Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 40, 2012, Pages 16234-16239

  Rahimov, Fedik ^a,b   King, Oliver D ^b,c   Leung, Doris G ^d,e   Bibat, Genila M ^d   Emerson, Charles P ^b,c   Kunkel, Louis M ^a,b,f   Wagner, Kathryn R ^d,e  

^a HARVARD MEDICAL SCHOOL   (United States)

^b The Senator Paul D Wellstone Muscular Dystrophy Cooperative Research Center   (United States)

^c BOSTON BIOMEDICAL RESEARCH INSTITUTE   (United States)

^d KENNEDY KRIEGER INSTITUTE   (United States)

^e JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

Microarray; Skeletal muscle

Indexed keywords

3 OXOACID COENZYME A TRANSFERASE; 3 OXOACID COENZYME A TRANSFERASE 1; ALPHA2 SMOOTH MUSCLE ACTIN; BIOLOGICAL MARKER; CALCIUM BINDING PROTEIN 39 LIKE; EXOSTOSES LIKE 1 PROTEIN; G0 G1 SWITCH 2 PROTEIN; GLYCOSYLTRANSFERASE; GLYCOSYLTRANSFERASE 25 DOMAIN CONTAINING 2 PROTEIN; INTERLEUKIN 32; ISOPENTENYL DIPHOSPHATE DELTA ISOMERASE; ISOPENTENYL DIPHOSPHATE DELTA ISOMERASE 2; LIPOPOLYSACCHARIDE BINDING PROTEIN; MYOSIN HEAVY CHAIN 8; PROFILIN; PROFILIN II; SMOOTH MUSCLE ACTIN; SOLUTE CARRIER FAMILY 25 MEMBER 33; THROMBIN RECEPTOR; TRANS 2,3 ENOYL COENZYME A REDUCTASE LIKE; UNCLASSIFIED DRUG;

ARTICLE; BICEPS BRACHII MUSCLE; CLINICAL ARTICLE; CONTROLLED STUDY; DELTOID MUSCLE; DISEASE SEVERITY; FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; HUMAN TISSUE; MUSCLE TISSUE; PRIORITY JOURNAL; RELATIVE;

EID: 84867059682     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1209508109     Document Type: Article

References (48)

1. Tawil R, Van Der Maarel SM (2006) Facioscapulohumeral muscular dystrophy. Muscle Nerve 34:1-15.
2. Padberg GW, et al. (1995) On the significance of retinal vascular disease and hearing loss in facioscapulohumeral muscular dystrophy. Muscle Nerve 2:S73-S80.
3. Fitzsimons RB (2011) Retinal vascular disease and the pathogenesis of facioscapulohumeral muscular dystrophy. A signalling message from Wnt? Neuromuscul Disord 21:263-271.
4. Wijmenga C, et al. (1992) Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy. Nat Genet 2:26-30.
5. van Deutekom JC, et al. (1993) FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. Hum Mol Genet 2: 2037-2042.
6. Mostacciuolo ML, et al. (2009) Facioscapulohumeral muscular dystrophy: Epidemiological and molecular study in a north-east Italian population sample. Clin Genet 75:550-555.
7. Tawil R, et al.; The FSH-DY Group (1996) Evidence for anticipation and association of deletion size with severity in facioscapulohumeral muscular dystrophy. Ann Neurol 39:744-748.
8. Lunt PW, et al. (1995) Correlation between fragment size at D4F104S1 and age at onset or at wheelchair use, with a possible generational effect, accounts for much phenotypic variation in 4q35-facioscapulohumeral muscular dystrophy (FSHD). Hum Mol Genet 4:951-958.
9. Kowaljow V, et al. (2007) The DUX4 gene at the FSHD1A locus encodes a pro-apoptotic protein. Neuromuscul Disord 17:611-623. (Pubitemid 47030917)
10. Bosnakovski D, et al. (2008) An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies. EMBO J 27:2766-2779.
11. Lemmers RJ, et al. (2010) A unifying genetic model for facioscapulohumeral muscular dystrophy. Science 329:1650-1653.
12. Geng LN, et al. (2012) DUX4 activates germline genes, retroelements, and immune mediators: Implications for facioscapulohumeral dystrophy. Dev Cell 22:38-51.
13. Ilyin SE, Belkowski SM, Plata-Salamán CR (2004) Biomarker discovery and validation: Technologies and integrative approaches. Trends Biotechnol 22:411-416. (Pubitemid 38993225)
14. Homma S, et al. (2012) A unique library of myogenic cells from facioscapulohumeral muscular dystrophy subjects and unaffected relatives: Family, disease and cell function. Eur J Hum Genet 20:404-410.
15. Orrell RW, et al. (1999) Definitive molecular diagnosis of facioscapulohumeral dystrophy. Neurology 52:1822-1826. (Pubitemid 29260895)
16. Kang PB, et al. (2005) Variations in gene expression among different types of human skeletal muscle. Muscle Nerve 32:483-491. (Pubitemid 41395981)
17. Osborne RJ, Welle S, Venance SL, Thornton CA, Tawil R (2007) Expression profile of FSHD supports a link between retinal vasculopathy and muscular dystrophy. Neurology 68:569-577.
18. Chen YW, Zhao P, Borup R, Hoffman EP (2000) Expression profiling in the muscular dystrophies: Identification of novel aspects of molecular pathophysiology. J Cell Biol 151:1321-1336.
19. Pescatori M, et al. (2007) Gene expression profiling in the early phases of DMD: A constant molecular signature characterizes DMD muscle from early postnatal life throughout disease progression. FASEB J 21:1210-1226. (Pubitemid 46495710)
20. Greenberg SA, et al. (2002) Molecular profiles of inflammatory myopathies. Neurology 59:1170-1182. (Pubitemid 35192386)
21. Sáenz A, et al. (2008) Gene expression profiling in limb-girdle muscular dystrophy 2A. PLoS ONE 3:e3750.
22. Winokur ST, et al. (2003) Expression profiling of FSHD muscle supports a defect in specific stages of myogenic differentiation. Hum Mol Genet 12:2895-2907. (Pubitemid 37442018)
23. Arashiro P, et al. (2009) Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers. Proc Natl Acad Sci USA 106:6220-6225.
24. Dixit M, et al. (2007) DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proc Natl Acad Sci USA 104: 18157-18162. (Pubitemid 350210837)
25. Wallace LM, et al. (2011) DUX4, a candidate gene for facioscapulohumeral muscular dystrophy, causes p53-dependent myopathy in vivo. Ann Neurol 69:540-552.
26. Wu D, et al. (2010) ROAST: Rotation gene set tests for complex microarray experiments. Bioinformatics 26:2176-2182.
27. Kumar D, Shadrach JL, Wagers AJ, Lassar AB (2009) Id3 is a direct transcriptional target of Pax7 in quiescent satellite cells. Mol Biol Cell 20:3170-3177.
28. Geng LN, et al. (2011) DUX4 activates germline genes, retroelements, and immune mediators: Implications for facioscapulohumeral dystrophy. Dev Cell 22:38-51.
29. Snider L, et al. (2010) Facioscapulohumeral dystrophy: Incomplete suppression of a retrotransposed gene. PLoS Genet 6:e1001181.
30. Snider L, et al. (2009) RNA transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: New candidates for the pathophysiology of facioscapulohumeral dystrophy. Hum Mol Genet 18:2414-2430.
31. Jones TI, et al. (2012) Facioscapulohumeral muscular dystrophy family studies of DUX4 expression: Evidence for disease modifiers and a quantitative model of pathogenesis. Hum Mol Genet, 10.1093/hmg/dds284.
32. Celegato B, et al. (2006) 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. Proteomics 6:5303-5321. (Pubitemid 44547168)
33. Morley M, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430:743-747.
34. Cheung VG, Spielman RS (2009) Genetics of human gene expression: Mapping DNA variants that influence gene expression. Nat Rev Genet 10:595-604.
35. Clizbe DB, Owens ML, Masuda KR, Shackelford JE, Krisans SK (2007) IDI2, a second isopentenyl diphosphate isomerase in mammals. J Biol Chem 282:6668-6676. (Pubitemid 47100820)
36. Ramos-Valdivia AC, van der Heijden R, Verpoorte R (1997) Isopentenyl diphosphate isomerase: A core enzyme in isoprenoid biosynthesis. A review of its biochemistry and function. Nat Prod Rep 14:591-603. (Pubitemid 28010213)
37. Kato T, et al. (2010) Segmental copy-number gain within the region of isopentenyl diphosphate isomerase genes in sporadic amyotrophic lateral sclerosis. Biochem Biophys Res Commun 402:438-442.
38. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210. (Pubitemid 34679544)
39. Vilà-Brau A, De Sousa-Coelho AL, Mayordomo C, Haro D, Marrero PF (2011) Human HMGCS2 regulates mitochondrial fatty acid oxidation and FGF21 expression in HepG2 cell line. J Biol Chem 286:20423-20430.
40. Cheli S, et al. (2011) Expression profiling of FSHD-1 and FSHD-2 cells during myogenic differentiation evidences common and distinctive gene dysregulation patterns. PLoS ONE 6:e20966.
41. Toydemir RM, et al. (2006) Trismus-pseudocamptodactyly syndrome is caused by recurrent mutation of MYH8. Am J Med Genet A 140:2387-2393. (Pubitemid 44684933)
42. Bandman E (1985) Continued expression of neonatal myosin heavy chain in adult dystrophic skeletal muscle. Science 227:780-782.
43. Engel AG, Biesecker G (1982) Complement activation in muscle fiber necrosis: Demonstration of the membrane attack complex of complement in necrotic fibers. Ann Neurol 12:289-296. (Pubitemid 12053038)
44. Spuler S, Engel AG (1998) Unexpected sarcolemmal complement membrane attack complex deposits on nonnecrotic muscle fibers in muscular dystrophies. Neurology 50: 41- 46.
45. Porter JD, et al. (2002) A chronic inflammatory response dominates the skeletal muscle molecular signature in dystrophin-deficient mdx mice. Hum Mol Genet 11: 263-272. (Pubitemid 34173355)
46. Irizarry RA, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.
47. Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
48. Reiner A, Yekutieli D, Benjamini Y (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19:368-375. (Pubitemid 36284936)