Review of Recurrently Mutated Genes in Craniosynostosis Supports Expansion of Diagnostic Gene Panels
Abstract
:1. Introduction
2. Materials and Methods
2.1. Literature Search
2.2. Panel-Based Sequencing of a Cohort of Genetically Unsolved Patients with Craniosynostosis
2.3. Analysis of Single Cell Transcriptomic Data
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Tønne, E.; Due-Tønnessen, B.J.; Wiig, U.; Stadheim, B.F.; Meling, T.R.; Helseth, E.; Heimdal, K.R. Epidemiology of craniosynostosis in Norway. J. Neurosurg. Pediatr. 2020, 26, 68–75. [Google Scholar] [CrossRef] [PubMed]
- Cornelissen, M.; Ottelander, B.; Rizopoulos, D.; van der Hulst, R.; Mink van der Molen, A.; van der Horst, C.; Delye, H.; van Veelen, M.L.; Bonsel, G.; Mathijssen, I. Increase of prevalence of craniosynostosis. J. Craniomaxillofac. Surg. 2016, 44, 1273–1279. [Google Scholar] [CrossRef] [PubMed]
- Justice, C.M.; Yagnik, G.; Kim, Y.; Peter, I.; Jabs, E.W.; Erazo, M.; Ye, X.; Ainehsazan, E.; Shi, L.; Cunningham, M.L.; et al. A genome-wide association study identifies susceptibility loci for nonsyndromic sagittal craniosynostosis near BMP2 and within BBS9. Nat. Genet. 2012, 44, 1360–1364. [Google Scholar] [CrossRef] [PubMed]
- Justice, C.M.; Cuellar, A.; Bala, K.; Sabourin, J.A.; Cunningham, M.L.; Crawford, K.; Phipps, J.M.; Zhou, Y.; Cilliers, D.; Byren, J.C.; et al. A genome-wide association study implicates the BMP7 locus as a risk factor for nonsyndromic metopic craniosynostosis. Hum. Genet. 2020, 139, 1077–1090. [Google Scholar] [CrossRef] [PubMed]
- Sanchez-Lara, P.A.; Carmichael, S.L.; Graham, J.M.; Jr Lammer, E.J.; Shaw, G.M.; Ma, C.; Rasmussen, S.A. National Birth Defects Prevention Study: Fetal constraint as a potential risk factor for craniosynostosis. Am. J. Med. Genet. A 2010, 152A, 394–400. [Google Scholar] [CrossRef] [PubMed]
- Wilkie, A.O.M.; Johnson, D.; Wall, S.A. Clinical genetics of craniosynostosis. Curr. Opin. Pediatr. 2017, 29, 622–628. [Google Scholar] [CrossRef]
- Timberlake, A.T.; Furey, C.G.; Choi, J.; Nelson-Williams, C.; Yale Center for Genome Analysis; Loring, E.; Galm, A.; Kahle, K.T.; Steinbacher, D.M.; Larysz, D.; et al. De novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis. Proc. Natl. Acad. Sci. USA 2017, 114, E7341–E7347. [Google Scholar] [CrossRef]
- Calpena, E.; Cuellar, A.; Bala, K.; Swagemakers, S.M.A.; Koelling, N.; McGowan, S.J.; Phipps, J.M.; Balasubramanian, M.; Cunningham, M.L.; Douzgou, S.; et al. SMAD6 variants in craniosynostosis: Genotype and phenotype evaluation. Genet. Med. 2020, 22, 1498–1506. [Google Scholar] [CrossRef]
- Twigg, S.R.F.; Wilkie, A.O.M. A Genetic-Pathophysiological Framework for Craniosynostosis. Am. J. Hum. Genet. 2015, 97, 359–377. [Google Scholar] [CrossRef]
- Goos, J.A.C.; Mathijssen, I.M.J. Genetic Causes of Craniosynostosis: An Update. Mol. Syndromol. 2019, 10, 6–23. [Google Scholar] [CrossRef]
- Hyder, Z.; Calpena, E.; Pei, Y.; Tooze, R.S.; Brittain, H.; Twigg, S.R.F.; Cilliers, D.; Morton, J.E.V.; McCann, E.; Weber, A.; et al. Evaluating the performance of a clinical genome sequencing program for diagnosis of rare genetic disease, seen through the lens of craniosynostosis. Genet. Med. 2021, 23, 2360–2368. [Google Scholar] [CrossRef]
- Smedley, D.; Smith, K.R.; Martin, A.; Thomas, E.A.; McDonagh, E.M.; Cipriani, V.; Ellingford, J.M.; Arno, G.; Tucci, A.; Vandrovcova, J.; et al. 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care-Preliminary Report. N. Eng. J. Med. 2021, 385, 1868–1880. [Google Scholar]
- Martin, A.R.; Williams, E.; Foulger, R.E.; Leigh, S.; Daugherty, L.C.; Niblock, O.; Leong, I.U.S.; Smith, K.R.; Gerasimenko, O.; Haraldsdottir, E.; et al. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat. Genet. 2019, 51, 1560–1565. [Google Scholar] [CrossRef]
- Lee, E.; Le, T.; Zhu, Y.; Elakis, G.; Turner, A.; Lo, W.; Venselaar, H.; Verrenkamp, C.A.; Snow, N.; Mowat, D.; et al. A craniosynostosis massively parallel sequencing panel study in 309 Australian and New Zealand patients: Findings and recommendations. Genet. Med. 2018, 20, 1061–1068. [Google Scholar] [CrossRef]
- Clarke, C.M.; Fok, V.T.; Gustafson, J.A.; Smyth, M.D.; Timms, A.E.; Frazar, C.D.; Smith, J.D.; Birgfeld, C.B.; Lee, A.; Ellenbogen, R.G.; et al. Single suture craniosynostosis: Identification of rare variants in genes associated with syndromic forms. Am. J. Med. Genet. A 2018, 176, 290–300. [Google Scholar] [CrossRef]
- Topa, A.; Rohlin, A.; Andersson, M.K.; Fehr, A.; Lovmar, L.; Stenman, G.; Kolby, L. NGS targeted screening of 100 Scandinavian patients with coronal synostosis. Am. J. Med. Genet. A 2020, 182, 348–356. [Google Scholar] [CrossRef]
- Timberlake, A.T.; Jin, S.C.; Nelson-Williams, C.; Wu, R.; Furey, C.G.; Islam, B.; Haider, S.; Loring, E.; Galm, A.; Yale Center for Genome Analysis; et al. Mutations in TFAP2B and previously unimplicated genes of the BMP, Wnt, and Hedgehog pathways in syndromic craniosynostosis. Proc. Natl. Acad. Sci. USA 2019, 116, 15116–15121. [Google Scholar] [CrossRef]
- Suzuki, T.; Suzuki, T.; Raveau, M.; Miyake, N.; Sudo, G.; Tsurusaki, Y.; Watanabe, T.; Sugaya, Y.; Tatsukawa, T.; Mazaki, E.; et al. A recurrent PJA1 variant in trigonocephaly and neurodevelopmental disorders. Ann. Clin. Transl. Neurol. 2020, 7, 1117–1131. [Google Scholar] [CrossRef]
- Yoon, J.G.; Hahn, H.M.; Choi, S.; Kim, S.J.; Aum, S.; Yu, J.W.; Park, E.K.; Shim, K.W.; Lee, M.G.; Kim, Y.O. Molecular Diagnosis of Craniosynostosis Using Targeted Next-Generation Sequencing. Neurosurgery 2020, 87, 294–302. [Google Scholar] [CrossRef]
- Wu, Y.; Peng, M.; Chen, J.; Suo, J.; Zou, S.; Xu, Y.; Wilkie, A.O.M.; Zou, W.; Mu, X.; Wang, S. A custom-designed panel sequencing study in 201 Chinese patients with craniosynostosis revealed novel variants and distinct mutation spectra. J. Genet. Genom. 2021, 48, 167–171. [Google Scholar] [CrossRef]
- Alghamdi, M.; Alhumsi, T.R.; Altweijri, I.; Alkhamis, W.H.; Barasain, O.; Cardona-Londono, K.J.; Ramakrishnan, R.; Guzman-Vega, F.J.; Arold, S.T.; Ali, G.; et al. Clinical and Genetic Characterization of Craniosynostosis in Saudi Arabia. Front. Pediatr. 2021, 9, 582816. [Google Scholar] [CrossRef] [PubMed]
- Tønne, E.; Due-Tønnessen, B.J.; Mero, I.L.; Wiig, U.S.; Kulseth, M.A.; Vigeland, M.D.; Sheng, Y.; von der Lippe, C.; Tveten, K.; Meling, T.R.; et al. Benefits of clinical criteria and high-throughput sequencing for diagnosing children with syndromic craniosynostosis. Eur. J. Hum. Genet. 2021, 29, 920–929. [Google Scholar] [CrossRef] [PubMed]
- Chen, J.; Zhang, P.; Peng, M.; Liu, B.; Wang, X.; Du, S.; Lu, Y.; Mu, X.; Lu, Y.; Wang, S.; et al. An additional whole-exome sequencing study in 102 panel-undiagnosed patients: A retrospective study in a Chinese craniosynostosis cohort. Front. Genet. 2022, 13, 967688. [Google Scholar] [CrossRef] [PubMed]
- Tønne, E.; Due-Tønnessen, B.J.; Vigeland, M.D.; Amundsen, S.S.; Ribarska, T.; Asten, P.M.; Sheng, Y.; Helseth, E.; Gilfillan, G.D.; Mero, I.L.; et al. Whole-exome sequencing in syndromic craniosynostosis increases diagnostic yield and identifies candidate genes in osteogenic signaling pathways. Am. J. Med. Genet. A 2022, 188, 1464–1475. [Google Scholar] [CrossRef] [PubMed]
- Timberlake, A.T.; Kiziltug, E.; Jin, S.C.; Nelson-Williams, C.; Loring, E.; Yale Center for Genome Analysis; Allocco, A.; Marlier, A.; Banka, S.; Stuart, H.; et al. De novo mutations in the BMP signaling pathway in lambdoid craniosynostosis. Hum. Genet. 2023, 142, 21–32. [Google Scholar] [CrossRef]
- Tooze, R.S.; Calpena, E.; Twigg, S.R.F.; D’Arco, F. Genomics England Research C, Wakeling EL, Wilkie AOM: Craniosynostosis, inner ear, and renal anomalies in a child with complete loss of SPRY1 (sprouty homolog 1) function. J. Med. Genet. 2022. Epub ahead of print. [Google Scholar] [CrossRef]
- Koelling, N.; Bernkopf, M.; Calpena, E.; Maher, G.J.; Miller, K.A.; Ralph, H.K.; Goriely, A.; Wilkie, A.O.M. Amplimap: A versatile tool to process and analyze targeted NGS data. Bioinformatics 2019, 35, 5349–5350. [Google Scholar] [CrossRef]
- Whiffin, N.; Minikel, E.; Walsh, R.; O’Donnell-Luria, A.H.; Karczewski, K.; Ing, A.Y.; Barton, P.J.R.; Funke, B.; Cook, S.A.; MacArthur, D.; et al. Using high-resolution variant frequencies to empower clinical genome interpretation. Genet. Med. 2017, 19, 1151–1158. [Google Scholar] [CrossRef]
- Farmer, D.T.; Mlcochova, H.; Zhou, Y.; Koelling, N.; Wang, G.; Ashley, N.; Bugacov, H.; Chen, H.J.; Parvez, R.; Tseng, K.C.; et al. The developing mouse coronal suture at single-cell resolution. Nat. Commun. 2021, 12, 4797. [Google Scholar] [CrossRef]
- Tooze, R.S.; Miller, K.; Swagemakers, S.; Mcgowan, S.; Boute, O.; Collet, C.; Johnson, D.; Laffargue, F.; Leeuw, N.D.; Morton, J.; et al. Pathogenic variants in the paired-related homeobox 1 (PRRX1) gene are associated with craniosynostosis [Conference Abstract]. In Proceedings of the European Society of Human Genetics Conference, Vienna, Austria, 11–14 June 2022. [Google Scholar]
- Durmaz, C.D.; Altiner, S. MASP1-related 3MC syndrome in a patient from Turkey. Am. J. Med. Genet. A 2021, 185, 2267–2270. [Google Scholar] [CrossRef]
- Atik, T.; Koparir, A.; Bademci, G.; Foster, J., 2nd; Altunoglu, U.; Mutlu, G.Y.; Bowdin, S.; Elcioglu, N.; Tayfun, G.A.; Atik, S.S.; et al. Novel MASP1 mutations are associated with an expanded phenotype in 3MC1 syndrome. Orphanet J. Rare Dis. 2015, 10, 128. [Google Scholar] [CrossRef]
- Tolchin, D.; Yeager, J.P.; Prasad, P.; Dorrani, N.; Russi, A.S.; Martinez-Agosto, J.A.; Haseeb, A.; Angelozzi, M.; Santen, G.W.E.; Ruivenkamp, C.; et al. De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas. Am. J. Hum. Genet. 2020, 106, 830–845. [Google Scholar] [CrossRef]
- Tagariello, A.; Heller, R.; Greven, A.; Kalscheuer, V.M.; Molter, T.; Rauch, A.; Kress, W.; Winterpacht, A. Balanced translocation in a patient with craniosynostosis disrupts the SOX6 gene and an evolutionarily conserved non-transcribed region. J. Med. Genet. 2006, 43, 534–540. [Google Scholar] [CrossRef]
- Gustafson, J.; Bjork, M.; van Ravenswaaij-Arts, C.M.A.; Cunningham, M.L. Mechanism of Disease: Recessive ADAMTSL4 Mutations and Craniosynostosis with Ectopia Lentis. Case Rep. Genet. 2022, 2022, 3239260. [Google Scholar] [CrossRef]
- Gumus, E. Extending the phenotype of Xia-Gibbs syndrome in a two-year-old patient with craniosynostosis with a novel de novo AHDC1 missense mutation. Eur. J. Med. Genet. 2020, 63, 103637. [Google Scholar] [CrossRef]
- Miller, K.A.; Twigg, S.R.; McGowan, S.J.; Phipps, J.M.; Fenwick, A.L.; Johnson, D.; Wall, S.A.; Noons, P.; Rees, K.E.; Tidey, E.A.; et al. Diagnostic value of exome and whole genome sequencing in craniosynostosis. J. Med. Genet. 2017, 54, 260–268. [Google Scholar] [CrossRef]
- Ritter, A.L.; McDougall, C.; Skraban, C.; Medne, L.; Bedoukian, E.C.; Asher, S.B.; Balciuniene, J.; Campbell, C.D.; Baker, S.W.; Denenberg, E.H.; et al. Variable Clinical Manifestations of Xia-Gibbs syndrome: Findings of Consecutively Identified Cases at a Single Children’s Hospital. Am. J. Med. Genet. A 2018, 176, 1890–1896. [Google Scholar] [CrossRef]
- Danda, S.; Datar, C.; Kher, A.; Deshpande, T.; Thomas, M.M.; Oommen, S.P. First reported cases with Xia-Gibbs syndrome from India harboring novel variants in AHDC1. Am. J. Med. Genet. A 2022, 188, 2501–2504. [Google Scholar] [CrossRef]
- Adès, L.C.; Sullivan, K.; Biggin, A.; Haan, E.A.; Brett, M.; Holman, K.J.; Dixon, J.; Robertson, S.; Holmes, A.D.; Rogers, J.; et al. FBN1, TGFBR1, and the Marfan-craniosynostosis/mental retardation disorders revisited. Am. J. Med. Genet. A 2006, 140, 1047–1058. [Google Scholar] [CrossRef]
- Takenouchi, T.; Hida, M.; Sakamoto, Y.; Torii, C.; Kosaki, R.; Takahashi, T.; Kosaki, K. Severe congenital lipodystrophy and a progeroid appearance: Mutation in the penultimate exon of FBN1 causing a recognizable phenotype. Am. J. Med. Genet. A 2013, 161A, 3057–3062. [Google Scholar] [CrossRef]
- Hiraki, Y.; Moriuchi, M.; Okamoto, N.; Ishikawa, N.; Sugimoto, Y.; Eguchi, K.; Sakai, H.; Saitsu, H.; Mizuguchi, T.; Harada, N.; et al. Craniosynostosis in a patient with a de novo 15q15-q22 deletion. Am. J. Med. Genet. A 2008, 146A, 1462–1465. [Google Scholar] [CrossRef] [PubMed]
- Sentchordi-Montané, L.; Diaz-Gonzalez, F.; Cátedra-Vallés, E.V.; Heath, K.E. Identification of the third FGF9 variant in a girl with multiple synostosis-comparison of the genotype:phenotype of FGF9 variants in humans and mice. Clin. Genet. 2021, 99, 309–312. [Google Scholar] [CrossRef] [PubMed]
- Wu, X.L.; Gu, M.M.; Huang, L.; Liu, X.S.; Zhang, H.X.; Ding, X.Y.; Xu, J.Q.; Cui, B.; Wang, L.; Lu, S.Y.; et al. Multiple synostoses syndrome is due to a missense mutation in exon 2 of FGF9 gene. Am. J. Hum. Genet. 2009, 85, 53–63. [Google Scholar] [CrossRef] [PubMed]
- Rodriguez-Zabala, M.; Aza-Carmona, M.; Rivera-Pedroza, C.I.; Belinchon, A.; Guerrero-Zapata, I.; Barraza-Garcia, J.; Vallespin, E.; Lu, M.; Del Pozo, A.; Glucksman, M.J.; et al. FGF9 mutation causes craniosynostosis along with multiple synostoses. Hum. Mutat. 2017, 38, 1471–1476. [Google Scholar] [CrossRef]
- Murakami, H.; Okawa, A.; Yoshida, H.; Nishikawa, S.; Moriya, H.; Koseki, H. Elbow knee synostosis (Eks): A new mutation on mouse Chromosome 14. Mamm. Genome 2002, 13, 341–344. [Google Scholar] [CrossRef]
- Bashir, R.A.; Dixit, A.; Goedhart, C.; Parboosingh, J.S.; Innes, A.M.; Ferreira, P.; Hasan, S.U.; Au, P.B. Lin-Gettig syndrome: Craniosynostosis expands the spectrum of the KAT6B related disorders. Am. J. Med. Genet. A 2017, 173, 2596–2604. [Google Scholar] [CrossRef]
- Mignot, C.; Moutard, M.L.; Rastetter, A.; Boutaud, L.; Heide, S.; Billette, T.; Doummar, D.; Garel, C.; Afenjar, A.; Jacquette, A.; et al. ARID1B mutations are the major genetic cause of corpus callosum anomalies in patients with intellectual disability. Brain 2016, 139, e64. [Google Scholar] [CrossRef]
- Goos, J.A.C.; Vogel, W.K.; Mlcochova, H.; Millard, C.J.; Esfandiari, E.; Selman, W.H.; Calpena, E.; Koelling, N.; Carpenter, E.L.; Swagemakers, S.M.A.; et al. A de novo substitution in BCL11B leads to loss of interaction with transcriptional complexes and craniosynostosis. Hum. Mol. Genet. 2019, 28, 2501–2513. [Google Scholar] [CrossRef]
- Zhao, X.; Wu, B.; Chen, H.; Zhang, P.; Qian, Y.; Peng, X.; Dong, X.; Wang, Y.; Li, G.; Dong, C.; et al. Case report: A novel truncating variant of BCL11B associated with rare feature of craniosynostosis and global developmental delay. Front. Pediatr. 2022, 10, 982361. [Google Scholar] [CrossRef]
- Eto, K.; Machida, O.; Yanagishita, T.; Shimojima Yamamoto, K.; Chiba, K.; Aihara, Y.; Hasegawa, Y.; Nagata, M.; Ishihara, Y.; Miyashita, Y.; et al. Novel BCL11B truncation variant in a patient with developmental delay, distinctive features, and early craniosynostosis. Hum. Genome Var. 2022, 9, 43. [Google Scholar] [CrossRef]
- Bostwick, B.L.; McLean, S.; Posey, J.E.; Streff, H.E.; Gripp, K.W.; Blesson, A.; Powell-Hamilton, N.; Tusi, J.; Stevenson, D.A.; Farrelly, E.; et al. Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders. Genome Med. 2017, 9, 73. [Google Scholar] [CrossRef]
- Gregor, A.; Sadleir, L.G.; Asadollahi, R.; Azzarello-Burri, S.; Battaglia, A.; Ousager, L.B.; Boonsawat, P.; Bruel, A.L.; Buchert, R.; Calpena, E.; et al. De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder. Am. J. Hum. Genet. 2018, 103, 305–316. [Google Scholar] [CrossRef]
- Schwerd, T.; Krause, F.; Twigg, S.R.F.; Aschenbrenner, D.; Chen, Y.-H.; Borgmeyer, U.; Müller, M.; Manrique, S.; Schumacher, N.; Wall, S.A.; et al. A variant in IL6ST with a selective IL-11 signaling defect in human and mouse. Bone Res. 2020, 8, 24. [Google Scholar] [CrossRef]
- Schwerd, T.; Twigg, S.R.F.; Aschenbrenner, D.; Manrique, S.; Miller, K.A.; Taylor, I.B.; Capitani, M.; McGowan, S.J.; Sweeney, E.; Weber, A.; et al. A biallelic mutation in IL6ST encoding the GP130 co-receptor causes immunodeficiency and craniosynostosis. J. Exp. Med. 2017, 214, 2547–2562. [Google Scholar] [CrossRef]
- Lipiński, P.; Różdżyńska-Świątkowska, A.; Iwanicka-Pronicka, K.; Perkowska, B.; Pokora, P.; Tylki-Szymańska, A. Long-term outcome of patients with α-mannosidosis—A single center study. Mol. Genet. Metab. Rep. 2022, 30, 100826. [Google Scholar] [CrossRef]
- Strande, N.T.; Riggs, E.R.; Buchanan, A.H.; Ceyhan-Birsoy, O.; DiStefano, M.; Dwight, S.S.; Goldstein, J.; Ghosh, R.; Seifert, B.A.; Sneddon, T.P.; et al. Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource. Am. J. Hum. Genet. 2017, 100, 895–906. [Google Scholar] [CrossRef]
- Wright, C.F.; Fitzgerald, T.W.; Jones, W.D.; Clayton, S.; McRae, J.F.; van Kogelenberg, M.; King, D.A.; Ambridge, K.; Barrett, D.M.; Bayzetinova, T.; et al. Genetic diagnosis of developmental disorders in the DDD study: A scalable analysis of genome-wide research data. Lancet 2015, 385, 1305–1314. [Google Scholar] [CrossRef]
- Holland, P.W.; Booth, H.A.; Bruford, E.A. Classification and nomenclature of all human homeobox genes. BMC Biol. 2007, 5, 47. [Google Scholar] [CrossRef]
- Wilk, K.; Yeh, S.A.; Mortensen, L.J.; Ghaffarigarakani, S.; Lombardo, C.M.; Bassir, S.H.; Aldawood, Z.A.; Lin, C.P.; Intini, G. Postnatal Calvarial Skeletal Stem Cells Expressing PRX1 Reside Exclusively in the Calvarial Sutures and Are Required for Bone Regeneration. Stem Cell Rep. 2017, 8, 933–946. [Google Scholar] [CrossRef]
- Opperman, L.A. Cranial Sutures as Intramembranous Bone Growth Sites. Dev. Dyn. 2000, 219, 472–485. [Google Scholar] [CrossRef]
- Levi, B.; Wan, D.C.; Wong, V.W.; Nelson, E.; Hyun, J.; Longaker, M.T. Cranial suture biology: From pathways to patient care. J. Craniofac. Surg. 2012, 23, 13–19. [Google Scholar] [CrossRef] [PubMed]
- Ornitz, D.M.; Marie, P.J. Fibroblast growth factor signaling in skeletal development and disease. Genes Dev. 2015, 29, 1463–1486. [Google Scholar] [CrossRef] [PubMed]
- Rice, D.P.; Aberg, T.; Chan, Y.; Tang, Z.; Kettunen, P.J.; Pakarinen, L.; Maxson, R.E.; Thesleff, I. Integration of FGF and TWIST in calvarial bone and suture development. Development 2000, 127, 1845–1855. [Google Scholar] [CrossRef] [PubMed]
- Kim, H.J.; Rice, D.P.; Kettunen, P.J.; Thesleff, I. FGF-, BMP- and Shh-mediated signalling pathways in the regulation of cranial suture morphogenesis and calvarial bone development. Development 1998, 125, 1241–1251. [Google Scholar] [CrossRef]
- Harada, M.; Murakami, H.; Okawa, A.; Okimoto, N.; Hiraoka, S.; Nakahara, T.; Akasaka, R.; Shiraishi, Y.; Futatsugi, N.; Mizutani-Koseki, Y.; et al. FGF9 monomer-dimer equilibrium regulates extracellular matrix affinity and tissue diffusion. Nat. Genet. 2009, 41, 289–298. [Google Scholar] [CrossRef]
- Harada, M.; Akita, K. Mouse fibroblast growth factor 9 N143T mutation leads to wide chondrogenic condensation of long bones. Histochem. Cell Biol. 2020, 153, 215–223. [Google Scholar] [CrossRef]
- Gabriel, L.A.; Wang, L.W.; Bader, H.; Ho, J.C.; Majors, A.K.; Hollyfield, J.G.; Traboulsi, E.I.; Apte, S.S. ADAMTSL4, a secreted glycoprotein widely distributed in the eye, binds fibrillin-1 microfibrils and accelerates microfibril biogenesis. Investig. Ophthalmol. Vis. Sci. 2012, 53, 461–469. [Google Scholar] [CrossRef]
- Bader, H.L.; Wang, L.W.; Ho, J.C.; Tran, T.; Holden, P.; Fitzgerald, J.; Atit, R.P.; Reinhardt, D.P.; Apte, S.S. A disintegrin-like and metalloprotease domain containing thrombospondin type 1 motif-like 5 (ADAMTSL5) is a novel fibrillin-1-, fibrillin-2-, and heparin-binding member of the ADAMTS superfamily containing a netrin-like module. Matrix Biol. 2012, 31, 398–411. [Google Scholar] [CrossRef]
- Tsutsui, K.; Manabe, R.; Yamada, T.; Nakano, I.; Oguri, Y.; Keene, D.R.; Sengle, G.; Sakai, L.Y.; Sekiguchi, K. ADAMTSL-6 is a novel extracellular matrix protein that binds to fibrillin-1 and promotes fibrillin-1 fibril formation. J. Biol. Chem. 2010, 285, 4870–4882. [Google Scholar] [CrossRef]
- Ding, L.; Cao, J.; Lin, W.; Chen, H.; Xiong, X.; Ao, H.; Yu, M.; Lin, J.; Cui, Q. The Roles of Cyclin-Dependent Kinases in Cell-Cycle Progression and Therapeutic Strategies in Human Breast Cancer. Int. J. Mol. Sci. 2020, 21, 1960. [Google Scholar] [CrossRef]
- Kipreos, E.T.; Pagano, M. The F-box protein family. Genome Biol. 2000, 1, reviews3002.1. [Google Scholar] [CrossRef]
- Silverman, J.S.; Skaar, J.R.; Pagano, M. SCF ubiquitin ligases in the maintenance of genome stability. Trends Biochem. Sci. 2012, 37, 66–73. [Google Scholar] [CrossRef]
- Zollino, M.; Lattante, S.; Orteschi, D.; Frangella, S.; Doronzio, P.N.; Contaldo, I.; Mercuri, E.; Marangi, G. Syndromic Craniosynostosis Can Define New Candidate Genes for Suture Development or Result from the Non-specifc Effects of Pleiotropic Genes: Rasopathies and Chromatinopathies as Examples. Front. Neurosci. 2017, 11, 587. [Google Scholar] [CrossRef]
- Bjornsson, H.T. The Mendelian disorders of the epigenetic machinery. Genome Res. 2015, 25, 1473–1481. [Google Scholar] [CrossRef]
- Matsuoka, K.; Park K-a Ito, M.; Ikeda, K.; Takeshita, S. Osteoclast-Derived Complement Component 3a Stimulates Osteoblast Differentiation. J. Bone Miner. Res. 2014, 29, 1522–1530. [Google Scholar] [CrossRef]
- Mödinger, Y.; Löffler, B.; Huber-Lang, M.; Ignatius, A. Complement involvement in bone homeostasis and bone disorders. Semin. Immunol. 2018, 37, 53–65. [Google Scholar] [CrossRef]
- Wang, Z.; Li, J.; Li, K.; Xu, J. SOX6 is downregulated in osteosarcoma and suppresses the migration, invasion and epithelial-mesenchymal transition via TWIST1 regulation. Mol. Med. Rep. 2018, 17, 6803–6811. [Google Scholar] [CrossRef]
- An, C.I.; Ichihashi, Y.; Peng, J.; Sinha, N.R.; Hagiwara, N. Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart. PLoS ONE 2016, 11, e0166574. [Google Scholar] [CrossRef]
- Kyrylkova, K.; Iwaniec, U.T.; Philbrick, K.A.; Leid, M. BCL11B regulates sutural patency in the mouse craniofacial skeleton. Dev. Biol. 2016, 415, 251–260. [Google Scholar] [CrossRef]
- Senaratne, T.N.; Quintero-Rivera, F. NFIA-Related Disorder. In GeneReviews(®); Adam, M.P., Everman, D.B., Mirzaa, G.M., Pagon, R.A., Wallace, S.E., Bean, L.J.H., Gripp, K.W., Amemiya, A., Eds.; University of Washington: Seattle, WA, USA, 1993. [Google Scholar]
Cohort | Number of Probands Screened | Sequencing Technology | Phenotypes Included in the Screen a | Number of Pathogenic/Likely Pathogenic Variants Identified in Each Screen Corresponding to Current PanelApp (v3) Status | |||
---|---|---|---|---|---|---|---|
Green | Amber | Red | Null | ||||
Australia/New Zealand (Lee et al., 2018) [14] | 309 | 20-gene panel | Patients recruited with a range of sutures fused, with or without syndromic features | 40 | 2 | 1 | |
Seattle (Clarke et al., 2018) [15] | 397 | RNA-sequencing, 61 genes screened | Single suture craniosynostosis | 43 | 1 | 19 | |
Scandinavia (Topa et al., 2019) [16] | 100 | 63-gene panel | Syndromic craniosynostosis (78% of the cohort), predominately coronal synostosis | 66 | |||
Yale (Timberlake et al., 2019) [17] | 12 | Whole exome | All syndromic, with single and multi-suture synostosis | 5 | 4 | ||
Japan (Suzuki et al., 2020) [18] b | 51 | Whole exome | All with trigonocephaly | 4 | 17 | ||
Korea (Yoon et al., 2020) [19] | 110 | 34-gene panel | Patients recruited with syndromic or non-syndromic craniosynostosis and all sutures considered | 24 | 1 | ||
China (Wu et al., 2021) [20] | 201 | 17-gene panel | Cohort consists of patients with syndromic and non-syndromic craniosynostosis | 51 | |||
Saudi Arabia (Alghamdi et al., 2021) [21] | 28 | Whole exome | Syndromic craniosynostosis with all sutures considered | 13 | 2 | ||
100 kGP (Hyder et al., 2021) [11] | 114 | Whole genome | Patients recruited with syndromic or non-syndromic craniosynostosis and all sutures considered | 12 | 3 | 3 | 16 |
Norway (Tønne et al., 2021) [22] | 381 | 72-gene panel | Patients recruited with syndromic or non-syndromic craniosynostosis and all sutures considered | 59 | 4 | 5 | |
China (Chen et al., 2022) [23] | 264 | 17-gene panel (264 individuals), whole-exome sequencing (n = 102, 39%) | Patients recruited with syndromic or non-syndromic craniosynostosis and all sutures considered | 143 | 2 | 4 | |
Norway (Tønne et al., 2022) [24] | 10 | Whole exome | All patients with syndromic craniosynostosis that were negative in the previous Tønne screen [22] | 1 | 4 | ||
Yale (Timberlake et al., 2023) [25] | 25 | Whole exome | All patients displayed lambdoid synostosis | 1 | 14 | ||
Oxford (Tooze et al., 2022) [26] | 617 | 42-gene panel (Table S2) | Patients recruited with syndromic or non-syndromic craniosynostosis and all sutures considered | 4 | 6 |
Gene. | Current Panel | Mode of Inheritance | Broad Categories of Pathophysiology | Literature |
---|---|---|---|---|
MASP1 | Amber | Biallelic | Bone osteogenesis, resorption, and homeostasis | Two reviews identify a prevalence of 27–31% of patients with craniosynostosis and 3MC syndrome and a variant in MASP1 [31,32]. |
NFIA | Amber | Monoallelic | Regulator of cell fate and differentiation | Four patients identified in independent screens [19,22,23,24]. |
PRRX1 | Amber | Monoallelic | Regulator of cell fate and differentiation | There are 17 patients from 14 independent families with rare heterozygous variants in PRRX1, predicting loss of function variants or missense variants affecting the homeodomain [30]. |
SOX6 | Amber | Monoallelic | Regulator of cell fate and differentiation | Seven independent families with loss of function variants in SOX6 and craniosynostosis; five of these are published [23,33,34] and two were identified in a screen of 617 patients without a genetic diagnosis to their craniosynostosis [this study; Table S3]. |
ADAMTSL4 | Red | Biallelic | Regulator of the extracellular matrix | More than 12 cases of ectopia lentis and craniosynostosis are associated with recessive variants in ADAMTSL4 [35]. |
AHDC1 | Red | Monoallelic | Regulator of cell fate and differentiation | There are three individuals reported with bona fide craniosynostosis and variants in AHDC1 [36,37,38], a further four individuals are described with variants in AHDC1 and suspected craniosynostosis [22,39]. |
FBN1 | Red | Monoallelic | Regulator of the extracellular matrix | There are five likely pathogenic de novo variants reported in independent families and one deletion which includes FBN1 [19,37,40,41,42]. |
FGF9 | Red | Monoallelic | Regulator of cell fate and differentiation | Three likely pathogenic variants have been reported in independent families; one variant segregates in 12 individuals in the same family and another variant was inherited from an affected father [43,44,45]. A missense substitution, p.(Asn143Thr), in murine Fgf9 results in a phenotype similar to multiple synostoses syndrome 3, with craniosynostosis [46]. |
KAT6B | Red | Monoallelic | Chromatinopathy | Three loss of function variants have been identified in patients with craniosynostosis and a phenotype similar to Lin-Gettig syndrome [22,47]. |
NFIX | Red | Monoallelic | Regulator of cell fate and differentiation | Four families are reported with variants in NFIX. Only one of these variants does not affect a functional domain (p.(Met48Lys)), but it is reported in ClinVar as likely pathogenic for Malan overgrowth syndrome [22,25]. |
ARID1B | Absent | Monoallelic | Chromatinopathy | Four independent families have been described with loss-of-function variants in ARID1B and craniosynostosis with developmental delay [11,18,23,48]. |
BCL11B | Absent | Monoallelic | Regulator of cell fate and differentiation | There are seven families with variants in BCL11B and confirmed craniosynostosis [49,50,51]. |
CDK13 | Absent | Monoallelic | Cell-cycle regulator/genome stability | Four independent cases identified within the literature in patients with craniosynostosis [11,22,52]. |
FBXO11 | Absent | Monoallelic | Cell-cycle regulator/genome stability | Three independent cases confirmed in patients [11,53]. |
IL6ST | Absent | Biallelic | Bone osteogenesis, resorption, and homeostasis | Two cases of recessive variants in IL6ST and craniosynostosis with additional animal models which phenocopy the human presentation [54,55]. |
MAN2B1 | Absent | Biallelic | Bone osteogenesis, resorption, and homeostasis | Three independent families with recessive variants in MAN2B1 and craniosynostosis, although not all individuals with recessive variants in MAN2B1 develop craniosynostosis [11,22,56]. |
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Tooze, R.S.; Calpena, E.; Weber, A.; Wilson, L.C.; Twigg, S.R.F.; Wilkie, A.O.M. Review of Recurrently Mutated Genes in Craniosynostosis Supports Expansion of Diagnostic Gene Panels. Genes 2023, 14, 615. https://doi.org/10.3390/genes14030615
Tooze RS, Calpena E, Weber A, Wilson LC, Twigg SRF, Wilkie AOM. Review of Recurrently Mutated Genes in Craniosynostosis Supports Expansion of Diagnostic Gene Panels. Genes. 2023; 14(3):615. https://doi.org/10.3390/genes14030615
Chicago/Turabian StyleTooze, Rebecca S., Eduardo Calpena, Astrid Weber, Louise C. Wilson, Stephen R. F. Twigg, and Andrew O. M. Wilkie. 2023. "Review of Recurrently Mutated Genes in Craniosynostosis Supports Expansion of Diagnostic Gene Panels" Genes 14, no. 3: 615. https://doi.org/10.3390/genes14030615
APA StyleTooze, R. S., Calpena, E., Weber, A., Wilson, L. C., Twigg, S. R. F., & Wilkie, A. O. M. (2023). Review of Recurrently Mutated Genes in Craniosynostosis Supports Expansion of Diagnostic Gene Panels. Genes, 14(3), 615. https://doi.org/10.3390/genes14030615