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

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 and progression to inform clinical trial design. For drugs that inhibit the expression of DUX4, measuring DUX4 or DUX4 target gene expression might be an interim outcome measure of drug activity, however, only a subset of muscle biopsies in FSHD show 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 one-year follow-up assessment of the same muscle with repeat MRI and muscle biopsy. There was very little change in the muscle MRI characteristics over the one-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 one-year period, however, there was some variability for each individual muscle biopsied. We pooled the data from both the initial and one-year follow-up evaluations and identified several subgroups based on gene expression, as well as a set of genes that distinguished all of the FSHD samples from the controls that include DUX4-regulated genes, inflammatory immune genes, and cell cycle control genes. These candidate markers of disease activity need to be validated on independent datasets, but will hopefully be useful in studies of disease progression and response to therapy. A total of 36 patients were recruited through the Seattle Paul D. Wellstone Muscular Dystrophy Cooperative Research Center. 35 patients (mean age 54, range 19-75; 22 male/13 female; clinical severity score 0-8) underwent muscle biopsy at the first visit. All patients had genetically confirmed FSHD1 or 2. 31 patients had muscle biopsies at the second visit. The inital visit RNA-seq biopsy samples were deposited to GSE115650. This raw dataset includes the RNA-seq performed on 27 out of the 31 follow-up biopsies plus the eight control muscle biopsies from the initial investigation. Definitions: sizeFactor: normalization factor calculated by DESeq2 T1_rating: MRI signal: T1 fat rating fat_fraction: MRI signal: T1 fat fraction STIR_rating: MRI signal: STIR rating Inflammation: Histopathologic inflammations core Variability.in.Fiber.Size: Pathology score: Variabilituy in fiber size Extent.of.Central.Nucleation: Pathology score: Extent of centrl nucleation Necrosis.Regeneration.Inflammation: Pathology score: Variabilituy in fiber size Fibrosis: Pathology score: Fibrosis Pathology.Score: Accumulated pathology score dux4.rlogsum: DUX4 score = summation of four DUX4 biomarkers dux4.group: Group by DUX4 score