Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?

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Abstract

Variants have been identified in the embryonic ectoderm development (EED) gene in seven patients with syndromic overgrowth similar to that observed in Weaver syndrome. Here, we present three additional patients with missense variants in the EED gene. All the missense variants reported to date (including the three presented here) have localized to one of seven WD40 domains of the EED protein, which are necessary for interaction with enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2). In addition, among the seven patients reported in the literature and the three new patients presented here, all of the reported pathogenic variants except one occurred at one of four amino acid residues in the EED protein. The recurrence of pathogenic variation at these loci suggests that these residues are functionally important (mutation hotspots). In silico modeling and calculations of the free energy changes resulting from these variants suggested that they not only destabilize the EED protein structure but also adversely affect interactions between EED, EZH2, and/or H3K27me3. These cases help demonstrate the mechanism(s) by which apparently deleterious variants in the EED gene might cause overgrowth and lend further support that amino acid residues in the WD40 domain region may be mutation hotspots.

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References

  1. 1.

    O’Meara MM, Simon JA. Inner workings and regulatory inputs that control Polycomb repressive complex 2. Chromosoma. 2012;121:221–34.

  2. 2.

    Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science. 2002;298:1039–43.

  3. 3.

    Bracken AP, Helin K. Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer. 2009;9:773–84.

  4. 4.

    Bachmann IM, Halvorsen OJ, Collett K, Stefansson IM, Straume O, Haukaas SA, et al. EZH2 expression is associated with high proliferation rate and aggressive tumor subgroups in cutaneous melanoma and cancers of the endometrium, prostate, and breast. J Clin Oncol. 2006;24:268–73.

  5. 5.

    Pasini D, Bracken AP, Jensen MR, Lazzerini Denchi E, Helin K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J. 2004;23:4061–71.

  6. 6.

    Ciferri C, Lander GC, Maiolica A, Herzog F, Aebersold R, Nogales E. Molecular architecture of human polycomb repressive complex 2. eLife. 2012;1:e00005.

  7. 7.

    Jiao L, Liu X. Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2. Science. 2015;350:aac4383.

  8. 8.

    Justin N, Zhang Y, Tarricone C, Martin SR, Chen S, Underwood E, et al. Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2. Nat Commun. 2016;7:11316.

  9. 9.

    Cohen ASA, Tuysuz B, Shen Y, Bhalla SK, Jones SJM, Gibson WT. A novel mutation in EED associated with overgrowth. J Hum Genet. 2015;60:339–42.

  10. 10.

    Cohen AS. Gibson WT EED-associated overgrowth in a second male patient. J Hum Genet. 2016;61:831–4.

  11. 11.

    Cooney E, Bi W, Schlesinger AE, Vinson S, Potocki L, Novel EED. Mutation in patient with Weaver syndrome. Am J Med Genet A. 2017;173:541–5.

  12. 12.

    Imagawa E, Higashimoto K, Sakai Y, Numakura C, Okamoto N, Matsunaga S, et al. Mutations in genes encoding polycomb repressive complex 2 subunits cause Weaver syndrome. Hum Mutat. 2017;38:637–48.

  13. 13.

    Smigiel R, Biernacka A, Biela M, Murcia-Pienkowski V, Szmida E, Gasperowicz P, et al. Novel de novo mutation affecting two adjacent aminoacids in the EED gene in a patient with Weaver syndrome. J Hum Genet. 2018;63:517–20.

  14. 14.

    Kasinath V, Faini M, Poepsel S, Reif D, Feng XA, Stjepanovic G, et al. Structures of human PRC2 with its cofactors AEBP2 and JARID2. Science. 2018;359:940–4.

  15. 15.

    Xiang J, Honig, B. Jackal: A protein structure modeling package. New York: Columbia University and Howard Hughes Medical Institute; 2002.

  16. 16.

    Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–802.

  17. 17.

    Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33–8.

  18. 18.

    UniProt Consortium.UniProt: a hub for protein information. Nucleic Acids Res. 2015;43:D204–12.

  19. 19.

    Magis C, Taly JF, Bussotti G, Chang JM, Di PT, Erb I, et al. T-Coffee: tree-based consistency objective function for alignment evaluation. Methods Mol Biol. 2014;1079:117–29.

  20. 20.

    Getov I, Petukh M, Alexov E. SAAFEC: predicting the effect of single point mutations on protein folding free energy using a knowledge-modified MM/PBSA approach. Int J Mol Sci. 2016;17:512.

  21. 21.

    Pires DEV, Ascher DB, Blundell TL. mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics. 2014;30:335–42.

  22. 22.

    Worth CL, Preissner R, Blundell TL. SDM--a server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res. 2011;39:W215–22.

  23. 23.

    Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 2005;33:W306–10.

  24. 24.

    Dehouck Y, Kwasigroch JM, Gilis D, Rooman M. PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality. BMC Bioinformatics. 2011;12:151.

  25. 25.

    Petukh M, Dai L, Alexov E. SAAMBE: webserver to predict the charge of binding free energy caused by amino acids mutations. Int J Mol Sci. 2016;17:547.

  26. 26.

    Dehouck Y, Kwasigroch JM, Rooman M, Gilis D. BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations. Nucleic Acids Res. 2013;41:W333–9.

  27. 27.

    Li M, Simonetti FL, Goncearenco A, Panchenko AR. MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. Nucleic Acids Res. 2016;44):W494–501.

  28. 28.

    Cao Q, Wang X, Zhao M, Yang R, Malik R, Qiao Y, et al. The central role of EED in the orchestration of polycomb group complexes. Nat Commun. 2014;5:3127.

  29. 29.

    Montgomery ND, Yee D, Montgomery SA, Magnuson T. Molecular and functional mapping of EED motifs required for PRC2-dependent histone methylation. J Mol Biol. 2007;374:1145–57.

  30. 30.

    Denisenko O, Shnyreva M, Suzuki H, Bomsztyk K. Point mutations in the WD40 domain of Eed block its interaction with Ezh2. Mol Cell Biol. 1998;18:5634–42.

  31. 31.

    Xu C, Bian C, Yang W, Galka M, Ouyang H, Chen C, et al. Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc Natl Acad Sci USA. 2010;107:19266–71.

  32. 32.

    Margueron R, Justin N, Ohno K, Sharpe ML, Son J, Drury WJ, et al. Role of the polycomb protein EED in the propagation of repressive histone marks. Nature. 2009;461:762–7.

  33. 33.

    Lee C-H, Yu J-R, Kumar S, Jin Y, LeRoy G, Bhanu N, et al. Allosteric activation dictates PRC2 activity independent of its recruitment tochromatin. Mol Cell. 2018;70:422–34.e6.

  34. 34.

    Tatton-Brown K, Loveday C, Yost S, Clarke M, Ramsay E, Zachariou A, et al. Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability. Am J Hum Genet. 2017;100:725–36.

  35. 35.

    Ueda T, Sanada M, Matsui H, Yamasaki N, Honda Z-I, Shih L-Y, et al. EED mutants impair polycomb repressive complex 2 in myelodysplastic syndrome and related neoplasms. Leukemia . 2012;26:2557–60.

  36. 36.

    Sewalt RG, van der Vlag J, Gunster MJ, Hamer KM, den Blaauwen JL, Satijn DP, et al. Characterization of interactions between the mammalian polycomb-group proteins Enx1/EZH2 and EED suggests the existence of different mammalian polycomb-group protein complexes. Mol Cell Biol. 1998;18:3586–95.

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Acknowledgements

We thank the patients and their families for their participation in this study. We also recognize the contributions of our laboratory staff and the clinical team at the Greenwood Genetic Center for their considerable efforts.

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Correspondence to Julie R. Jones.

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The Greenwood Genetic Center receives revenue from diagnostic testing performed in the GGC Molecular Diagnostic Laboratory.

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