Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells

Jagannathan, Sujatha; Shadle, Sean C.; Resnick, Rebecca; Snider, Lauren; Tawil, Rabi; Maarel, Silvère M. van der; Bradley, Robert K.; Tapscott, Stephen J.

doi:10.1093/hmg/ddw271

Cited by 88 publications

(177 citation statements)

References 28 publications

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“…We define 59 "FSHD-induced genes" as the set of known DUX4 target genes, genes upregulated in previous FSHD studies, and novel genes upregulated across this FSHD2 differentiation time-course ( Figure 1C red box). Previously published FSHD-induced genes [20,22,24] were upregulated in waves starting at day 2, such as TRIM43, MBD3L2, MBD3L3, KHDC1L and LEUTX, followed by day 3, such as PRAMEF1, PRAMEF2, PRAMEF12, ZSCAN4 and MBD3L5, and day 4, such as CCNA1, KDM4E, PRAMEF17, PRAMEF6 [20] ( Figure 1C, S3). After being significantly upregulated, most FSHD-induced genes remained upregulated through the end of the time-course ( Figure 1C).…”

Section: Upregulation Of Fshd-induced Genes During Fshd2 Myotube Diffmentioning

confidence: 71%

“…To identify correlated gene regulation between the populations, we used the distinct expression profiles of DUX4, DUXA, DUXB, CHI3L1 and CYTL1 to mark the three FSHD2 myotube nuclei populations mentioned above and to observe their coexpression patterns with FSHD-induced genes ( Figure 3D). We found that 19 FSHD-induced genes were coexpressed in both "FSHD-Hi" and "FSHD-Lo" populations, including reported DUX4 targets LEUTX, ZSCAN4, MBD3L2, TRIM43, KHDC1L and CCNA1 [4,20,24], indicating that they may perform as a core set of responsive and interactive genes during FSHD progression ( Figure 3D). We observed that 15 FSHD-induced genes were coexpressed only in the "FSHD-Hi" population, such as KDM4E, PRAMEF1, PRAMEF11, PRAMEF12 and SLC34A2, and 9 genes were exclusively coexpressed in the "FSHD-Lo" population.…”

Section: Detection Of Nuclei With Dux4 Expression From Fshd2 Myotubesmentioning

confidence: 99%

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Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei

Jiang

Williams

Kong

et al. 2018

Preprint

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AbstractFSHD is characterized by the misexpression of DUX4 in skeletal muscle. However, DUX4 is lowly expressed in patient samples and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we performed pooled RNA-seq differentiation time-course in FSHD2 patient-derived primary myoblasts and identified early-and late-induced sets of FSHD-associated genes. Using single-cell and single-nucleus RNA-seq on FSHD2 myoblasts and myotubes respectively, we captured DUX4 expression in single-nuclei and found that only some DUX4 targets are coexpressed. We identified two populations of FSHD myotube nuclei with distinct transcriptional profiles. One population is highly enriched with DUX4 and FSHD related genes, including the DUX4 paralog DUXA (“FSHD-Hi”). The other population has no expression of DUX4 and expresses low amounts of FSHD related genes (“FSHD-Lo”), but is marked by the expression of CYTL1 and CHI3L1. “FSHD-Hi” myotube nuclei upregulated a set of transcription factors (TFs) that may form a self-sustaining network of gene dysregulation, which perpetuates this disease after DUX4 is no longer expressed.

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Section: Upregulation Of Fshd-induced Genes During Fshd2 Myotube Diffmentioning

confidence: 71%

Section: Detection Of Nuclei With Dux4 Expression From Fshd2 Myotubesmentioning

confidence: 99%

Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei

Jiang

Williams

Kong

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Therefore, to determine whether DUX4 expression in FSHD cells correlates with higher levels of MYC mRNA, we used an RNA-seq dataset from FSHD cells FACS sorted based on the expression of a DUX4-reporter gene [7]. Based on our previous analysis of this dataset (see Supplemental Table 1 in Jagannathan, et al [29]), muscle cells expressing the DUX4-responsive promoter showed an almost 2-fold increase in the level of MYC mRNA (log2 fold-change ~0.9 and adjusted p-value = ~0.003); however, EGR1, PMAIP1/NOXA and BCL2L11 were not significantly upregulated. Therefore, DUX4 expression is associated with higher levels of MYC mRNA in FSHD muscle cells, but the role in activating an apoptotic pathway requires further study.…”

Section: Resultsmentioning

confidence: 99%

DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy

et al. 2017

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Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of DUX4 in skeletal muscle cells. DUX4 is a transcription factor that activates genes normally associated with stem cell biology and its mis-expression in FSHD cells results in apoptosis. To identify genes and pathways necessary for DUX4-mediated apoptosis, we performed an siRNA screen in an RD rhabdomyosarcoma cell line with an inducible DUX4 transgene. Our screen identified components of the MYC-mediated apoptotic pathway and the double-stranded RNA (dsRNA) innate immune response pathway as mediators of DUX4-induced apoptosis. Further investigation revealed that DUX4 expression led to increased MYC mRNA, accumulation of nuclear dsRNA foci, and activation of the dsRNA response pathway in both RD cells and human myoblasts. Nuclear dsRNA foci were associated with aggregation of the exon junction complex component EIF4A3. The elevation of MYC mRNA, dsRNA accumulation, and EIF4A3 nuclear aggregates in FSHD muscle cells suggest that these processes might contribute to FSHD pathophysiology.

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“…1c), we found that Dux and DUX4 18 activated orthologous genes in myoblasts of their respective species, including genes in the mouse 2C-like gene signature. For this analysis we only considered genes with simple 1:1 mouse-to-human orthology according to HomoloGene 19 .…”

mentioning

confidence: 77%

Conservation and innovation in the DUX4-family gene network

et al. 2017

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Facioscapulohumeral dystrophy (FSHD; OMIM #158900, #158901) is caused by mis-expression of the DUX4 transcription factor in skeletal muscle1. Animal models of FSHD are hampered by incomplete knowledge of the conservation of the DUX4 transcriptional program in other species2–5. Despite divergence of their binding motifs, both mouse Dux and human DUX4 activate genes associated with cleavage-stage embryos, including MERV-L and ERVL-MaLR retrotransposons, in mouse and human muscle cells respectively. When expressed in mouse cells, human DUX4 maintained modest activation of cleavage-stage genes driven by conventional promoters, but did not activate MERV-L-promoted genes. These findings indicate that the ancestral DUX4-factor regulated genes characteristic of cleavage-stage embryos driven by conventional promoters, whereas divergence of the DUX4/Dux homeodomains correlates with retrotransposon specificity. These results provide insight into how species balance conservation of a core transcriptional program with innovation at retrotransposon promoters and provide a basis for animal models that recreate the FSHD transcriptome.

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Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells

Cited by 88 publications

References 28 publications

Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei

Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei

DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy

Conservation and innovation in the DUX4-family gene network

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