Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy, linked to hypomethylation of D4Z4 repeats on chromosome 4q causing expression of the DUX4 transcription factor. However, DUX4 is difficult to detect in FSHD muscle biopsies and it is debatable how robust changes in DUX4 target gene expression are as an FSHD biomarker. PAX7 is a master regulator of myogenesis that rescues DUX4-mediated apoptosis. Here, we show that suppression of PAX7 target genes is a hallmark of FSHD, and that it is as major a signature of FSHD muscle as DUX4 target gene expression. This is shown using meta-analysis of over six FSHD muscle biopsy gene expression studies, and validated by RNA-sequencing on FSHD patient-derived myoblasts. DUX4 also inhibits PAX7 from activating its transcriptional target genes and vice versa. Furthermore, PAX7 target gene repression can explain oxidative stress sensitivity and epigenetic changes in FSHD. Thus, PAX7 target gene repression is a hallmark of FSHD that should be considered in the investigation of FSHD pathology and therapy.
Highlights
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy, linked to hypomethylation of D4Z4 repeats on chromosome 4q causing expression of the double homeobox 4 (DUX4) transcription factor
We find that only the new biomarker based on Pax[7] target gene repression is consistently able to discriminate FSHD from control skeletal muscle biopsies in every FSHD biopsy data set, while the discriminatory power of DUX4 target gene expression is limited to just two studies[10, 28]
Transcriptomic biomarkers of FSHD muscle are important both for understanding molecular processes perturbed in pathology and for monitoring therapeutic responses in clinical trials[3]
Summary
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy, linked to hypomethylation of D4Z4 repeats on chromosome 4q causing expression of the DUX4 transcription factor. The Geng et al.[35] DUX4 target gene signature was significantly upregulated on the FSHD muscle biopsy samples from the Yao et al.[10] RNA-seq data set.
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