Selected Publications
Kalita B, Martinez-Cebrian G, McEvoy J, Allensworth M, Knight M, Magli A, Perlingeiro RCR, Dyer MA, Stewart E, Dynlacht BD. PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma. Cell (in press, 2025).
Norrie J, Lupo M, Shirinifard A, Djekidel N, Ramirez C, Xu B, Dundee J, Dyer MA. Latent epigenetic programs in Müller glia contribute to stress, injury and disease response in retina. Developmental Cell, 2025 PMCID: PMC10614790
Honnell, V, Sweeney, S, Norrie, J, Parks, M, Ramirez, C, Jannu, AJ, Xu, B, Teubner, B, Lee, AY, Bell, C, Dyer, MA. Evolutionary conservation of VSX2 super-enhancer modules in retinal development. Development July 2025. PMCID: PMC11266796.
Zeineldin M, Patel AG, Dyer MA. Neuroblastoma: When differentiation goes awry. Neuron 2022 Sep 21;110(18):2916-2928. PMCID: PMC9509448.
Patel AG, Chen X, Huang X, Clay MR, Komorova N, Krasin MJ, Pappo A, Tillman H, Orr BA, McEvoy J, Gordon B, Blankenship K, Reilly C, Zhou X, Norrie JL, Karlstrom A, Yu J, Wodarz D, Stewart E, Dyer MA. The Myogenesis Program Drives Clonal Selection and Drug Resistance in Rhabdomyosarcoma. Developmental Cell 2022 May;57(10):1226-1240. PMCID: PMC9133224.
Honnell V, Norrie JL, Patel AG, Ramirez C, Zhang J, Lai YH, Wan S, Dyer MA. Identification of a modular superenhancer in murine retinal development. Nature Communications. 2022 Jan 11;13(1):253. PMCID: PMC8752785.
Norrie JL, Nityanandam A, Lai K, Chen X, Wilson M, Stewart E, Griffiths L, Jin H, Wu G, Orr B, Tran Q, Allen S, Reilly C, Zhou X, Zhang J, Newman K, Johnson D, Brennan R, Dyer MA. Retinoblastoma from human stem cell-derived retinal organoids. Nat Communications 2021 Jul 27;12(1):4535. PMCID: PMC8316454.
Zeineldin M, Federico S, Chen X, Fan Y, Xu B, Stewart E, Zhou X, Jeon J, Griffiths L, Nguyen R, Norrie J, Easton J, Mulder H, Yergeau D, Liu Y, Wu J, Van Ryn C, Naranjo A, Hogarty MD, Kamiński MM, Valentine M, Pruett-Miller SM, Pappo A, Zhang J, Clay MR, Bahrami A, Vogel P, Lee S, Shelat A, Sarthy JF, Meers MP, George RE, Mardis ER, Wilson RK, Henikoff S, Downing JR, Dyer MA. MYCN amplification and ATRX mutations are incompatible in neuroblastoma. Nature Communications 11, 913 (2020). PMCID: PMC7021759.
Norrie JL, Lupo MS, Xu B, Al Diri I, Valentine M, Putnam D, Griffiths L, Zhang J, Johnson D, Easton J, Shao Y, Honnell V, Frase S, Miller S, Stewart V, Zhou X, Chen X, Dyer MA. Nucleome Dynamics During Retinal Development. Neuron 104(3):512-528, 2019 Nov 6. PMCID: PMC6842117
Stewart E, McEvoy J, Wang H, Chen X, Honnell V, Ocarz M, Gordon B, Dapper J, Blankenship K, Yang Y, Li Y, Shaw TI, Cho JH, Wang X, Xu B, Gupta P, Fan Y, Liu Y, Rusch M, Griffiths L, Jeon J, Freeman BB 3rd, Clay MR, Pappo A, Easton J, Shurtleff S, Shelat A, Zhou X, Boggs K, Mulder H, Yergeau D, Bahrami A, Mardis ER, Wilson RK, Zhang J, Peng J, Downing JR, Dyer MA; St. Jude Children's Research Hospital – Washington University Pediatric Cancer Genome Project. Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell Sep 10;34(3):411-426.e19, 2018. doi: 10.1016/j.ccell.2018.07.012. Epub 2018 Aug 23. PMID: 30146332
Wang L, Hiler D, Xu B, AlDiri I, Chen X, Zhou X, Griffiths L, Valentine M, Shirinifard A, Sablauer A, Thiagarajan S, Barabas ME, Zhang J, Johnson D, Frase S, Dyer MA. Retinal Cell Type DNA Methylation and Histone Modifications Predict Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures. Cell Rep Mar 6;22(10):2601-2614, 2018. doi: 10.1016/j.celrep.2018.01.075. PMID: 29514090
Stewart E, McEvoy J, Wang H, Chen X, Honnell V, Ocarz M, Gordon B, Dapper J, Blankenship K, Yang Y, Li Y, Shaw TI, Cho JH, Wang X, Xu B, Gupta P, Fan Y, Liu Y, Rusch M, Griffiths L, Jeon J, Freeman BB rd, Clay MR, Pappo A, Easton J, Shurtleff S, Shelat A, Zhou X, Boggs K, Mulder H, Yergeau D, Bahrami A, Mardis ER, Wilson RK, Zhang J, Peng J, Downing JR, and Dyer MA; St. Jude Children's Research Hospital – Washington University Pediatric Cancer Genome Project.. Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell 34(3):411-426, 2018 Sep 10. PMCID: PMC6158019.
Stewart E, Federico SM, Chen X, Shelat AA, Bradley C, Gordon B, Karlstrom A, Nathaniel R. Twarog NR, Clay MR, Bahrami A, Freeman III BB, Xu B, Zhou X, Wu J, Honnell V, Monica M, Blankenship K, Dapper J, Mardis ER, Wilson RK, Downing J, Zhang J, Easton J, Pappo A, and Dyer MA. Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors. Nature 2017 Sep 7;549(7670):96-100. PMCID: PMC5659286.
Aldiri I, Xu B, Wang L, Chen X, Hiler D, Griffiths L, Valentine M, Shirinifard A, Thiagarajan S, Sablauer A, Barabas ME, Zhang J, Johnson D, Frase S, Zhou X, Easton J, Zhang J, Mardis ER, Wilson RK, Downing JR, Dyer MA. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis. Neuron 2017 May 3;94(3):550-568.e10. PMCID: PMC5508517.
Hiler DJ, Barabas ME, Griffiths LM, Dyer MA. Reprogramming retinal neurons and standardized quantification of their differentiation in 3-dimensional retinal cultures. Nature Protocols 2016 (in press). (PMCID: PMC Journal–in process).
Dyer MA. Stem Cells Expand Insights into Human Brain Evolution. Cell Stem Cell Apr 7;18(4):425-6, 2016. PMID: 27058930 (PMCID: PMC Journal–in process).
Stewart E, Federico S, Karlstrom A, Shelat A, Sablauer A, Pappo A, Dyer MA. The Childhood Solid Tumor Network: A new resource for the developmental biology and oncology research communities. Dev Biol June 9, 2015. Epub ahead of print. pii: S0012-1606(15)00105-0. doi: 10.1016/j.ydbio.2015.03.001.
Chen X, Pappo A, Dyer MA. Pediatric solid tumor genomics and developmental pliancy. Oncogene Feb 2, 2015. Epub ahead of print. doi: 10.1038/onc.2014.474.
Hiler D, Chen X, Hazen J, Kupriyanov S, Carroll PA, Qu C, Xu B, Johnson D, Griffiths L, Frase S, Rodriguez AR, Martin G, Zhang J, Jeon J, Fan Y, Finkelstein D, Eisenman RN, Baldwin K, Dyer MA. Quantification of Retinogenesis in 3D Cultures Reveals Epigenetic Memory and Higher Efficiency in iPSCs Derived from Rod Photoreceptors. Cell Stem Cell 17(1):101-15, 2015.
Stewart E, Goshorn R, Bradley C, Griffiths LM, Benavente C, Twarog NR, Miller GM, Caufield W, Freeman BB 3rd, Bahrami A, Pappo A, Wu J, Loh A, Karlström Å, Calabrese C, Gordon B, Tsurkan L, Hatfield MJ, Potter PM, Snyder SE, Thiagarajan S, Shirinifard A, Sablauer A, Shelat AA, Dyer MA. Targeting the DNA repair pathway in Ewing sarcoma. Cell Rep 9(3):829-41, 2014.
Chen X, Bahrami A, Pappo A, Easton J, Dalton J, Hedlund E, Dyer MA. Recurrent Somatic Structural Variations Contribute to Tumorigenesis in Pediatric Osterosarcoma. Cell Reports 7(1);104-112, 2014.
Chen X, Stewart E, Shelat A, Qu c, Bahrami A, Hatley M, Wu G, Bradley C, McEvoy J, Pappo P, Spunt S, Valentine M, Dyer MA. Targeting Oxidative Stress in Embryonal Rhabdomyosarcoma. Cancer Cell Dec 9;24(6):710-24, 2013.
Cheung NK, Zhang J, Lu C, Parker M, Bahrami A, Tickoo SK, Heguy A, Pappo AS, Federico S, Dalton J, Cheung IY, Ding L, Fulton R, Wang J, Chen X, Becksfort J, Wu J, Billups CA, Ellison D, Mardis ER, Wilson RK, Downing JR, Dyer MA. St Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project. Association of age at diagnosis and genetic mutations in patients with neuroblastoma. JAMA Mar 14;307(10):1062-71, 2012. (PMCID:PMC3527076)
Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, Ulyanov A, Wu G, Wilson W, Wang J, Brennan R, Rusch M, Manning AL, Ma J, Easton J, Shurtleff S, Mullighan C, Pounds S, Mukatira S, Gupta P, Neale G, Zhao D, Lu C, Fulton RS, Fulton LL, Hong X, Dooling DJ, Ochoa K, Naeve C, Dyson NJ, Mardis ER, Bahrami A, Ellison D, Wilson RK, Downing J, Dyer MA. A Novel Retinoblastoma Therapy from Genomic and Epigenetic Analyses. Nature Jan 11;481(7381):329-34, 2012. doi: 10.1038/nature10733. PMCID:PMC3289956. Faculty of 1000 (F1000)
McEvoy J, Flores-Otero J, Zhang J, Nemeth K, Brennan RC, Rodriguez-Galindo C, Wilson M, Xiong S, Lozano G, Sage J, Fu L, Louhibi L, Trimarchi J, Pani A, Smeyne R, Johnson D, Dyer MA. Coexpression of Normally Incompatible Developmental Pathways in Retinoblastoma, Cancer cell. Cancer Cell Aug 16;20(2):260-75, 2011. Faculty of 1000 (F1000)
Brennan RC, Federico S, Bradley C, Zhang J, Flores-Otero J, Wilson M, Stewart CF, Zhu F, Guy K, Dyer MA. Targeting the p53 Pathway in Retinoblastoma with Subconjunctival Nutlin-3a. Cancer Res Apr 22, 2011. [Epub ahead of print]. PMCID: PMC3116943. Faculty of 1000 (F1000)
Nemeth K, Federico S, Angel MC, Shen Y, Schaiquevich P, Zhang J, Egorin M, Stewart C, Dyer MA. Subconjunctival Carboplatin and Systemic Topotecan Treatment in Preclinical Models of Retinoblastoma. Cancer Jan 15;117(2):421-34, 2011. PMCID: PMC3000447.
Reed D, Shen Y, Shelat AA, Arnold LA, Ferreira AM, Zhu F, Mills N, Smithson DC, Regni CA, Bashford D, Cicero SA, Schulman BA, Jochemsen AG, Guy RK, Dyer MA. Identification and characterization of the first small molecule inhibitor of MDMX. Biol Chem 285(14):10786-96, 2010. (Epub 2010 Jan 15, 2010 Apr 2). PMCID: PMC2856285.
Laurie N, Mohan A, McEvoy J, Reed D, Zhang J, Schweers B, Ajioka I, Valentine V, Johnson D, Ellison D, Dyer MA. Changes in retinoblastoma cell adhesion associated with optic nerve invasion. Mol Cell Biol Dec;29(23):6268-82, 2009. Epub 2009 Sep 28. PMCID: PMC2786692
Dyer MA, Martins R, da Silva Filho M, Muniz JA, Silveira LC, Cepko CL, Finlay BL. Developmental sources of conservation and variation in the evolution of the primate eye. Proc Natl Acad Sci USA Jun 2;106(22):8963-8968, 2009. Epub 2009 May 18.
Cicero SA, Johnson D, Reyntjens S, Frase S, Connell S, Chow LM, Baker SJ, Sorrentino BP, Dyer MA. Cells previously identified as retinal stem cells are pigmented ciliary epithelial cells. Proc Natl Acad Sci USA Apr 21;106(16):6685-90, 2009. Epub 2009 Apr 3.
Martins RAP, Zindy F, Donovan S, Zhang J, Pounds S, Knoepfler PS, Eisenman RN, Roussel M, Dyer MA. N-myc coordinates retinal growth with eye size during mouse development. Genes and Development 15;22(2):179-193, 2008. PMCID: PMC2192753
MacPherson D, Dyer MA. Retinoblastoma: from the two-hit hypothesis to targeted chemotherapy. Cancer Res 67(16):7547-50, 2007.
Johnson DA, Zhang J, Frase S, Dyer MA. Neuronal differentiation and synaptogenesis in retinoblastoma. Cancer Res 67(6):2701-11, 2007.
Laurie N, Donovan S, Gray J, Fuller C, Johnson D, Wilson M, Rodriguez-Galindo C, Marine J-C, Jochemsen AG, Mendrysa S, Dyer MA. Inactivation the p53 pathway in retinoblastoma. Nature 444:61-66, 2006.
Johnson D, Donovan S, Dyer MA. Mosaic deletion of Rb arrests rod differentiation and stimulates ectopic synaptogenesis in the mouse retina. J Comp Neurol 498:112-128, 2006.
Donovan SL, Schweers BA, Zhang J, Martins RA, Johnson DJ, Dyer MA. Compensation by tumor suppressor genes during retinal development in mice and humans. BMC Biology 4:14 (open access), 2006.
Laurie NA, Gray JK, Zhang J, Leggas M, Relling M, Egorin M, Stewart C, Dyer MA. Topotecan combination chemotherapy in two new rodent models of retinoblastoma. Clin Cancer Res 11:7569-7578, 2005.
Dyer MA, Bremner R. The search for the retinoblastoma cell of origin. Nat Rev Cancer 5:91-101, 2005.
Zhang J, Gray J, Wu L, Leone G, Rowan S, Cepko CL, Zhu X, Craft CM, Dyer MA. Rb regulates proliferation and rod photoreceptor development in the mouse retina. Nat Genet 36:351-360, 2004.
Last update: April 2025