; however, only a subset of FHSD muscle biopsies shows evidence of DUX4 expression. Our prior study showed that MRI T2-STIR-positive muscles had a higher probability of showing DUX4 expression than muscles with normal MRI characteristics. In the current study, we performed a 1-year follow-up assessment of the same muscle with repeat MRI and muscle biopsy. There was little change in MRI characteristics over the 1-year period and, similar to the initial evaluation, MRI T2-STIR-postive muscles had a higher expression of DUX4-regulated genes, as well as genes associated with inflammation, extracellular matrix and cell cycle. Compared to the initial evaluation, overall the level of expression in these gene categories remained stable over the 1-year period; however, there was some variability for each individual muscle biopsied. The pooled data from both the initial and 1-year follow-up evaluations identified several FSHD subgroups based on gene expression, as well as a set of genes—composed of DUX4-target genes, inflammatory and immune genes and cell cycle control genes—that distinguished all of the FSHD samples from the controls. These candidate markers of disease activity need to be replicated in independent datasets and, if validated, may provide useful measures of disease progression and response to therapy.

Skeletal muscle regeneration in facioscapulohumeral muscular dystrophy is correlated with pathological severity

“…Consistent with this, an early microarray-based transcriptomic study found that many genes engaged in differentiation were altered in FSHD muscle, suggesting a partial block in the myogenic differentiation program ( 58 ). Moreover, a recent RNA-seq-based transcriptomic study identified a subset of FSHD samples displaying a ‘muscle-low’ transcriptome, suppressing genes typically involved in myogenesis ( 59 ). For DM2, myoblasts from adult DM2 patients differentiate as effectively as controls ex vivo ( 60–62 ) but are characterized by a premature proliferative growth arrest, halting cell division earlier than controls ( 61 ).…”

Longitudinal study of MRI and functional outcome measures in facioscapulohumeral muscular dystrophy

“…Multi-level DIXON analysis: Dixon data was imported into ITK-snap (Version 3.6.0) for individual muscle labelling (sartorius, vastus lateralis, semimembranosus, tibialis anterior, tibialis posterior, soleus, medial gastrocnemius, and lateral gastrocnemius) on the raw DIXON opposing phase image, owing to the ease of conspicuity of muscle borders. These regions were chosen for parallel work (MRI-biopsy association [ 10 , 11 ]) and to survey a “control” region that is rarely affected (tibialis posterior). A continuous series of axial images of approximately 100 mm in the center of the calf and proximal thigh was selected for segmentation, involving tracing every third slice and interpolating, then manual cleaning up of the result.…”

Designed U7 snRNAs inhibit DUX4 expression and improve FSHD-associated outcomes in DUX4 overexpressing cells and FSHD patient myotubes

“…With the emergence of prospective FSHD therapies came a need in the FSHD field to develop clinical outcome measures and biomarkers that could be used to establish therapeutic efficacy. 41 , 42 , 43 , 44 Although DUX4 expression is the most direct measure of target engagement by a prospective drug or gene therapy, it is difficult to detect and relatively scarce in FSHD muscle biopsies. Thus, DUX4 expression in human muscle biopsies is currently not a reliable outcome measure for FSHD clinical trials, and several groups have now turned to examining DUX4-activated biomarkers as an indirect measure of DUX4 expression.…”