BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is a dominant disease 
linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35. 
Within each repeat unit is a gene, DUX4, that can encode a protein containing 
two homeodomains. A DUX4 transcript derived from the last repeat unit in a 
contracted array is associated with pathogenesis but it is unclear how.
METHODS: Using exon-based microarrays, the expression profiles of myogenic 
precursor cells were determined. Both undifferentiated myoblasts and myoblasts 
differentiated to myotubes derived from FSHD patients and controls were studied 
after immunocytochemical verification of the quality of the cultures. To further 
our understanding of FSHD and normal myogenesis, the expression profiles 
obtained were compared to those of 19 non-muscle cell types analyzed by 
identical methods.
RESULTS: Many of the ~17,000 examined genes were differentially expressed 
(>2-fold, p<0.01) in control myoblasts or myotubes vs. non-muscle cells (2185 
and 3006, respectively) or in FSHD vs. control myoblasts or myotubes (295 and 
797, respectively). Surprisingly, despite the morphologically normal 
differentiation of FSHD myoblasts to myotubes, most of the disease-related 
dysregulation was seen as dampening of normal myogenesis-specific expression 
changes, including in genes for muscle structure, mitochondrial function, stress 
responses, and signal transduction. Other classes of genes, including those 
encoding extracellular matrix or pro-inflammatory proteins, were upregulated in 
FSHD myogenic cells independent of an inverse myogenesis association. 
Importantly, the disease-linked DUX4 RNA isoform was detected by RT-PCR in FSHD 
myoblast and myotube preparations only at extremely low levels. Unique insights 
into myogenesis-specific gene expression were also obtained. For example, all 
four Argonaute genes involved in RNA-silencing were significantly upregulated 
during normal (but not FSHD) myogenesis relative to non-muscle cell types.
CONCLUSIONS: DUX4's pathogenic effect in FSHD may occur transiently at or before 
the stage of myoblast formation to establish a cascade of gene dysregulation. 
This contrasts with the current emphasis on toxic effects of experimentally 
upregulated DUX4 expression at the myoblast or myotube stages. Our model could 
explain why DUX4's inappropriate expression was barely detectable in myoblasts 
and myotubes but nonetheless linked to FSHD.