The Costello laboratory focuses on genetic and epigenetic mechanisms in gene regulation, as well as technology development and application to stem cells and brain cancer. We apply next-generation sequencing to study DNA methylation, histone methylation, RNA expression, genetic variation and mutations. My laboratory has a long standing interest in understanding how genetic and epigenetic mechanisms regulate gene expression in human cells and tissues during development and during initiation and progression of human brain tumors. We also use deep integration of patient imaging and treatment data with longitudinal genomics of tumor subclones to understand tumor evolution.
Costello JF. Stem Cells: Tips for priming potency (editorial). Nature 2008 July 3, 454, 45-46.
Maunakea AK, Nagarajan, RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielson C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SSJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Evolutionarily Conserved Role of Intragenic DNA Methylation in Regulating Alternative Promoters. Nature, 2010 Jul 8;466(7303):253-7.
Harris RA, Wang T, Coarfa C, Zhou X, Xi Y, Nagarajan RP, Hong C, Downey S, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker J, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Sequence-based profiling of DNA methylation: comparisons of methods and catalogue of allelic epigenetic modifications. Nature Biotechnology 2010 Oct;28(10):1097-105. Epub 2010 Sep 19.
Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, *Costello JF, *Wang T. Exploring long-range genome interactions using the WashU Epigenome Browser. Nat Methods. 2013 May;10(5):375-5. doi: 10.1038/nmeth.2440. *co-corresponding authors
Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, *Costello JF, *Wang T. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet. 2013 May 26. doi: 10.1038/ng.2649. *co-corresponding authors