HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles

Abstract

Fibro-adipogenic progenitors (FAPs) are important components of the skeletal muscle regenerative environment. Whether FAPs support muscle regeneration or promote fibro-adipogenic degeneration is emerging as a key determinant in the pathogenesis of muscular diseases, including Duchenne muscular dystrophy (DMD). However, the molecular mechanism that controls FAP lineage commitment and activity is currently unknown. We show here that an HDAC-myomiR-BAF60 variant network regulates the fate of FAPs in dystrophic muscles of mdx mice. Combinatorial analysis of gene expression microarray, genome-wide chromatin remodeling by nuclease accessibility (NA) combined with next-generation sequencing (NA-seq), small RNA sequencing (RNA-seq), and microRNA (miR) high-throughput screening (HTS) against SWI/SNF BAF60 variants revealed that HDAC inhibitors (HDACis) derepress a ''latent'' myogenic program in FAPs from dystrophic muscles at early stages of disease. Specifically, HDAC inhibition induces two core components of the myogenic transcriptional machinery, MYOD and BAF60C, and up-regulates the myogenic miRs (myomiRs) (miR-1.2, miR-133, and miR-206), which target the alternative BAF60 variants BAF60A and BAF60B, ultimately directing promyogenic differentiation while suppressing the fibro-adipogenic phenotype. In contrast, FAPs from late stage dystrophic muscles are resistant to HDACi-induced chromatin remodeling at myogenic loci and fail to activate the promyogenic phenotype. These results reveal a previously unappreciated disease stage-specific bipotency of mesenchimal cells within the regenerative environment of dystrophic muscles. Resolution of such bipotency by epigenetic intervention with HDACis provides a molecular rationale for the in situ reprogramming of target cells to promote therapeutic regeneration of dystrophic muscles.

Autophagy regulates satellite cell ability to regenerate normal and dystrophic muscles

“…49 Accordingly, pharmacological treatment with HDAC inhibitors (HDACi) leads to morphological and functional recovery of the dystrophic phenotype in mdx mice. [50][51][52][53] Still a stage-dependent beneficial effect of HDACi treatment has been reported being HDACi efficacy restricted to early stages of the disease. 52,54 Interestingly, the refractoriness to HDACi treatment coincides with the premature block of autophagy reported in this work.…”

“…[50][51][52][53] Still a stage-dependent beneficial effect of HDACi treatment has been reported being HDACi efficacy restricted to early stages of the disease. 52,54 Interestingly, the refractoriness to HDACi treatment coincides with the premature block of autophagy reported in this work. Recent evidence underscores a role of HDACi in inducing autophagy 55,56 by directly regulating LC3 levels.…”

HDAC inhibitors for muscular dystrophies: progress and prospects

“…Interestingly, FAPs from dystrophic muscles at advanced stage of disease are resistant to the beneficial effects of HDACi, accounting for the stage-specific effect of HDACi previously observed by Mozzetta et al [9] Genome-wide studies of chromatin accessibility showed that at early stages of the disease, HDACi promote an extensive chromatin remodeling, which was not observed at late stage of the disease. [14] This finding indicates that pharmacological interventions that target FAPs could be used to promote compensatory regeneration, while preventing fibroadipogenic degeneration of DMD muscles. It also suggests that FAPs of dystrophic muscles at late stages of DMD progression might acquire a chromatin conformation that confers resistance to treatments that are…”

“…MyomiRs in turn target two alternative BAF60 variants -BAF60 A and B -that when incorporated into the Switch/Sucrose NonFermentable (SWI/SNF) chromatin-remodeling complex would otherwise promote the activation of the fibro-adipogenic program. [14] Thus, HDACi-mediated selection of BAF60 C-based SWI/SNF complex appears to mediate a therapeutic switch of FAP phenotype from pro-fibroadipogenic to pro-myogenic one. Interestingly, FAPs from dystrophic muscles at advanced stage of disease are resistant to the beneficial effects of HDACi, accounting for the stage-specific effect of HDACi previously observed by Mozzetta et al [9] Genome-wide studies of chromatin accessibility showed that at early stages of the disease, HDACi promote an extensive chromatin remodeling, which was not observed at late stage of the disease.…”

“…[12] Moreover, recent studies have revealed complex epigenetic networks targeted by HDACi in MuSCs and FAPs. [13,14] In particular, studies from Saccone et al have identified an HDAC-regulated network that controls the functional phenotype of FAPs from dystrophic muscles. Treatment with HDACi promotes the expression of two core components of the myogenic transcriptional machinery, MyoD and BAF60c [15] and upregulates three myogenic microRNA involved into muscle differentiation (myomiRs; miR-1.2, miR-133 and miR-206) in FAPs.…”