Publications by authors named "Stephen J Tapscott"

141 Publications

Chromosome 10q-linked FSHD identifies as principal disease gene.

Authors:
Richard J L F Lemmers Patrick J van der Vliet Ana Blatnik Judit Balog Janez Zidar Don Henderson Rianne Goselink Stephen J Tapscott Nicol C Voermans Rabi Tawil George W A M Padberg Baziel Gm van Engelen Silvère M van der Maarel

J Med Genet 2021 Jan 12. Epub 2021 Jan 12.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Background: Facioscapulohumeral dystrophy (FSHD) is an inherited muscular dystrophy clinically characterised by muscle weakness starting with the facial and upper extremity muscles. A disease model has been developed that postulates that failure in somatic repression of the transcription factor DUX4 embedded in the D4Z4 repeat on chromosome 4q causes FSHD. However, due to the position of the D4Z4 repeat close to the telomere and the complex genetic and epigenetic aetiology of FSHD, there is ongoing debate about the transcriptional deregulation of closely linked genes and their involvement in FSHD.

Method: Detailed genetic characterisation and gene expression analysis of patients with clinically confirmed FSHD and control individuals.

Results: Identification of two FSHD families in which the disease is caused by repeat contraction and expression from chromosome 10 due to a de novo D4Z4 repeat exchange between chromosomes 4 and 10. We show that the genetic lesion causal to FSHD in these families is physically separated from other candidate genes on chromosome 4. We demonstrate that muscle cell cultures from affected family members exhibit the characteristic molecular features of FSHD, including and DUX4 target gene expression, without showing evidence for transcriptional deregulation of other chromosome 4-specific candidate genes.

Conclusion: This study shows that in rare situations, FSHD can occur on chromosome 10 due to an interchromosomal rearrangement with the FSHD locus on chromosome 4q. These findings provide further evidence that derepression is the dominant disease pathway for FSHD. Hence, therapeutic strategies should focus on DUX4 as the primary target.
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http://dx.doi.org/10.1136/jmedgenet-2020-107041DOI Listing
January 2021

Adapting MRI as a clinical outcome measure for a facioscapulohumeral muscular dystrophy trial of prednisone and tacrolimus: case report.

Authors:
Leo H Wang Laura M Johnstone Michael Bindschadler Stephen J Tapscott Seth D Friedman

BMC Musculoskelet Disord 2021 Jan 9;22(1):56. Epub 2021 Jan 9.

Radiology Clinical Research Imaging Core/Improvement and Innovation, Seattle Children's Hospital, Seattle, Washington, USA.

Background: Facioscapulohumeral muscular dystrophy (FSHD) is a patchy and slowly progressive disease of skeletal muscle. MRI short tau inversion recovery (STIR) sequences of patient muscles often show increased hyperintensity that is hypothesized to be associated with inflammation. This is supported by the presence of inflammatory changes on biopsies of STIR-positive muscles. We hypothesized that the STIR positivity would normalize with targeted immunosuppressive therapy.

Case Presentation: 45-year-old male with FSHD type 1 was treated with 12 weeks of immunosuppressive therapy, tacrolimus and prednisone. Tacrolimus was treated to a goal serum trough of > 5 ng/mL and prednisone was tapered every month. Quantitative strength exam, functional outcome measures, and muscle MRI were performed at baseline, week 6, and week 12. The patient reported subjective worsening as reflected in quantitative strength exam. The MRI STIR signal was slightly increased from 0.02 to 0.03 of total muscle; while the T1 fat fraction was stable. Functional outcome measures also were stable.

Conclusions: Immunosuppressive therapy in refractive autoimmune myopathy in other contexts has been shown to reverse STIR signal hyperintensity, however this treatment did not reverse STIR signal in this patient with FSHD. In fact, STIR signal slightly increased throughout the treatment period. This is the first study of using MRI STIR and T1 fat fraction to follow treatment effect in FSHD. We find that STIR might not be a dynamic marker for suppressing inflammation in FSHD.
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http://dx.doi.org/10.1186/s12891-020-03910-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7797109PMC
January 2021

Longitudinal measures of RNA expression and disease activity in FSHD muscle biopsies.

Authors:
Chao-Jen Wong Leo H Wang Seth D Friedman Dennis Shaw Amy E Campbell Chris B Budech Leann M Lewis Richard J F L Lemmers Jeffrey M Statland Silvère M van der Maarel Rabi N Tawil Stephen J Tapscott

Hum Mol Genet 2020 04;29(6):1030-1043

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Advances in understanding the pathophysiology of facioscapulohumeral dystrophy (FSHD) have led to the discovery of candidate therapeutics, and it is important to identify markers of disease activity to inform clinical trial design. For drugs that inhibit DUX4 expression, measuring DUX4 or DUX4-target gene expression might be an interim measure of drug activity; however, only a subset of FHSD muscle biopsies shows evidence of DUX4 expression. Our prior study showed that MRI T2-STIR-positive muscles had a higher probability of showing DUX4 expression than muscles with normal MRI characteristics. In the current study, we performed a 1-year follow-up assessment of the same muscle with repeat MRI and muscle biopsy. There was little change in MRI characteristics over the 1-year period and, similar to the initial evaluation, MRI T2-STIR-postive muscles had a higher expression of DUX4-regulated genes, as well as genes associated with inflammation, extracellular matrix and cell cycle. Compared to the initial evaluation, overall the level of expression in these gene categories remained stable over the 1-year period; however, there was some variability for each individual muscle biopsied. The pooled data from both the initial and 1-year follow-up evaluations identified several FSHD subgroups based on gene expression, as well as a set of genes-composed of DUX4-target genes, inflammatory and immune genes and cell cycle control genes-that distinguished all of the FSHD samples from the controls. These candidate markers of disease activity need to be replicated in independent datasets and, if validated, may provide useful measures of disease progression and response to therapy.
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http://dx.doi.org/10.1093/hmg/ddaa031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158378PMC
April 2020

DUX4-Induced Histone Variants H3.X and H3.Y Mark DUX4 Target Genes for Expression.

Authors:
Rebecca Resnick Chao-Jen Wong Danielle C Hamm Sean R Bennett Peter J Skene Sandra B Hake Steven Henikoff Silvère M van der Maarel Stephen J Tapscott

Cell Rep 2019 11;29(7):1812-1820.e5

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Electronic address:

The DUX4 transcription factor is briefly expressed in the early cleavage-stage embryo, where it induces an early wave of zygotic gene transcription, whereas its mis-expression in skeletal muscle causes the muscular dystrophy facioscapulohumeral dystrophy (FSHD). Here, we show that DUX4 induces the expression of the histone variants H3.X and H3.Y. We have used a myoblast cell line with doxycycline-inducible DUX4 to show that these histone variants are incorporated throughout the body of DUX4-induced genes. Following a brief pulse of DUX4, these histones contribute to greater perdurance and to enhanced re-activation of DUX4 target gene expression. These findings provide a model for H3.X/Y as a chromatin mechanism that facilitates the expression of DUX4 target genes subsequent to a brief pulse of DUX4 expression.
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http://dx.doi.org/10.1016/j.celrep.2019.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6886682PMC
November 2019

Intronic variants in FSHD: testing the potential for CRISPR-Cas9 genome editing.

Authors:
Remko Goossens Marlinde L van den Boogaard Richard J L F Lemmers Judit Balog Patrick J van der Vliet Iris M Willemsen Julie Schouten Ignazio Maggio Nienke van der Stoep Rob C Hoeben Stephen J Tapscott Niels Geijsen Manuel A F V Gonçalves Sabrina Sacconi Rabi Tawil Silvère M van der Maarel

J Med Genet 2019 12 1;56(12):828-837. Epub 2019 Nov 1.

Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

Background: Facioscapulohumeral dystrophy (FSHD) is associated with partial chromatin relaxation of the retrogene containing D4Z4 macrosatellite repeats on chromosome 4, and transcriptional de-repression of in skeletal muscle. The common form of FSHD, FSHD1, is caused by a D4Z4 repeat array contraction. The less common form, FSHD2, is generally caused by heterozygous variants in .

Methods: We employed whole exome sequencing combined with Sanger sequencing to screen uncharacterised FSHD2 patients for extra-exonic mutations. We also used CRISPR-Cas9 genome editing to repair a pathogenic intronic variant from patient myoblasts.

Results: We identified intronic variants in two FSHD families. In the first family, an intronic variant resulted in partial intron retention and inclusion of the distal 14 nucleotides of intron 13 into the transcript. In the second family, a deep intronic variant in intron 34 resulted in exonisation of 53 nucleotides of intron 34. In both families, the aberrant transcripts are predicted to be non-functional. Deleting the pseudo-exon by CRISPR-Cas9 mediated genome editing in primary and immortalised myoblasts from the index case of the second family restored wild-type SMCHD1 expression to a level that resulted in efficient suppression of .

Conclusions: The estimated intronic mutation frequency of almost 2% in FSHD2, as exemplified by the two novel intronic variants identified here, emphasises the importance of screening for intronic variants in . Furthermore, the efficient suppression of after restoring SMCHD1 levels by genome editing of the mutant allele provides further guidance for therapeutic strategies.
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http://dx.doi.org/10.1136/jmedgenet-2019-106402DOI Listing
December 2019

DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double-stranded RNA foci in human cell models of FSHD.

Authors:
Sean C Shadle Sean R Bennett Chao-Jen Wong Nancy A Karreman Amy E Campbell Silvère M van der Maarel Brenda L Bass Stephen J Tapscott

Hum Mol Genet 2019 12;28(23):3997-4011

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

The DUX4 transcription factor is normally expressed in the cleavage-stage embryo and regulates genes involved in embryonic genome activation. Misexpression of DUX4 in skeletal muscle, however, is toxic and causes facioscapulohumeral muscular dystrophy (FSHD). We recently showed DUX4-induced toxicity is due, in part, to the activation of the double-stranded RNA (dsRNA) response pathway and the accumulation of intranuclear dsRNA foci. Here, we determined the composition of DUX4-induced dsRNAs. We found that a subset of DUX4-induced dsRNAs originate from inverted Alu repeats embedded within the introns of DUX4-induced transcripts and from DUX4-induced dsRNA-forming intergenic transcripts enriched for endogenous retroviruses, Alu and LINE-1 elements. However, these repeat classes were also represented in dsRNAs from cells not expressing DUX4. In contrast, pericentric human satellite II (HSATII) repeats formed a class of dsRNA specific to the DUX4 expressing cells. Further investigation revealed that DUX4 can initiate the bidirectional transcription of normally heterochromatin-silenced HSATII repeats. DUX4-induced HSATII RNAs co-localized with DUX4-induced nuclear dsRNA foci and with intranuclear aggregation of EIF4A3 and ADAR1. Finally, gapmer-mediated knockdown of HSATII transcripts depleted DUX4-induced intranuclear ribonucleoprotein aggregates and decreased DUX4-induced cell death, suggesting that HSATII-formed dsRNAs contribute to DUX4 toxicity.
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http://dx.doi.org/10.1093/hmg/ddz242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342170PMC
December 2019

TWIST1 Heterodimerization with E12 Requires Coordinated Protein Phosphorylation to Regulate Periostin Expression.

Authors:
Svetlana A Mikheeva Nathan D Camp Lei Huang Antrix Jain Sung Yun Jung Naze G Avci Mari Tokita Alejandro Wolf-Yadlin Jing Zhang Stephen J Tapscott Robert C Rostomily Andrei M Mikheev

Cancers (Basel) 2019 Sep 18;11(9). Epub 2019 Sep 18.

Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA.

Diffuse invasion into adjacent brain matter by glioblastoma (GBM) is largely responsible for their dismal prognosis. Previously, we showed that the TWIST1 (TW) bHLH transcription factor and its regulated gene periostin () promote invasive phenotypes of GBM cells. Since TW functional effects are regulated by phosphorylation and dimerization, we investigated how phosphorylation of serine 68 in TW regulates TW dimerization, expression, and invasion in glioma cells. Compared with wild-type TW, the hypophosphorylation mutant, TW(S68A), impaired TW heterodimerization with the E12 bHLH transcription factor and cell invasion in vitro but had no effect on TW homodimerization. Overexpression of TW:E12 forced dimerization constructs (FDCs) increased glioma cell invasion and upregulated pro-invasive proteins, including POSTN, in concert with cytoskeletal reorganization. By contrast, TW:TW homodimer FDCs inhibited POSTN expression and cell invasion in vitro. Further, phosphorylation of analogous PXSP phosphorylation sites in TW:E12 FDCs (TW S68 and E12 S139) coordinately regulated and mRNA expression. These results suggested that TW regulates pro-invasive phenotypes in part through coordinated phosphorylation events in TW and E12 that promote heterodimer formation and regulate downstream targets. This new mechanistic understanding provides potential therapeutic strategies to inhibit TW-POSTN signaling in GBM and other cancers.
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http://dx.doi.org/10.3390/cancers11091392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770789PMC
September 2019

DUX4 Suppresses MHC Class I to Promote Cancer Immune Evasion and Resistance to Checkpoint Blockade.

Authors:
Guo-Liang Chew Amy E Campbell Emma De Neef Nicholas A Sutliff Sean C Shadle Stephen J Tapscott Robert K Bradley

Dev Cell 2019 09 18;50(5):658-671.e7. Epub 2019 Jul 18.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Electronic address:

Advances in cancer immunotherapies make it critical to identify genes that modulate antigen presentation and tumor-immune interactions. We report that DUX4, an early embryonic transcription factor that is normally silenced in somatic tissues, is re-expressed in diverse solid cancers. Both cis-acting inherited genetic variation and somatically acquired mutations in trans-acting repressors contribute to DUX4 re-expression in cancer. Although many DUX4 target genes encode self-antigens, DUX4-expressing cancers were paradoxically characterized by reduced markers of anti-tumor cytolytic activity and lower major histocompatibility complex (MHC) class I gene expression. We demonstrate that DUX4 expression blocks interferon-γ-mediated induction of MHC class I, implicating suppressed antigen presentation in DUX4-mediated immune evasion. Clinical data in metastatic melanoma confirmed that DUX4 expression was associated with significantly reduced progression-free and overall survival in response to anti-CTLA-4. Our results demonstrate that cancers can escape immune surveillance by reactivating a normal developmental pathway and identify a therapeutically relevant mechanism of cell-intrinsic immune evasion.
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http://dx.doi.org/10.1016/j.devcel.2019.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736738PMC
September 2019

Insights into pediatric rhabdomyosarcoma research: Challenges and goals.

Authors:
Marielle E Yohe Christine M Heske Elizabeth Stewart Peter C Adamson Nabil Ahmed Cristina R Antonescu Eleanor Chen Natalie Collins Alan Ehrlich Rene L Galindo Berkley E Gryder Heidi Hahn Sharon Hammond Mark E Hatley Douglas S Hawkins Madeline N Hayes Andrea Hayes-Jordan Lee J Helman Simone Hettmer Myron S Ignatius Charles Keller Javed Khan David G Kirsch Corinne M Linardic Philip J Lupo Rossella Rota Jack F Shern Janet Shipley Sivasish Sindiri Stephen J Tapscott Christopher R Vakoc Leonard H Wexler David M Langenau

Pediatr Blood Cancer 2019 10 21;66(10):e27869. Epub 2019 Jun 21.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts.

Overall survival rates for pediatric patients with high-risk or relapsed rhabdomyosarcoma (RMS) have not improved significantly since the 1980s. Recent studies have identified a number of targetable vulnerabilities in RMS, but these discoveries have infrequently translated into clinical trials. We propose streamlining the process by which agents are selected for clinical evaluation in RMS. We believe that strong consideration should be given to the development of combination therapies that add biologically targeted agents to conventional cytotoxic drugs. One example of this type of combination is the addition of the WEE1 inhibitor AZD1775 to the conventional cytotoxic chemotherapeutics, vincristine and irinotecan.
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http://dx.doi.org/10.1002/pbc.27869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707829PMC
October 2019

Clinically Advanced p38 Inhibitors Suppress DUX4 Expression in Cellular and Animal Models of Facioscapulohumeral Muscular Dystrophy.

Authors:
Jonathan Oliva Scott Galasinski Amelia Richey Amy E Campbell Marvin J Meyers Neal Modi Jun Wen Zhong Rabi Tawil Stephen J Tapscott Francis M Sverdrup

J Pharmacol Exp Ther 2019 08 12;370(2):219-230. Epub 2019 Jun 12.

Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)

Facioscapulohumeral muscular dystrophy (FSHD) is characterized by misexpression of the double homeobox 4 (DUX4) developmental transcription factor in mature skeletal muscle, where it is responsible for muscle degeneration. Preventing expression of DUX4 mRNA is a disease-modifying therapeutic strategy with the potential to halt or reverse the course of disease. We previously reported that agonists of the -2 adrenergic receptor suppress expression by activating adenylate cyclase to increase cAMP levels. Efforts to further explore this signaling pathway led to the identification of p38 mitogen-activated protein kinase as a major regulator of expression. In vitro experiments demonstrate that clinically advanced p38 inhibitors suppress expression in FSHD type 1 and 2 myoblasts and differentiating myocytes in vitro with exquisite potency. Individual small interfering RNA-mediated knockdown of either p38 or p38 suppresses expression, demonstrating that each kinase isoform plays a distinct requisite role in activating Finally, p38 inhibitors effectively suppress expression in a mouse xenograft model of human FSHD gene regulation. These data support the repurposing of existing clinical p38 inhibitors as potential therapeutics for FSHD. The surprise finding that p38 and p38 isoforms each independently contribute to DUX4 expression offers a unique opportunity to explore the utility of p38 isoform-selective inhibitors to balance efficacy and safety in skeletal muscle. We propose p38 inhibition as a disease-modifying therapeutic strategy for FSHD. SIGNIFICANCE STATEMENT: Facioscapulohumeral muscular dystrophy (FSHD) currently has no treatment options. This work provides evidence that repurposing a clinically advanced p38 inhibitor may provide the first disease-modifying drug for FSHD by suppressing toxic DUX4 expression, the root cause of muscle degeneration in this disease.
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http://dx.doi.org/10.1124/jpet.119.259663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6652132PMC
August 2019

Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of facioscapulohumeral muscular dystrophy.

Authors:
Sujatha Jagannathan Yuko Ogata Philip R Gafken Stephen J Tapscott Robert K Bradley

Elife 2019 01 15;8. Epub 2019 Jan 15.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

DUX4 is a transcription factor whose misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). DUX4's transcriptional activity has been extensively characterized, but the DUX4-induced proteome remains undescribed. Here, we report concurrent measurement of RNA and protein levels in DUX4-expressing cells via RNA-seq and quantitative mass spectrometry. DUX4 transcriptional targets were robustly translated, confirming the likely clinical relevance of proposed FSHD biomarkers. However, a multitude of mRNAs and proteins exhibited discordant expression changes upon DUX4 expression. Our dataset revealed unexpected proteomic, but not transcriptomic, dysregulation of diverse molecular pathways, including Golgi apparatus fragmentation, as well as extensive post-transcriptional buffering of stress-response genes. Key components of RNA degradation machineries, including UPF1, UPF3B, and XRN1, exhibited suppressed protein, but not mRNA, levels, explaining the build-up of aberrant RNAs that characterizes DUX4-expressing cells. Our results provide a resource for the FSHD community and illustrate the importance of post-transcriptional processes in DUX4-induced pathology.
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http://dx.doi.org/10.7554/eLife.41740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349399PMC
January 2019

Single-cell RNA sequencing in facioscapulohumeral muscular dystrophy disease etiology and development.

Authors:
Anita van den Heuvel Ahmed Mahfouz Susan L Kloet Judit Balog Baziel G M van Engelen Rabi Tawil Stephen J Tapscott Silvère M van der Maarel

Hum Mol Genet 2019 04;28(7):1064-1075

Department of Human Genetics, Leiden University Medical Center, ZC Leiden, Zuid-Holland, The Netherlands.

Facioscapulohumeral muscular dystrophy (FSHD) is characterized by sporadic de-repression of the transcription factor DUX4 in skeletal muscle. DUX4 activates a cascade of muscle disrupting events, eventually leading to muscle atrophy and apoptosis. Yet, how sporadic DUX4 expression leads to the generalized muscle wasting remains unclear. Transcriptome analyses have systematically been challenged by the majority of nuclei being DUX4neg, weakening the DUX4 transcriptome signature. Moreover, DUX4 has been shown to be expressed in a highly dynamic burst-like manner, likely resulting in the detection of the downstream cascade of events long after DUX4 expression itself has faded. Identifying the FSHD transcriptome in individual cells and unraveling the cascade of events leading to FSHD development may therefore provide important insights in the disease process. We employed single-cell RNA sequencing, combined with pseudotime trajectory modeling, to study FSHD disease etiology and cellular progression in human primary myocytes. We identified a small FSHD-specific cell population in all tested patient-derived cultures and detected new genes associated with DUX4 de-repression. We furthermore generated an FSHD cellular progression model, reflecting both the early burst-like DUX4 expression as well as the downstream activation of various FSHD-associated pathways, which allowed us to correlate DUX4 expression signature dynamics with that of regulatory complexes, thereby facilitating the prioritization of epigenetic targets for DUX4 silencing. Single-cell transcriptomics combined with pseudotime modeling thus holds valuable information on FSHD disease etiology and progression that can potentially guide biomarker and target selection for therapy.
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http://dx.doi.org/10.1093/hmg/ddy400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423425PMC
April 2019

MRI-informed muscle biopsies correlate MRI with pathology and DUX4 target gene expression in FSHD.

Authors:
Leo H Wang Seth D Friedman Dennis Shaw Lauren Snider Chao-Jen Wong Chris B Budech Sandra L Poliachik Nancy E Gove Leann M Lewis Amy E Campbell Richard J F L Lemmers Silvère M Maarel Stephen J Tapscott Rabi N Tawil

Hum Mol Genet 2019 02;28(3):476-486

Neuromuscular Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA.

Facioscapulohumeral muscular dystrophy (FSHD) is a common, dominantly inherited disease caused by the epigenetic de-repression of the DUX4 gene, a transcription factor normally repressed in skeletal muscle. As targeted therapies are now possible in FSHD, a better understanding of the relationship between DUX4 activity, muscle pathology and muscle magnetic resonance imaging (MRI) changes is crucial both to understand disease mechanisms and for the design of future clinical trials. Here, we performed MRIs of the lower extremities in 36 individuals with FSHD, followed by needle muscle biopsies in safely accessible muscles. We examined the correlation between MRI characteristics, muscle pathology and expression of DUX4 target genes. Results show that the presence of elevated MRI short tau inversion recovery signal has substantial predictive value in identifying muscles with active disease as determined by histopathology and DUX4 target gene expression. In addition, DUX4 target gene expression was detected only in FSHD-affected muscles and not in control muscles. These results support the use of MRI to identify FSHD muscles most likely to have active disease and higher levels of DUX4 target gene expression and might be useful in early phase therapeutic trials to demonstrate target engagement in therapies aiming to suppress DUX4 expression.
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http://dx.doi.org/10.1093/hmg/ddy364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337697PMC
February 2019

Identification of SMCHD1 domains for nuclear localization, homo-dimerization, and protein cleavage.

Authors:
Yosuke Hiramuki Stephen J Tapscott

Skelet Muscle 2018 08 2;8(1):24. Epub 2018 Aug 2.

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.

Background: SMCHD1 is a disease modifier and a causative gene for facioscapulohumeral muscular dystrophy (FSHD) type 1 and type 2, respectively. A large variety of different mutations in SMCHD1 have been identified as causing FSHD2. In many cases, it is unclear how these mutations disrupt the normal function of SMCHD1.

Methods: We made and analyzed lenti-viral vectors that express Flag-tagged full-length or different mutant SMCHD1 proteins to better understand the functional domains of SMCHD1 in muscle cells.

Results: We identified regions necessary for nuclear localization, dimerization, and cleavage sites. Moreover, we confirmed that some mutants increased DUX4 expression in FSHD1 myoblasts.

Conclusions: These findings provide an additional basis for understanding the molecular consequences of SMCHD1 mutations.
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http://dx.doi.org/10.1186/s13395-018-0172-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090946PMC
August 2018

FSHD type 2 and Bosma arhinia microphthalmia syndrome: Two faces of the same mutation.

Authors:
Karlien Mul Richard J L F Lemmers Marjolein Kriek Patrick J van der Vliet Marlinde L van den Boogaard Umesh A Badrising John M Graham Angela E Lin Harrison Brand Steven A Moore Katherine Johnson Teresinha Evangelista Ana Töpf Volker Straub Solange Kapetanovic García Sabrina Sacconi Rabi Tawil Stephen J Tapscott Nicol C Voermans Baziel G M van Engelen Corinne G C Horlings Natalie D Shaw Silvère M van der Maarel

Neurology 2018 08 6;91(6):e562-e570. Epub 2018 Jul 6.

From the Department of Neurology (K.M., N.C.V., B.G.M.v.E., C.G.C.H.), Radboud University Medical Center, Nijmegen; Departments of Human Genetics (R.J.L.F.L., P.J.v.d.V., M.L.v.d.B., S.M.v.d.M.), Clinical Genetics (M.K.), and Neurology (U.A.B.), Leiden University Medical Center, Leiden, the Netherlands; Department of Pediatrics (J.M.G.), Cedars Sinai Medical Center, Los Angeles, CA; Department of Medical Genetics (A.E.L.), MassGeneral Hospital for Children, Boston, MA; Center for Genomic Medicine and Department of Neurology (H.B.), Massachusetts General Hospital, Boston; Department of Pathology (S.A.M.), University of Iowa Hospitals and Clinics, Iowa City; The John Walton Muscular Dystrophy Research Centre (K.J., T.E., A.T., V.S.), Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK; Neuromuscular Consult Unit (S.K.G.), Bilbo-Basurtu Erakunde Sanitario Integratua, Organización Sanitaria Integrada Bilbao-Basurto, Spain; Centre de Référence des Maladies Neuromusculaires (S.S.), Nice, France; Department of Neurology (R.T.), University of Rochester Medical Center, NY; Division of Human Biology (S.J.T.), Fred Hutchinson Cancer Research Center, Seattle, WA; and National Institute of Environmental Health Sciences (N.D.S.), Research Triangle Park, NC.

Objective: To determine whether congenital arhinia/Bosma arhinia microphthalmia syndrome (BAMS) and facioscapulohumeral muscular dystrophy type 2 (FSHD2), 2 seemingly unrelated disorders both caused by heterozygous pathogenic missense variants in the gene, might represent different ends of a broad single phenotypic spectrum associated with SMCHD1 dysfunction.

Methods: We examined and/or interviewed 14 patients with FSHD2 and 4 unaffected family members with N-terminal pathogenic missense variants to identify BAMS subphenotypes.

Results: None of the patients with FSHD2 or family members demonstrated any congenital defects or dysmorphic features commonly found in patients with BAMS. One patient became anosmic after nasal surgery and one patient was hyposmic; one man was infertile (unknown cause) but reported normal pubertal development.

Conclusion: These data suggest that arhinia/BAMS and FSHD2 do not represent one phenotypic spectrum and that pathogenic variants by themselves are insufficient to cause either of the 2 disorders. More likely, both arhinia/BAMS and FSHD2 are caused by complex oligogenic or multifactorial mechanisms that only partially overlap at the level of
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http://dx.doi.org/10.1212/WNL.0000000000005958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105048PMC
August 2018

Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures.

Authors:
Jong-Won Lim Chao-Jen Wong Zizhen Yao Rabi Tawil Silvère M van der Maarel Daniel G Miller Stephen J Tapscott Galina N Filippova

Hum Mol Genet 2018 08;27(15):2644-2657

Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Facioscapulohumeral muscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4 macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defects mostly due to SMCHD1 mutation. Previous reports showed DUX4-induced gene expression changes as well as changes in microRNA expression in FSHD muscle cells. However, a genome wide analysis of small noncoding RNAs that might be regulated by DUX4 or by mutations in SMCHD1 has not been reported yet. Here, we identified several types of small noncoding RNAs including known microRNAs that are differentially expressed in FSHD2 muscle cells compared to control. Although fewer small RNAs were differentially expressed during muscle differentiation in FSHD2 cells compared to controls, most of the known myogenic microRNAs, such as miR1, miR133a and miR206 were induced in both FSHD2 and control muscle cells during differentiation. Our small RNA sequencing data analysis also revealed both DUX4- and SMCHD1-specific changes in FSHD2 muscle cells. Six FSHD2 microRNAs were affected by DUX4 overexpression in control myoblasts, whereas increased expression of tRNAs and 5S rRNAs in FSHD2 muscle cells was largely recapitulated in SMCHD1-depleted control myoblasts. Altogether, our studies suggest that the small noncoding RNA transcriptome changes in FSHD2 might be different from those in FSHD1 and that these differences may provide new diagnostic and therapeutic tools specific to FSHD2.
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http://dx.doi.org/10.1093/hmg/ddy173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048983PMC
August 2018

Facioscapulohumeral dystrophy: activating an early embryonic transcriptional program in human skeletal muscle.

Authors:
Amy E Campbell Andrea E Belleville Rebecca Resnick Sean C Shadle Stephen J Tapscott

Hum Mol Genet 2018 08;27(R2):R153-R162

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

Facioscapulohumeral dystrophy (FSHD) is the third most prevalent muscular dystrophy. A progressive disease, it presents clinically as weakness and wasting of the face, shoulder and upper arm muscles, with later involvement of the trunk and lower extremities. FSHD develops through complex genetic and epigenetic events that converge on a common mechanism of toxicity with mis-expression of the transcription factor double homeobox 4 (DUX4). There is currently no treatment available for FSHD. However, the consensus that ectopic DUX4 expression in skeletal muscle is the root cause of FSHD pathophysiology has allowed research efforts to turn toward cultivating a deeper understanding of DUX4 biology and the pathways that underlie FSHD muscle pathology, and to translational studies aimed at developing targeted therapeutics using ever more sophisticated cell and animal-based models of FSHD. This review summarizes recent advances in our understanding of FSHD, including the regulation and activity of DUX4 in its normal developmental roles as well as its pathological contexts. We highlight how these advances raise new questions and challenges for the field as it moves into the next decade of FSHD research.
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http://dx.doi.org/10.1093/hmg/ddy162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061842PMC
August 2018

Monosomy 18p is a risk factor for facioscapulohumeral dystrophy.

Authors:
Judit Balog Remko Goossens Richard J L F Lemmers Kirsten R Straasheijm Patrick J van der Vliet Anita van den Heuvel Chiara Cambieri Nicolas Capet Léonard Feasson Veronique Manel Julian Contet Marjolein Kriek Colleen M Donlin-Smith Claudia A L Ruivenkamp Patricia Heard Stephen J Tapscott Jannine D Cody Rabi Tawil Sabrina Sacconi Silvère M van der Maarel

J Med Genet 2018 07 21;55(7):469-478. Epub 2018 Mar 21.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Background: 18p deletion syndrome is a rare disorder caused by partial or full monosomy of the short arm of chromosome 18. Clinical symptoms caused by 18p hemizygosity include cognitive impairment, mild facial dysmorphism, strabismus and ptosis. Among other genes, structural maintenance of chromosomes flexible hinge domain containing 1 () is hemizygous in most patients with 18p deletions. Digenic inheritance of a mutation and a moderately sized D4Z4 repeat on a facioscapulohumeral muscular dystrophy (FSHD) permissive genetic background of chromosome 4 can cause FSHD type 2 (FSHD2).

Objectives: Since 12% of Caucasian individuals harbour moderately sized D4Z4 repeats on an FSHD permissive background, we tested if people with 18p deletions are at risk of developing FSHD.

Methods: To test our hypothesis we studied different cellular systems originating from individuals with 18p deletions not presenting FSHD2 phenotype for transcriptional and epigenetic characteristics of FSHD at D4Z4. Furthermore, individuals with an idiopathic muscle phenotype and an 18p deletion were subjected to neurological examination.

Results: Primary fibroblasts hemizygous for have a D4Z4 chromatin structure comparable with FSHD2 concomitant with DUX4 expression after transdifferentiation into myocytes. Neurological examination of 18p deletion individuals from two independent families with a moderately sized D4Z4 repeat identified muscle features compatible with FSHD.

Conclusions: 18p deletions leading to haploinsufficiency of , together with a moderately sized FSHD permissive D4Z4 allele, can associate with symptoms and molecular features of FSHD. We propose that patients with 18p deletion should be characterised for their D4Z4 repeat size and haplotype and monitored for clinical features of FSHD.
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http://dx.doi.org/10.1136/jmedgenet-2017-105153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019561PMC
July 2018

NuRD and CAF-1-mediated silencing of the D4Z4 array is modulated by DUX4-induced MBD3L proteins.

Authors:
Amy E Campbell Sean C Shadle Sujatha Jagannathan Jong-Won Lim Rebecca Resnick Rabi Tawil Silvère M van der Maarel Stephen J Tapscott

Elife 2018 03 13;7. Epub 2018 Mar 13.

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

The DUX4 transcription factor is encoded by a retrogene embedded in each unit of the D4Z4 macrosatellite repeat. DUX4 is normally expressed in the cleavage-stage embryo, whereas chromatin repression prevents DUX4 expression in most somatic tissues. Failure of this repression causes facioscapulohumeral muscular dystrophy (FSHD) due to mis-expression of DUX4 in skeletal muscle. In this study, we used CRISPR/Cas9 engineered chromatin immunoprecipitation (enChIP) locus-specific proteomics to characterize D4Z4-associated proteins. These and other approaches identified the Nucleosome Remodeling Deacetylase (NuRD) and Chromatin Assembly Factor 1 (CAF-1) complexes as necessary for DUX4 repression in human skeletal muscle cells and induced pluripotent stem (iPS) cells. Furthermore, DUX4-induced expression of MBD3L proteins partly relieved this repression in FSHD muscle cells. Together, these findings identify NuRD and CAF-1 as mediators of DUX4 chromatin repression and suggest a mechanism for the amplification of DUX4 expression in FSHD muscle cells.
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http://dx.doi.org/10.7554/eLife.31023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849414PMC
March 2018

Smchd1 haploinsufficiency exacerbates the phenotype of a transgenic FSHD1 mouse model.

Authors:
Jessica C de Greef Yvonne D Krom Bianca den Hamer Lauren Snider Yosuke Hiramuki Rob F P van den Akker Kelsey Breslin Miha Pakusch Daniela C F Salvatori Bram Slütter Rabi Tawil Marnie E Blewitt Stephen J Tapscott Silvère M van der Maarel

Hum Mol Genet 2018 02;27(4):716-731

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

In humans, a copy of the DUX4 retrogene is located in each unit of the D4Z4 macrosatellite repeat that normally comprises 8-100 units. The D4Z4 repeat has heterochromatic features and does not express DUX4 in somatic cells. Individuals with facioscapulohumeral muscular dystrophy (FSHD) have a partial failure of somatic DUX4 repression resulting in the presence of DUX4 protein in sporadic muscle nuclei. Somatic DUX4 derepression is caused by contraction of the D4Z4 repeat to 1-10 units (FSHD1) or by heterozygous mutations in genes responsible for maintaining the D4Z4 chromatin structure in a repressive state (FSHD2). One of the FSHD2 genes is the structural maintenance of chromosomes hinge domain 1 (SMCHD1) gene. SMCHD1 mutations have also been identified in FSHD1; patients carrying a contracted D4Z4 repeat and a SMCHD1 mutation are more severely affected than relatives with only a contracted repeat or a SMCHD1 mutation. To evaluate the modifier role of SMCHD1, we crossbred mice carrying a contracted D4Z4 repeat (D4Z4-2.5 mice) with mice that are haploinsufficient for Smchd1 (Smchd1MommeD1 mice). D4Z4-2.5/Smchd1MommeD1 mice presented with a significantly reduced body weight and developed skin lesions. The same skin lesions, albeit in a milder form, were also observed in D4Z4-2.5 mice, suggesting that reduced Smchd1 levels aggravate disease in the D4Z4-2.5 mouse model. Our study emphasizes the evolutionary conservation of the SMCHD1-dependent epigenetic regulation of the D4Z4 repeat array and further suggests that the D4Z4-2.5/Smchd1MommeD1 mouse model may be used to unravel the function of DUX4 in non-muscle tissues like the skin.
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http://dx.doi.org/10.1093/hmg/ddx437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886298PMC
February 2018

Impediment of Replication Forks by Long Non-coding RNA Provokes Chromosomal Rearrangements by Error-Prone Restart.

Authors:
Takaaki Watanabe Michael Marotta Ryusuke Suzuki Scott J Diede Stephen J Tapscott Atsushi Niida Xiongfong Chen Lila Mouakkad Anna Kondratova Armando E Giuliano Sandra Orsulic Hisashi Tanaka

Cell Rep 2017 Nov;21(8):2223-2235

Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA. Electronic address:

Naturally stalled replication forks are considered to cause structurally abnormal chromosomes in tumor cells. However, underlying mechanisms remain speculative, as capturing naturally stalled forks has been a challenge. Here, we captured naturally stalled forks in tumor cells and delineated molecular processes underlying the structural evolution of circular mini-chromosomes (double-minute chromosomes; DMs). Replication forks stalled on the DM by the co-directional collision with the transcription machinery for long non-coding RNA. RPA, BRCA2, and DNA polymerase eta (Polη) were recruited to the stalled forks. The recruitment of Polη was critical for replication to continue, as Polη knockdown resulted in DM loss. Rescued stalled forks were error-prone and switched replication templates repeatedly to create complex fusions of multiple short genomic segments. In mice, such complex fusions circularized the genomic region surrounding MYC to create a DM during tumorigenesis. Our results define a molecular path that guides stalled replication forks to complex chromosomal rearrangements.
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http://dx.doi.org/10.1016/j.celrep.2017.10.103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710012PMC
November 2017

Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2.

Authors:
Richard Jlf Lemmers Patrick J van der Vliet Judit Balog Jelle J Goeman Wibowo Arindrarto Yvonne D Krom Kirsten R Straasheijm Rashmie D Debipersad Gizem Özel Janet Sowden Lauren Snider Karlien Mul Sabrina Sacconi Baziel van Engelen Stephen J Tapscott Rabi Tawil Silvère M van der Maarel

Eur J Hum Genet 2018 01 21;26(1):94-106. Epub 2017 Nov 21.

Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.

Facioscapulohumeral muscular dystrophy is caused by incomplete repression of the transcription factor DUX4 in skeletal muscle as a consequence of D4Z4 macrosatellite repeat contraction in chromosome 4q35 (FSHD1) or variants in genes encoding D4Z4 chromatin repressors (FSHD2). A clinical hallmark of FSHD is variability in onset and progression suggesting the presence of disease modifiers. A well-known cis modifier is the polymorphic DUX4 polyadenylation signal (PAS) that defines FSHD permissive alleles: D4Z4 chromatin relaxation on non-permissive alleles which lack the DUX4-PAS cannot cause disease in the absence of stable DUX4 mRNA. We have explored the nature and relevance of a common variant of the major FSHD haplotype 4A161, which is defined by 1.6 kb size difference of the most distal D4Z4 repeat unit. While the short variant (4A161S) has been extensively studied, we demonstrate that the long variant (4A161L) is relatively common in the European population, is capable of expressing DUX4, but that DUX4 mRNA processing differs from 4A161S. While we do not find evidence for a difference in disease severity between FSHD carriers of an 4A161S or 4A161L allele, our study does uncover biallelic DUX4 expression in FSHD2 patients. Compared to control individuals, we observed an increased frequency of FSHD2 patients homozygous for disease permissive alleles, and who are thus capable of biallelic DUX4 expression, while SMCHD1 variant carriers with only one permissive allele were significantly more often asymptomatic. This suggests that biallelic DUX4 expression lowers the threshold for disease presentation and is a modifier for disease severity in FSHD2.
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http://dx.doi.org/10.1038/s41431-017-0015-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838976PMC
January 2018

BET bromodomain inhibitors and agonists of the beta-2 adrenergic receptor identified in screens for compounds that inhibit DUX4 expression in FSHD muscle cells.

Authors:
Amy E Campbell Jonathan Oliva Matthew P Yates Jun Wen Zhong Sean C Shadle Lauren Snider Nikita Singh Shannon Tai Yosuke Hiramuki Rabi Tawil Silvère M van der Maarel Stephen J Tapscott Francis M Sverdrup

Skelet Muscle 2017 09 4;7(1):16. Epub 2017 Sep 4.

Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University, Saint Louis, MO, 63104, USA.

Background: Facioscapulohumeral dystrophy (FSHD) is a progressive muscle disease caused by mutations that lead to epigenetic derepression and inappropriate transcription of the double homeobox 4 (DUX4) gene in skeletal muscle. Drugs that enhance the repression of DUX4 and prevent its expression in skeletal muscle cells therefore represent candidate therapies for FSHD.

Methods: We screened an aggregated chemical library enriched for compounds with epigenetic activities and the Pharmakon 1600 library composed of compounds that have reached clinical testing to identify molecules that decrease DUX4 expression as monitored by the levels of DUX4 target genes in FSHD patient-derived skeletal muscle cell cultures.

Results: Our screens identified several classes of molecules that include inhibitors of the bromodomain and extra-terminal (BET) family of proteins and agonists of the beta-2 adrenergic receptor. Further studies showed that compounds from these two classes suppress the expression of DUX4 messenger RNA (mRNA) by blocking the activity of bromodomain-containing protein 4 (BRD4) or by increasing cyclic adenosine monophosphate (cAMP) levels, respectively.

Conclusions: These data uncover pathways involved in the regulation of DUX4 expression in somatic cells, provide potential candidate classes of compounds for FSHD therapeutic development, and create an important opportunity for mechanistic studies that may uncover additional therapeutic targets.
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http://dx.doi.org/10.1186/s13395-017-0134-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584331PMC
September 2017

SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes.

Authors:
Amanda G Mason Roderick C Slieker Judit Balog Richard J L F Lemmers Chao-Jen Wong Zizhen Yao Jong-Won Lim Galina N Filippova Enrico Ne Rabi Tawil Bas T Heijmans Stephen J Tapscott Silvère M van der Maarel

Skelet Muscle 2017 06 6;7(1):12. Epub 2017 Jun 6.

Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Background: Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance.

Methods: To investigate the global effects of harboring heterozygous SMCHD1 mutations on DNA methylation in humans, we combined 450k methylation analysis on mononuclear monocytes from female heterozygous SMCHD1 mutation carriers and unaffected controls with reduced representation bisulfite sequencing (RRBS) on FSHD2 and control myoblast cell lines. Candidate loci were then evaluated for SMCHD1 binding using ChIP-qPCR and expression was evaluated using RT-qPCR.

Results: We identified a limited number of clustered autosomal loci with CpG hypomethylation in SMCHD1 mutation carriers: the protocadherin (PCDH) cluster on chromosome 5, the transfer RNA (tRNA) and 5S rRNA clusters on chromosome 1, the HOXB and HOXD clusters on chromosomes 17 and 2, respectively, and the D4Z4 repeats on chromosomes 4 and 10. Furthermore, minor increases in RNA expression were seen in FSHD2 myoblasts for some of the PCDHβ cluster isoforms, tRNA isoforms, and a HOXB isoform in comparison to controls, in addition to the previously reported effects on DUX4 expression. SMCHD1 was bound at DNAseI hypersensitivity sites known to regulate the PCDHβ cluster and at the chromosome 1 tRNA cluster, with decreased binding in SMCHD1 mutation carriers at the PCDHβ cluster sites.

Conclusions: Our study is the first to investigate the global methylation effects in humans resulting from heterozygous mutations in SMCHD1. Our results suggest that SMCHD1 acts as a repressor on a limited set of autosomal gene clusters, as an observed reduction in methylation associates with a loss of SMCHD1 binding and increased expression for some of the loci.
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http://dx.doi.org/10.1186/s13395-017-0129-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461771PMC
June 2017

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons.

Authors:
Peter G Hendrickson Jessie A Doráis Edward J Grow Jennifer L Whiddon Jong-Won Lim Candice L Wike Bradley D Weaver Christian Pflueger Benjamin R Emery Aaron L Wilcox David A Nix C Matthew Peterson Stephen J Tapscott Douglas T Carrell Bradley R Cairns

Nat Genet 2017 Jun 1;49(6):925-934. Epub 2017 May 1.

Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA.

To better understand transcriptional regulation during human oogenesis and preimplantation development, we defined stage-specific transcription, which highlighted the cleavage stage as being highly distinctive. Here, we present multiple lines of evidence that a eutherian-specific multicopy retrogene, DUX4, encodes a transcription factor that activates hundreds of endogenous genes (for example, ZSCAN4, KDM4E and PRAMEF-family genes) and retroviral elements (MERVL/HERVL family) that define the cleavage-specific transcriptional programs in humans and mice. Remarkably, mouse Dux expression is both necessary and sufficient to convert mouse embryonic stem cells (mESCs) into 2-cell-embryo-like ('2C-like') cells, measured here by the reactivation of '2C' genes and repeat elements, the loss of POU5F1 (also known as OCT4) protein and chromocenters, and the conversion of the chromatin landscape (as assessed by transposase-accessible chromatin using sequencing (ATAC-seq)) to a state strongly resembling that of mouse 2C embryos. Thus, we propose mouse DUX and human DUX4 as major drivers of the cleavage or 2C state.
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http://dx.doi.org/10.1038/ng.3844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703070PMC
June 2017

Conservation and innovation in the DUX4-family gene network.

Authors:
Jennifer L Whiddon Ashlee T Langford Chao-Jen Wong Jun Wen Zhong Stephen J Tapscott

Nat Genet 2017 Jun 1;49(6):935-940. Epub 2017 May 1.

Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

Facioscapulohumeral dystrophy (FSHD; MIM158900, MIM158901) is caused by misexpression of the DUX4 transcription factor in skeletal muscle. Animal models of FSHD are hindered by incomplete knowledge regarding the conservation of the DUX4 transcriptional program in other species. Despite the divergence of their binding motifs, both mouse DUX and human DUX4 in mouse and human muscle cells, respectively, activate genes associated with cleavage-stage embryos, including MERVL and ERVL-MaLR retrotransposons. We found that human DUX4 expressed in mouse cells maintained modest activation of cleavage-stage genes driven by conventional promoters but did not activate MERVL-promoted genes. Thus, the ancestral DUX4-regulated genes are characteristic of cleavage-stage embryos and are driven by conventional promoters, whereas divergence of the DUX4 and 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 establish a basis for animal models recreating the FSHD transcriptome.
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http://dx.doi.org/10.1038/ng.3846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5446306PMC
June 2017

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

Authors:
Sean C Shadle Jun Wen Zhong Amy E Campbell Melissa L Conerly Sujatha Jagannathan Chao-Jen Wong Timothy D Morello Silvère M van der Maarel Stephen J Tapscott

PLoS Genet 2017 03 8;13(3):e1006658. Epub 2017 Mar 8.

Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

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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http://dx.doi.org/10.1371/journal.pgen.1006658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5362247PMC
March 2017

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

Authors:
Sujatha Jagannathan Sean C Shadle Rebecca Resnick Lauren Snider Rabi N Tawil Silvère M van der Maarel Robert K Bradley Stephen J Tapscott

Hum Mol Genet 2016 10;25(20):4419-4431

Division of Human Biology.

Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of the double-homeodomain transcription factor DUX4 in skeletal muscle cells. Many different cell culture models have been developed to study the pathophysiology of FSHD, frequently based on endogenous expression of DUX4 in FSHD cells or by mis-expression of DUX4 in control human muscle cells. Although results generated using each model are generally consistent, differences have also been reported, making it unclear which model(s) faithfully recapitulate DUX4 and FSHD biology. In this study, we systematically compared RNA-seq data generated from three different models of FSHD—lentiviral-based DUX4 expression in myoblasts, doxycycline-inducible DUX4 in myoblasts, and differentiated human FSHD myocytes expressing endogenous DUX4—and show that the DUX4-associated gene expression signatures of each dataset are highly correlated (Pearson’s correlation coefficient, r ∼ 0.75-0.85). The few robust differences were attributable to different states of cell differentiation and other differences in experimental design. Our study describes a model system for inducible DUX4 expression that enables reproducible and synchronized experiments and validates the fidelity and FSHD relevance of multiple distinct models of DUX4 expression.
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http://dx.doi.org/10.1093/hmg/ddw271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078597PMC
October 2016

Mutations in DNMT3B Modify Epigenetic Repression of the D4Z4 Repeat and the Penetrance of Facioscapulohumeral Dystrophy.

Authors:
Marlinde L van den Boogaard Richard J L F Lemmers Judit Balog Mariëlle Wohlgemuth Mari Auranen Satomi Mitsuhashi Patrick J van der Vliet Kirsten R Straasheijm Rob F P van den Akker Marjolein Kriek Marlies E Y Laurense-Bik Vered Raz Monique M van Ostaijen-Ten Dam Kerstin B M Hansson Elly L van der Kooi Sari Kiuru-Enari Bjarne Udd Maarten J D van Tol Ichizo Nishino Rabi Tawil Stephen J Tapscott Baziel G M van Engelen Silvère M van der Maarel

Am J Hum Genet 2016 05;98(5):1020-1029

Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands. Electronic address:

Facioscapulohumeral dystrophy (FSHD) is associated with somatic chromatin relaxation of the D4Z4 repeat array and derepression of the D4Z4-encoded DUX4 retrogene coding for a germline transcription factor. Somatic DUX4 derepression is caused either by a 1-10 unit repeat-array contraction (FSHD1) or by mutations in SMCHD1, which encodes a chromatin repressor that binds to D4Z4 (FSHD2). Here, we show that heterozygous mutations in DNA methyltransferase 3B (DNMT3B) are a likely cause of D4Z4 derepression associated with low levels of DUX4 expression from the D4Z4 repeat and increased penetrance of FSHD. Recessive mutations in DNMT3B were previously shown to cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome. This study suggests that transcription of DUX4 in somatic cells is modified by variations in its epigenetic state and provides a basis for understanding the reduced penetrance of FSHD within families.
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http://dx.doi.org/10.1016/j.ajhg.2016.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863565PMC
May 2016

Corrigendum. Increased DUX4 expression during muscle differentiation correlates with decreased SMCHD1 protein levels at D4Z4.

Authors:
Judit Balog Peter E Thijssen Sean Shadle Kirsten R Straasheijm Patrick J van der Vliet Yvonne D Krom Marlinde L van den Boogaard Annika de Jong Richard J L F Lemmers Rabi Tawil Stephen J Tapscott Silvère M van der Maarel

Epigenetics 2016 ;11(2):175

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http://dx.doi.org/10.1080/15592294.2016.1161273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846112PMC
August 2016