A Recurrent Rare SOX9 Variant (M469V) is Associated with Congenital Vertebral Malformations

Author(s): Nan Wu, Lianlei Wang, Jianhua Hu*, Sen Zhao, Bowen Liu, Yaqi Li, Huakang Du, Yuanqiang Zhang, Xiaoxin Li, Zihui Yan, Shengru Wang, Yipeng Wang, Jianguo Zhang, Zhihong Wu, DISCO (Deciphering Disorders Involving Scoliosis & Comorbidities) study group, Guixing Qiu.

Journal Name: Current Gene Therapy

Volume 19 , Issue 4 , 2019

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Graphical Abstract:


Abstract:

Objective: The genetic variations contributed to a substantial proportion of congenital vertebral malformations (CVM). SOX9 gene, a member of the SOX gene family, has been implicated in CVM. To study the SOX9 mutation in CVM patients is of great significance to explain the pathogenesis of scoliosis (the clinical manifestation of CVM) and to explore the pathogenesis of SOX9-related skeletal deformities.

Methods: A total of 50 singleton patients with CVM were included in this study. Exome Sequencing (ES) was performed on all the patients. The recurrent candidate variant of SOX9 gene was validated by Sanger sequencing. Luciferase assay was performed to investigate the functional changes of this variant.

Results: A recurrent rare heterozygous missense variant in SOX9 gene (NM_000346.3: c.1405A>G, p.M469V) which had not been reported previously was identified in three CVM patients who had the clinical findings of congenital scoliosis without deformities in other systems. This variant was absent from our in-house database and it was predicted to be deleterious (CADD = 24.5). The luciferase assay demonstrated that transactivation capacity of the mutated SOX9 protein was significantly lower than that of the wild-type for the two luciferase reporters (p = 0.0202, p = 0.0082, respectively).

Conclusion: This SOX9 mutation (p.M469V) may contribute to CVM without other systematic deformity, which provides important implications and better understanding of phenotypic variability in SOX9-related skeletal deformities.

Keywords: SOX9 gene, campomelic dysplasia, acampomelic campomelic dysplasia, congenital vertebral malformations, congenital scoliosis, exome sequencing.

[1]
Wagner T, Wirth J, Meyer J, et al. Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9. Cell 1994; 79(6): 1111-20.
[http://dx.doi.org/10.1016/0092-8674(94)90041-8] [PMID: 8001137]
[2]
Houston CS, Opitz JM, Spranger JW, et al. The campomelic syndrome: Review, report of 17 cases, and follow-up on the currently 17-year-old boy first reported by Maroteaux et al. in 1971. Am J Med Genet 1983; 15(1): 3-28.
[http://dx.doi.org/10.1002/ajmg.1320150103] [PMID: 6344634]
[3]
Macpherson RI, Skinner SA, Donnenfeld AE. Acampomelic campomelic dysplasia. Pediatr Radiol 1989; 20(1-2): 90-3.
[http://dx.doi.org/10.1007/BF02010643] [PMID: 2602025]
[4]
von Bohlen AE, Böhm J, Pop R, et al. A mutation creating an upstream initiation codon in the SOX9 5′ UTR causes acampomelic campomelic dysplasia. Mol Genet Genomic Med 2017; 5(3): 261-8.
[http://dx.doi.org/10.1002/mgg3.282] [PMID: 28546996]
[5]
Wada Y, Nishimura G, Nagai T, et al. Mutation analysis of SOX9 and single copy number variant analysis of the upstream region in eight patients with campomelic dysplasia and acampomelic campomelic dysplasia. Am J Med Genet A 2009; 149A(12): 2882-5.
[http://dx.doi.org/10.1002/ajmg.a.33107] [PMID: 19921652]
[6]
Li Y, Zheng M, Lau YF. The sex-determining factors SRY and SOX9 regulate similar target genes and promote testis cord formation during testicular differentiation. Cell Rep 2014; 8(3): 723-33.
[http://dx.doi.org/10.1016/j.celrep.2014.06.055] [PMID: 25088423]
[7]
Tommerup N, Schempp W, Meinecke P, et al. Assignment of an autosomal sex reversal locus (SRA1) and campomelic dysplasia (CMPD1) to 17q24.3-q25.1. Nat Genet 1993; 4(2): 170-4.
[http://dx.doi.org/10.1038/ng0693-170] [PMID: 8348155]
[8]
Smyk M, Akdemir KC, Stankiewicz P. SOX9 chromatin folding domains correlate with its real and putative distant cis-regulatory elements. Nucleus 2017; 8(2): 182-7.
[http://dx.doi.org/10.1080/19491034.2017.1279776] [PMID: 28085555]
[9]
Foster JW, Dominguez-Steglich MA, Guioli S, et al. Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene. Nature 1994; 372(6506): 525-30.
[http://dx.doi.org/10.1038/372525a0] [PMID: 7990924]
[10]
Higeta D, Yamaguchi R, Takagi T, et al. Familial campomelic dysplasia due to maternal germinal mosaicism. Congenit Anom (Kyoto) 2018; 58(6): 194-7.
[http://dx.doi.org/10.1111/cga.12279] [PMID: 29542186]
[11]
Lefebvre V. Roles and regulation of SOX transcription factors in skeletogenesis. Curr Top Dev Biol 2019; 133: 171-93.
[http://dx.doi.org/10.1016/bs.ctdb.2019.01.007] [PMID: 30902252]
[12]
Alfares A, Aloraini T, Subaie LA, et al. Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing. Genet Med 2018; 20(11): 1328-33.
[http://dx.doi.org/10.1038/gim.2018.41] [PMID: 29565419]
[13]
Cheng L, Sun J, Xu W, Dong L, Hu Y, Zhou M. OAHG: An integrated resource for annotating human genes with multi-level ontologies. Sci Rep 2016; 6: 34820.
[http://dx.doi.org/10.1038/srep34820] [PMID: 27703231]
[14]
Cheng L, Hu Y, Sun J, Zhou M, Jiang Q. DincRNA: A comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function. Bioinformatics 2018; 34(11): 1953-6.
[http://dx.doi.org/10.1093/bioinformatics/bty002] [PMID: 29365045]
[15]
Retterer K, Juusola J, Cho MT, et al. Clinical application of whole-exome sequencing across clinical indications. Genet Med 2016; 18(7): 696-704.
[http://dx.doi.org/10.1038/gim.2015.148] [PMID: 26633542]
[16]
Wang K, Zhao S, Liu B, et al. Perturbations of BMP/TGF-β and VEGF/VEGFR signalling pathways in non-syndromic sporadic brain arteriovenous malformations (BAVM). J Med Genet 2018; 55(10): 675-84.
[http://dx.doi.org/10.1136/jmedgenet-2017-105224] [PMID: 30120215]
[17]
Wang K, Zhao S, Zhang Q, et al. Whole-exome sequencing reveals known and novel variants in a cohort of intracranial vertebral-basilar artery dissection (IVAD). J Hum Genet 2018; 63(11): 1119-28.
[http://dx.doi.org/10.1038/s10038-018-0496-x] [PMID: 30115950]
[18]
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLOS Comput Biol 2010; 6(12)e1001025
[http://dx.doi.org/10.1371/journal.pcbi.1001025] [PMID: 21152010]
[19]
Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 2014; 46(3): 310-5.
[http://dx.doi.org/10.1038/ng.2892] [PMID: 24487276]
[20]
Vaser R, Adusumalli S, Leng SN, Sikic M, Ng PC. SIFT missense predictions for genomes. Nat Protoc 2016; 11(1): 1-9.
[http://dx.doi.org/10.1038/nprot.2015.123] [PMID: 26633127]
[21]
Sherry ST, Ward MH, Kholodov M, et al. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res 2001; 29(1): 308-11.
[http://dx.doi.org/10.1093/nar/29.1.308] [PMID: 11125122]
[22]
Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet 2013; 7: Unit7.20.
[http://dx.doi.org/10.1002/0471142905.hg0720s76]
[23]
Landrum MJ, Lee JM, Riley GR, et al. ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 2014; 42: D980-5.
[http://dx.doi.org/10.1093/nar/gkt1113] [PMID: 24234437]
[24]
Sock E, Pagon RA, Keymolen K, Lissens W, Wegner M, Scherer G. Loss of DNA-dependent dimerization of the transcription factor SOX9 as a cause for campomelic dysplasia. Hum Mol Genet 2003; 12(12): 1439-47.
[http://dx.doi.org/10.1093/hmg/ddg158] [PMID: 12783851]
[25]
Thorne N, Inglese J, Auld DS. Illuminating insights into firefly luciferase and other bioluminescent reporters used in chemical biology. Chem Biol 2010; 17(6): 646-57.
[http://dx.doi.org/10.1016/j.chembiol.2010.05.012] [PMID: 20609414]
[26]
Geraldo MT, Valente GT, Nakajima RT, Martins C. Dimerization and transactivation domains as candidates for functional modulation and diversity of Sox9. PLoS One 2016; 11(5)e0156199
[http://dx.doi.org/10.1371/journal.pone.0156199] [PMID: 27196604]
[27]
Kozhemyakina E, Lassar AB, Zelzer E. A pathway to bone: Signaling molecules and transcription factors involved in chondrocyte development and maturation. Development 2015; 142(5): 817-31.
[http://dx.doi.org/10.1242/dev.105536] [PMID: 25715393]
[28]
Lefebvre V, Dvir-Ginzberg M. SOX9 and the many facets of its regulation in the chondrocyte lineage. Connect Tissue Res 2017; 58(1): 2-14.
[http://dx.doi.org/10.1080/03008207.2016.1183667] [PMID: 27128146]
[29]
Hattori T, Müller C, Gebhard S, et al. SOX9 is a major negative regulator of cartilage vascularization, bone marrow formation and endochondral ossification. Development 2010; 137(6): 901-11.
[http://dx.doi.org/10.1242/dev.045203] [PMID: 20179096]
[30]
Akiyama H. Control of chondrogenesis by the transcription factor Sox9. Mod Rheumatol 2008; 18(3): 213-9.
[http://dx.doi.org/10.3109/s10165-008-0048-x] [PMID: 18351289]
[31]
Lefebvre V, Huang W, Harley VR, Goodfellow PN, de Crombrugghe B. SOX9 is a potent activator of the chondrocyte-specific enhancer of the pro alpha1(II) collagen gene. Mol Cell Biol 1997; 17(4): 2336-46.
[http://dx.doi.org/10.1128/MCB.17.4.2336] [PMID: 9121483]
[32]
Huang W, Zhou X, Lefebvre V, de Crombrugghe B. Phosphorylation of SOX9 by cyclic AMP-dependent protein kinase A enhances SOX9's ability to transactivate a Col2a1 chondrocyte-specific enhancer. Mol Cell Biol 2000; 20(11): 4149-58.
[http://dx.doi.org/10.1128/MCB.20.11.4149-4158.2000] [PMID: 10805756]
[33]
Han Y, Lefebvre V. L-Sox5 and Sox6 drive expression of the aggrecan gene in cartilage by securing binding of Sox9 to a far-upstream enhancer. Mol Cell Biol 2008; 28(16): 4999-5013.
[http://dx.doi.org/10.1128/MCB.00695-08] [PMID: 18559420]
[34]
Topol L, Chen W, Song H, Day TF, Yang Y. SOX9 inhibits Wnt signaling by promoting beta-catenin phosphorylation in the nucleus. J Biol Chem 2009; 284(5): 3323-33.
[http://dx.doi.org/10.1074/jbc.M808048200] [PMID: 19047045]
[35]
Cheng A, Genever PG. SOX9 determines RUNX2 transactivity by directing intracellular degradation. J Bone Miner Res 2010; 25(12): 2680-9.
[http://dx.doi.org/10.1002/jbmr.174] [PMID: 20593410]
[36]
Wu N, Ming X, Xiao J, et al. TBX6 null variants and a common hypomorphic allele in congenital scoliosis. N Engl J Med 2015; 372(4): 341-50.
[http://dx.doi.org/10.1056/NEJMoa1406829] [PMID: 25564734]
[37]
Liu J, Wu N, Yang N, et al. TBX6-associated congenital scoliosis (TACS) as a clinically distinguishable subtype of congenital scoliosis: Further evidence supporting the compound inheritance and TBX6 gene dosage model. Genet Med 2019; 21(7): 1548-58.
[http://dx.doi.org/10.1038/s41436-018-0377-x] [PMID: 30636772]
[38]
Yang N, Wu N, Zhang L, et al. TBX6 compound inheritance leads to congenital vertebral malformations in humans and mice. Hum Mol Genet 2019; 28(4): 539-47.
[http://dx.doi.org/10.1093/hmg/ddy358] [PMID: 30307510]
[39]
Chen Y, Liu Z, Chen J, et al. The genetic landscape and clinical implications of vertebral anomalies in VACTERL association. J Med Genet 2016; 53(7): 431-7.
[http://dx.doi.org/10.1136/jmedgenet-2015-103554] [PMID: 27084730]


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VOLUME: 19
ISSUE: 4
Year: 2019
Page: [242 - 247]
Pages: 6
DOI: 10.2174/1566523219666190924120307
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