Parallel protein and transcript profiles of FSHD patient muscles correlate to the D4Z4 arrangement and reveal a common impairment of slow to fast fibre differentiation and a general deregulation of MyoD‐dependent genes

Abstract

Here, we present the first study of a human neuromuscular disorder at transcriptional and proteomic level. Autosomal dominant facio-scapulo-humeral muscular dystrophy (FSHD) is caused by a deletion of an integral number of 3.3-kb KpnI repeats inside the telomeric region D4Z4 at the 4q35 locus. We combined a muscle-specific cDNA microarray platform with a proteomic investigation to analyse muscle biopsies of patients carrying a variable number of KpnI repeats. Unsupervised cluster analysis divides patients into three classes, according to their KpnI repeat number. Expression data reveal a transition from fast-glycolytic to slow-oxidative phenotype in FSHD muscle, which is accompanied by a deficit of proteins involved in response to oxidative stress. Besides, FSHD individuals show a disruption in the MyoD-dependent gene network suggesting a coregulation at transcriptional level during myogenesis. We also discuss the hypothesis that D4Z4 contraction may affect in trans the expression of a set of genes involved in myogenesis, as well as in the regeneration pathway of satellite cells in adult tissue. Muscular wasting could result from the inability of satellite cells to successfully differentiate into mature fibres and from the accumulation of structural damages caused by a reactive oxygen species (ROS) imbalance induced by an increased oxidative metabolism in fibres.

Common epigenetic changes of D4Z4 in contraction-dependent and contraction-independent FSHD

“…The absence of FRG2 on the disease alleles in some FSHD patients with a proximal deletion makes this gene a less attractive candidate gene [39] . However, transcriptional deregulation of these candidate genes in patients with FSHD is still under debate, as several studies showed contradictory results [22,[40][41][42][43] . Based on our data showing that hypomethylation is restricted to the D4Z4 repeat and not spreading in a proximal direction in addition to previous data showing no change in the chromatin structure of proximal sequences in FSHD [22] , we do not support a cisspreading mechanism emanating from D4Z4 in FSHD.…”

Facioscapulohumeral Muscular Dystrophy: From Clinical Data to Molecular Genetics and Return

“…It has been also postulated that reduction of D4Z4 might have a more genome-wide effects, affecting other pathways, such the slow-to-fast fiber differentiation pathway (Celegato et al, 2006) and the response to oxidative stress and myogenic differentiation pathway (Winokur et al, 2003b). Because D4Z4 can be regarded as a docking platform for protein factors, loss of repeats may generate a local imbalance in the availability of D4Z4 proteins in the cell, and/or lead to new interaction with different proteins at the disease allele.…”

β - catenin is central to DUX4 -driven network rewiring in facioscapulohumeral muscular dystrophy

“…Many genes in this intersection have been associated with FSHD, e.g. TP53 [16], JUNB [20,17], HIF1A [20], WNT3 [4], LMO3 [20], ANXA4 [5] and HSPB1 [22]. Gene Set Enrichment Analysis (GSEA) [23] on the intersection also implicated many FSHD associated processes, such as myogenesis [17] and regulation of the actin cytoskeleton [15], and pathways, including, p53 [16], Wnt [4], and VEGF [5] To identify genes implicated as rewiring specifically in FSHD, we also ran InSpiRe on two datasets each describing skeletal muscle gene expression during ageing (GSE5086 [24] and GSE9676 [25]), disuse atrophy (GSE5110 [26] and GSE8872 [27]) and other muscle diseases involving inflammation and wasting (GSE3307 [19], where juvenile dermatomyositis and limb-girdle muscular dystrophy type 2A datasets were independently analysed).…”