Joseph Costello, PhD

Professor
Neurological Surgery
+1 415 514-1183

Joseph Costello, PhD studies the onset of tumorigenesis with an emphasis on discovering the mechanisms by which genes accumulate changes that may activate or inactivate tumor genes.

Publications: 

Longitudinal multimodal profiling of IDH-wildtype glioblastoma reveals the molecular evolution and cellular phenotypes underlying prognostically different treatment responses.

Neuro-oncology

Lucas CG, Al-Adli NN, Young JS, Gupta R, Morshed RA, Wu J, Ravindranathan A, Shai A, Oberheim Bush NA, Taylor JW, de Groot J, Villanueva-Meyer JE, Pekmezci M, Perry A, Bollen AW, Theodosopoulos PV, Aghi MK, Chang EF, Hervey-Jumper SL, Raleigh DR, Molinaro AM, Costello JF, Diaz AA, Clarke JL, Butowski NA, Phillips JJ, Chang SM, Berger MS, Solomon DA

Activating the dark genome to illuminate cancer vaccine targets.

Nature genetics

Kwok DW, Okada H, Costello JF

Functional Electrical Stimulation and Brain-Machine Interfaces for Simultaneous Control of Wrist and Finger Flexion.

bioRxiv : the preprint server for biology

Mender MJ, Ward AL, Cubillos LH, Kelberman MM, Costello JT, Temmar H, Wallace DM, Lin ET, Lam JLW, Willsey MS, Ganesh Kumar N, Kung TA, Patil PG, Chestek CA

Deconstructing Intratumoral Heterogeneity through Multiomic and Multiscale Analysis of Serial Sections.

Cancers

Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC

Quantitative assessment of preanalytic variables on clinical evaluation of PI3/AKT/mTOR signaling activity in diffuse glioma.

Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

Beccari S, Mohamed E, Voong V, Hilz S, Lafontaine M, Shai A, Lim Y, Martinez J, Switzman B, Yu RL, Lupo JM, Chang EF, Hervey-Jumper SL, Berger MS, Costello JF, Phillips JJ

Whole tumor analysis reveals early origin of the TERT promoter mutation and intercellular heterogeneity in TERT expression.

Neuro-oncology

Appin CL, Hong C, Suwala AK, Hilz S, Mathur R, Solomon DA, Smirnov IV, Stevers NO, Shai A, Wang A, Berger MS, Chang SM, Phillips JJ, Costello JF

Deconstructing Intratumoral Heterogeneity through Multiomic and Multiscale Analysis of Serial Sections.

bioRxiv : the preprint server for biology

Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC

Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma.

Scientific reports

Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker PB, Naik A, Shai A, Phillips JJ, Chang SM, Wiita AP, Wells JA, Costello JF, Diaz AA, Okada H

Artificial neural network for brain-machine interface consistently produces more naturalistic finger movements than linear methods.

bioRxiv : the preprint server for biology

Temmar H, Willsey MS, Costello JT, Mender MJ, Cubillos LH, Lam JL, Wallace DM, Kelberman MM, Patil PG, Chestek CA

Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective.

Cell

Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, Chang SM, Hervey-Jumper SL, Berger MS, Lupo JM, Okada H, Phillips JJ, Boutros PC, Gallo M, Oldham MC, Yue F, Costello JF

"De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade.

Acta neuropathologica

Hadad S, Gupta R, Oberheim Bush NA, Taylor JW, Villanueva-Meyer JE, Young JS, Wu J, Ravindranathan A, Zhang Y, Warrier G, McCoy L, Shai A, Pekmezci M, Perry A, Bollen AW, Phillips JJ, Braunstein SE, Raleigh DR, Theodosopoulos P, Aghi MK, Chang EF, Hervey-Jumper SL, Costello JF, de Groot J, Butowski NA, Clarke JL, Chang SM, Berger MS, Molinaro AM, Solomon DA

Novel SOX10 indel mutations drive schwannomas through impaired transactivation of myelination gene programs.

Neuro-oncology

Williams EA, Ravindranathan A, Gupta R, Stevers NO, Suwala AK, Hong C, Kim S, Yuan JB, Wu J, Barreto J, Lucas CG, Chan E, Pekmezci M, LeBoit PE, Mully T, Perry A, Bollen A, Van Ziffle J, Devine WP, Reddy AT, Gupta N, Basnet K, Macaulay R, Malafronte P, Lee H, Yong WH, Williams KJ, Juratli TA, Mata DA, Huang RSP, Hiemenz MC, Pavlick DC, Frampton GM, Janovitz T, Ross JS, Chang SM, Berger MS, Jacques L, Song JS, Costello JF, Solomon DA

Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma.

bioRxiv : the preprint server for biology

Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker P, Naik A, Shai A, Phillips JJ, Chang SM, Wiita AP, Wells JA, Costello JF, Diaz AA, Okada H

Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens.

bioRxiv : the preprint server for biology

Kwok DW, Stevers NO, Nejo T, Chen LH, Etxeberria I, Jung J, Okada K, Cove MC, Lakshmanachetty S, Gallus M, Barpanda A, Hong C, Chan GKL, Wu SH, Ramos E, Yamamichi A, Liu J, Watchmaker P, Ogino H, Saijo A, Du A, Grishanina N, Woo J, Diaz A, Chang SM, Phillips JJ, Wiita AP, Klebanoff CA, Costello JF, Okada H

Molecular biomarkers for assessing the heat-adapted phenotype: a narrative scoping review.

The journal of physiological sciences : JPS

Corbett J, Young JS, Tipton MJ, Costello JT, Williams TB, Walker EF, Lee BJ, Stevens CE

Balancing Memorization and Generalization in RNNs for High Performance Brain-Machine Interfaces.

bioRxiv : the preprint server for biology

Costello JT, Temmar H, Cubillos LH, Mender MJ, Wallace DM, Willsey MS, Patil PG, Chestek CA

Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance.

Clinical cancer research : an official journal of the American Association for Cancer Research

Carney SV, Banerjee K, Mujeeb A, Zhu B, Haase S, Varela ML, Kadiyala P, Tronrud CE, Zhu Z, Mukherji D, Gorla P, Sun Y, Tagett R, N??ez FJ, Luo M, Luo W, Ljungman M, Liu Y, Xia Z, Schwendeman A, Qin T, Sartor MA, Costello JF, Cahill DP, Lowenstein PR, Castro MG

Hyperpolarized d-[1- 13C]gluconolactone imaging visualizes response to TERT or GABPB1 targeting therapy for glioblastoma.

Scientific reports

Minami N, Hong D, Taglang C, Batsios G, Gillespie AM, Viswanath P, Stevers N, Barger CJ, Costello JF, Ronen SM

Single-cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects.

The Journal of clinical investigation

Jain S, Rick JW, Joshi RS, Beniwal A, Spatz J, Gill S, Chang AC, Choudhary N, Nguyen AT, Sudhir S, Chalif EJ, Chen JS, Chandra A, Haddad AF, Wadhwa H, Shah SS, Choi S, Hayes JL, Wang L, Yagnik G, Costello JF, Diaz A, Heiland DH, Aghi MK

Isocitrate dehydrogenase (IDH) mutant gliomas: A Society for Neuro-Oncology (SNO) consensus review on diagnosis, management, and future directions.

Neuro-oncology

Miller JJ, Gonzalez Castro LN, McBrayer S, Weller M, Cloughesy T, Portnow J, Andronesi O, Barnholtz-Sloan JS, Baumert BG, Berger MS, Bi WL, Bindra R, Cahill DP, Chang SM, Costello JF, Horbinski C, Huang RY, Jenkins RB, Ligon KL, Mellinghoff IK, Nabors LB, Platten M, Reardon DA, Shi DD, Schiff D, Wick W, Yan H, von Deimling A, van den Bent M, Kaelin WG, Wen PY

TERT promoter C228T mutation in neural progenitors confers growth advantage following telomere shortening in vivo.

Neuro-oncology

Miki S, Koga T, Mckinney AM, Parisian AD, Tadokoro T, Vadla R, Marsala M, Hevner RF, Costello JF, Furnari F

Real-time brain-machine interface in non-human primates achieves high-velocity prosthetic finger movements using a shallow feedforward neural network decoder.

Nature communications

Willsey MS, Nason-Tomaszewski SR, Ensel SR, Temmar H, Mender MJ, Costello JT, Patil PG, Chestek CA

Imaging biomarkers of TERT or GABPB1 silencing in TERT-positive glioblastoma.

Neuro-oncology

Minami N, Hong D, Stevers N, Barger CJ, Radoul M, Hong C, Chen L, Kim Y, Batsios G, Gillespie AM, Pieper RO, Costello JF, Viswanath P, Ronen SM

GABP couples oncogene signaling to telomere regulation in TERT promoter mutant cancer.

Cell reports

McKinney AM, Mathur R, Stevers NO, Molinaro AM, Chang SM, Phillips JJ, Costello JF

Conserved features of TERT promoter duplications reveal an activation mechanism that mimics hotspot mutations in cancer.

Nature communications

Barger CJ, Suwala AK, Soczek KM, Wang AS, Kim MY, Hong C, Doudna JA, Chang SM, Phillips JJ, Solomon DA, Costello JF

PI3K/AKT/mTOR signaling pathway activity in IDH-mutant diffuse glioma and clinical implications.

Neuro-oncology

Mohamed E, Kumar A, Zhang Y, Wang AS, Chen K, Lim Y, Shai A, Taylor JW, Clarke J, Hilz S, Berger MS, Solomon DA, Costello JF, Molinaro AM, Phillips JJ

Deuterium Metabolic Imaging Reports on TERT Expression and Early Response to Therapy in Cancer.

Clinical cancer research : an official journal of the American Association for Cancer Research

Batsios G, Taglang C, Tran M, Stevers N, Barger C, Gillespie AM, Ronen SM, Costello JF, Viswanath P

Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1.

Acta neuropathologica

Lucas CG, Sloan EA, Gupta R, Wu J, Pratt D, Vasudevan HN, Ravindranathan A, Barreto J, Williams EA, Shai A, Whipple NS, Bruggers CS, Maher O, Nabors B, Rodriguez M, Samuel D, Brown M, Carmichael J, Lu R, Mirchia K, Sullivan DV, Pekmezci M, Tihan T, Bollen AW, Perry A, Banerjee A, Mueller S, Gupta N, Hervey-Jumper SL, Oberheim Bush NA, Daras M, Taylor JW, Butowski NA, de Groot J, Clarke JL, Raleigh DR, Costello JF, Phillips JJ, Reddy AT, Chang SM, Berger MS, Solomon DA

Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.

Nature genetics

Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW, Qiu Z, Martin MV, Susko MS, Braunstein SE, Bush NAO, Schulte JD, Butowski N, Sneed PK, Berger MS, Krogan NJ, Perry A, Phillips JJ, Solomon DA, Costello JF, McDermott MW, Rich JN, Raleigh DR

Spatial concordance of DNA methylation classification in diffuse glioma.

Neuro-oncology

Verburg N, Barthel FP, Anderson KJ, Johnson KC, Koopman T, Yaqub MM, Hoekstra OS, Lammertsma AA, Barkhof F, Pouwels PJW, Reijneveld JC, Rozemuller AJM, Beli?n JAM, Boellaard R, Taylor MD, Das S, Costello JF, Vandertop WP, Wesseling P, de Witt Hamer PC, Verhaak RGW

Temozolomide-induced hypermutation is associated with distant recurrence and reduced survival after high-grade transformation of low-grade IDH-mutant gliomas.

Neuro-oncology

Yu Y, Villanueva-Meyer J, Grimmer MR, Hilz S, Solomon DA, Choi S, Wahl M, Mazor T, Hong C, Shai A, Phillips JJ, Wainer BH, McDermott M, Haas-Kogan D, Taylor JW, Butowski N, Clarke JL, Berger MS, Molinaro AM, Chang SM, Costello JF, Oberheim Bush NA

Metabolic imaging detects elevated glucose flux through the pentose phosphate pathway associated with TERT expression in low-grade gliomas.

Neuro-oncology

Viswanath P, Batsios G, Ayyappan V, Taglang C, Gillespie AM, Larson PEZ, Luchman HA, Costello JF, Pieper RO, Ronen SM

The Placenta - Fast, Loose, and in Control.

The New England journal of medicine

Costello JF, Fisher SJ

Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease.

Developmental cell

Zhang B, Kim MY, Elliot G, Zhou Y, Zhao G, Li D, Lowdon RF, Gormley M, Kapidzic M, Robinson JF, McMaster MT, Hong C, Mazor T, Hamilton E, Sears RL, Pehrsson EC, Marra MA, Jones SJM, Bilenky M, Hirst M, Wang T, Costello JF, Fisher SJ

Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors.

Neuro-oncology

Manjunath M, Yan J, Youn Y, Drucker KL, Kollmeyer TM, McKinney AM, Zazubovich V, Zhang Y, Costello JF, Eckel-Passow J, Selvin PR, Jenkins RB, Song JS

Cancer-specific loss of TERT activation sensitizes glioblastoma to DNA damage.

Proceedings of the National Academy of Sciences of the United States of America

Amen AM, Fellmann C, Soczek KM, Ren SM, Lew RJ, Knott GJ, Park JE, McKinney AM, Mancini A, Doudna JA, Costello JF

miRNA-independent function of long noncoding pri-miRNA loci.

Proceedings of the National Academy of Sciences of the United States of America

He D, Wu D, Muller S, Wang L, Saha P, Ahanger SH, Liu SJ, Cui M, Hong SJ, Jain M, Olson HE, Akeson M, Costello JF, Diaz A, Lim DA

Unique challenges for glioblastoma immunotherapy-discussions across neuro-oncology and non-neuro-oncology experts in cancer immunology. Meeting Report from the 2019 SNO Immuno-Oncology Think Tank.

Neuro-oncology

Chuntova P, Chow F, Watchmaker PB, Galvez M, Heimberger AB, Newell EW, Diaz A, DePinho RA, Li MO, Wherry EJ, Mitchell D, Terabe M, Wainwright DA, Berzofsky JA, Herold-Mende C, Heath JR, Lim M, Margolin KA, Chiocca EA, Kasahara N, Ellingson BM, Brown CE, Chen Y, Fecci PE, Reardon DA, Dunn GP, Liau LM, Costello JF, Wick W, Cloughesy T, Timmer WC, Wen PY, Prins RM, Platten M, Okada H

Early Noninvasive Metabolic Biomarkers of Mutant IDH Inhibition in Glioma.

Metabolites

Radoul M, Hong D, Gillespie AM, Najac C, Viswanath P, Pieper RO, Costello JF, Luchman HA, Ronen SM

Non-invasive assessment of telomere maintenance mechanisms in brain tumors.

Nature communications

Viswanath P, Batsios G, Mukherjee J, Gillespie AM, Larson PEZ, Luchman HA, Phillips JJ, Costello JF, Pieper RO, Ronen SM

Prostate Cancer Progression and the Epigenome.

The New England journal of medicine

Arap W, Pasqualini R, Costello JF

MGMT promoter methylation level in newly diagnosed low-grade glioma is a predictor of hypermutation at recurrence.

Neuro-oncology

Mathur R, Zhang Y, Grimmer MR, Hong C, Zhang M, Bollam S, Petrecca K, Clarke J, Berger MS, Phillips JJ, Oberheim-Bush NA, Molinaro AM, Chang SM, Costello JF

Multiplatform genomic profiling and magnetic resonance imaging identify mechanisms underlying intratumor heterogeneity in meningioma.

Nature communications

Magill ST, Vasudevan HN, Seo K, Villanueva-Meyer JE, Choudhury A, John Liu S, Pekmezci M, Findakly S, Hilz S, Lastella S, Demaree B, Braunstein SE, Bush NAO, Aghi MK, Theodosopoulos PV, Sneed PK, Abate AR, Berger MS, McDermott MW, Lim DA, Ullian EM, Costello JF, Raleigh DR

Glutamate Is a Noninvasive Metabolic Biomarker of IDH1-Mutant Glioma Response to Temozolomide Treatment.

Cancer research

Subramani E, Radoul M, Najac C, Batsios G, Molloy AR, Hong D, Gillespie AM, Santos RD, Viswanath P, Costello JF, Pieper RO, Ronen SM

Epigenomic programming in early fetal brain development.

Epigenomics

Li L, Maire CL, Bilenky M, Carles A, Heravi-Moussavi A, Hong C, Tam A, Kamoh B, Cho S, Cheung D, Li I, Wong T, Nagarajan RP, Mungall AJ, Moore R, Wang T, Kleinman CL, Jabado N, Jones SJ, Marra MA, Ligon KL, Costello JF, Hirst M

Patient-derived cells from recurrent tumors that model the evolution of IDH-mutant glioma.

Neuro-oncology advances

Jones LE, Hilz S, Grimmer MR, Mazor T, Najac C, Mukherjee J, McKinney A, Chow T, Pieper RO, Ronen SM, Chang SM, Phillips JJ, Costello JF

The DNA methylation landscape of advanced prostate cancer.

Nature genetics

Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sj?str?m M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY

Gliomas arising in the setting of Li-Fraumeni syndrome stratify into two molecular subgroups with divergent clinicopathologic features.

Acta neuropathologica

Sloan EA, Hilz S, Gupta R, Cadwell C, Ramani B, Hofmann J, Kline CN, Banerjee A, Reddy A, Oberheim Bush NA, Chang S, Braunstein S, Chang EF, Raffel C, Gupta N, Sun PP, Kim JYH, Moes G, Alva E, Li R, Bruggers CS, Alashari M, Wetmore C, Garg S, Dishop M, Van Ziffle J, Onodera C, Devine P, Grenert JP, Lee JC, Phillips JJ, Pekmezci M, Tihan T, Bollen AW, Berger MS, Costello JF, Perry A, Solomon DA

Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma.

Cell reports

Liu SJ, Magill ST, Vasudevan HN, Hilz S, Villanueva-Meyer JE, Lastella S, Daggubati V, Spatz J, Choudhury A, Orr BA, Demaree B, Seo K, Ferris SP, Abate AR, Oberheim Bush NA, Bollen AW, McDermott MW, Costello JF, Raleigh DR

Proceedings of the Comprehensive Oncology Network Evaluating Rare CNS Tumors (NCI-CONNECT) Oligodendroglioma Workshop.

Neuro-oncology advances

Penas-Prado M, Wu J, Cahill DP, Brat DJ, Costello JF, Kluetz PG, Cairncross JG, van den Bent M, Verhaak RGW, Aboud O, Burger P, Chang SM, Cordova C, Huang RY, Rowe LS, Taphoorn MJB, Gilbert MR, Armstrong TS, NCI-CONNECT Oligodendroglioma Workshop

Longitudinal molecular trajectories of diffuse glioma in adults.

Nature

Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW, GLASS Consortium

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.

Nature communications

Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N

Recurrent KBTBD4 small in-frame insertions and absence of DROSHA deletion or DICER1 mutation differentiate pineal parenchymal tumor of intermediate differentiation (PPTID) from pineoblastoma.

Acta neuropathologica

Lee JC, Mazor T, Lao R, Wan E, Diallo AB, Hill NS, Thangaraj N, Wendelsdorf K, Samuel D, Kline CN, Banerjee A, Auguste K, Raffel C, Gupta N, Berger M, Raleigh DR, Shai A, Phillips JJ, Bollen AW, Tihan T, Perry A, Costello J, Solomon DA

Genomic Profiling of BDE-47 Effects on Human Placental Cytotrophoblasts.

Toxicological sciences : an official journal of the Society of Toxicology

Robinson JF, Kapidzic M, Hamilton EG, Chen H, Puckett KW, Zhou Y, Ona K, Parry E, Wang Y, Park JS, Costello JF, Fisher SJ

Disruption of the �1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner.

Cancer cell

Mancini A, Xavier-Magalh?es A, Woods WS, Nguyen KT, Amen AM, Hayes JL, Fellmann C, Gapinske M, McKinney AM, Hong C, Jones LE, Walsh KM, Bell RJA, Doudna JA, Costa BM, Song JS, Perez-Pinera P, Costello JF

Temozolomide-associated hypermutation in gliomas.

Neuro-oncology

Choi S, Yu Y, Grimmer MR, Wahl M, Chang SM, Costello JF

To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes.

Frontiers in genetics

Wallace AD, Wendt GA, Barcellos LF, de Smith AJ, Walsh KM, Metayer C, Costello JF, Wiemels JL, Francis SS

Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas.

Neuro-oncology

Hayes J, Yu Y, Jalbert LE, Mazor T, Jones LE, Wood MD, Walsh KM, Bengtsson H, Hong C, Oberndorfer S, Roetzer T, Smirnov IV, Clarke JL, Aghi MK, Chang SM, Nelson SJ, Woehrer A, Phillips JJ, Solomon DA, Costello JF

The long non-coding RNA HOTAIR is transcriptionally activated by HOXA9 and is an independent prognostic marker in patients with malignant glioma.

Oncotarget

Xavier-Magalhães A, Gonçalves CS, Fogli A, Lourenço T, Pojo M, Pereira B, Rocha M, Lopes MC, Crespo I, Rebelo O, Tão H, Lima J, Moreira R, Pinto AA, Jones C, Reis RM, Costello JF, Arnaud P, Sousa N, Costa BM

Genome-wide DNA methylation is predictive of outcome in juvenile myelomonocytic leukemia.

Nature communications

Stieglitz E, Mazor T, Olshen AB, Geng H, Gelston LC, Akutagawa J, Lipka DB, Plass C, Flotho C, Chehab FF, Braun BS, Costello JF, Loh ML

Antigenic expression and spontaneous immune responses support the use of a selected peptide set from the IMA950 glioblastoma vaccine for immunotherapy of grade II and III glioma.

Oncoimmunology

Dutoit V, Migliorini D, Ranzanici G, Marinari E, Widmer V, Lobrinus JA, Momjian S, Costello J, Walker PR, Okada H, Weinschenk T, Herold-Mende C, Dietrich PY

Comprehensive Analysis of Hypermutation in Human Cancer.

Cell

Campbell BB, Light N, Fabrizio D, Zatzman M, Fuligni F, de Borja R, Davidson S, Edwards M, Elvin JA, Hodel KP, Zahurancik WJ, Suo Z, Lipman T, Wimmer K, Kratz CP, Bowers DC, Laetsch TW, Dunn GP, Johanns TM, Grimmer MR, Smirnov IV, Larouche V, Samuel D, Bronsema A, Osborn M, Stearns D, Raman P, Cole KA, Storm PB, Yalon M, Opocher E, Mason G, Thomas GA, Sabel M, George B, Ziegler DS, Lindhorst S, Issai VM, Constantini S, Toledano H, Elhasid R, Farah R, Dvir R, Dirks P, Huang A, Galati MA, Chung J, Ramaswamy V, Irwin MS, Aronson M, Durno C, Taylor MD, Rechavi G, Maris JM, Bouffet E, Hawkins C, Costello JF, Meyn MS, Pursell ZF, Malkin D, Tabori U, Shlien A

Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1.

Proceedings of the National Academy of Sciences of the United States of America

Mazor T, Chesnelong C, Pankov A, Jalbert LE, Hong C, Hayes J, Smirnov IV, Marshall R, Souza CF, Shen Y, Viswanath P, Noushmehr H, Ronen SM, Jones SJM, Marra MA, Cairncross JG, Perry A, Nelson SJ, Chang SM, Bollen AW, Molinaro AM, Bengtsson H, Olshen AB, Weiss S, Phillips JJ, Luchman HA, Costello JF

Treatment-Induced Mutagenesis and Selective Pressures Sculpt Cancer Evolution.

Cold Spring Harbor perspectives in medicine

Venkatesan S, Swanton C, Taylor BS, Costello JF

Probing the phosphatidylinositol 3-kinase/mammalian target of rapamycin pathway in gliomas: A phase 2 study of everolimus for recurrent adult low-grade gliomas.

Cancer

Wahl M, Chang SM, Phillips JJ, Molinaro AM, Costello JF, Mazor T, Alexandrescu S, Lupo JM, Nelson SJ, Berger M, Prados M, Taylor JW, Butowski N, Clarke JL, Haas-Kogan D

DNA methylation: an epigenetic mark of cellular memory.

Experimental & molecular medicine

Kim M, Costello J

Isocitrate dehydrogenase mutations suppress STAT1 and CD8+ T cell accumulation in gliomas.

The Journal of clinical investigation

Kohanbash G, Carrera DA, Shrivastav S, Ahn BJ, Jahan N, Mazor T, Chheda ZS, Downey KM, Watchmaker PB, Beppler C, Warta R, Amankulor NA, Herold-Mende C, Costello JF, Okada H

Chemotherapy for adult low-grade gliomas: clinical outcomes by molecular subtype in a phase II study of adjuvant temozolomide.

Neuro-oncology

Wahl M, Phillips JJ, Molinaro AM, Lin Y, Perry A, Haas-Kogan DA, Costello JF, Dayal M, Butowski N, Clarke JL, Prados M, Nelson S, Berger MS, Chang SM

Effect of acute hypoxia on cognition: A systematic review and meta-regression analysis.

Neuroscience and biobehavioral reviews

McMorris T, Hale BJ, Barwood M, Costello J, Corbett J

Mutant IDH1 Expression Drives TERT Promoter Reactivation as Part of the Cellular Transformation Process.

Cancer research

Ohba S, Mukherjee J, Johannessen TC, Mancini A, Chow TT, Wood M, Jones L, Mazor T, Marshall RE, Viswanath P, Walsh KM, Perry A, Bell RJ, Phillips JJ, Costello JF, Ronen SM, Pieper RO

Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors.

Clinical cancer research : an official journal of the American Association for Cancer Research

Sherborne AL, Lavergne V, Yu K, Lee L, Davidson PR, Mazor T, Smirnoff IV, Horvai AE, Loh M, DuBois SG, Goldsby RE, Neglia JP, Hammond S, Robison LL, Wustrack R, Costello JF, Nakamura AO, Shannon KM, Bhatia S, Nakamura JL

Mutant IDH1 expression is associated with down-regulation of monocarboxylate transporters.

Oncotarget

Viswanath P, Najac C, Izquierdo-Garcia JL, Pankov A, Hong C, Eriksson P, Costello JF, Pieper RO, Ronen SM

Intratumoral Heterogeneity of the Epigenome.

Cancer cell

Mazor T, Pankov A, Song JS, Costello JF

Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome.

G3 (Bethesda, Md.)

Gu J, Stevens M, Xing X, Li D, Zhang B, Payton JE, Oltz EM, Jarvis JN, Jiang K, Cicero T, Costello JF, Wang T

Understanding TERT Promoter Mutations: A Common Path to Immortality.

Molecular cancer research : MCR

Bell RJ, Rube HT, Xavier-Magalh?es A, Costa BM, Mancini A, Song JS, Costello JF

Corrigendum: The genomic landscape of juvenile myelomonocytic leukemia.

Nature genetics

Stieglitz E, Taylor-Weiner AN, Chang TY, Gelston LC, Wang YD, Mazor T, Esquivel E, Yu A, Seepo S, Olsen SR, Rosenberg M, Archambeault SL, Abusin G, Beckman K, Brown PA, Briones M, Carcamo B, Cooper T, Dahl GV, Emanuel PD, Fluchel MN, Goyal RK, Hayashi RJ, Hitzler J, Hugge C, Liu YL, Messinger YH, Mahoney DH, Monteleone P, Nemecek ER, Roehrs PA, Schore RJ, Stine KC, Takemoto CM, Toretsky JA, Costello JF, Olshen AB, Stewart C, Li Y, Ma J, Gerbing RB, Alonzo TA, Getz G, Gruber TA, Golub TR, Stegmaier K, Loh ML

Cancer: Oncogene brought into the loop.

Nature

Grimmer MR, Costello JF

The genomic landscape of juvenile myelomonocytic leukemia.

Nature genetics

Stieglitz E, Taylor-Weiner AN, Chang TY, Gelston LC, Wang YD, Mazor T, Esquivel E, Yu A, Seepo S, Olsen S, Rosenberg M, Archambeault SL, Abusin G, Beckman K, Brown PA, Briones M, Carcamo B, Cooper T, Dahl GV, Emanuel PD, Fluchel MN, Goyal RK, Hayashi RJ, Hitzler J, Hugge C, Liu YL, Messinger YH, Mahoney DH, Monteleone P, Nemecek ER, Roehrs PA, Schore RJ, Stine KC, Takemoto CM, Toretsky JA, Costello JF, Olshen AB, Stewart C, Li Y, Ma J, Gerbing RB, Alonzo TA, Getz G, Gruber T, Golub T, Stegmaier K, Loh ML

DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors.

Cancer cell

Mazor T, Pankov A, Johnson BE, Hong C, Hamilton EG, Bell RJA, Smirnov IV, Reis GF, Phillips JJ, Barnes MJ, Idbaih A, Alentorn A, Kloezeman JJ, Lamfers MLM, Bollen AW, Taylor BS, Molinaro AM, Olshen AB, Chang SM, Song JS, Costello JF

Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer.

Science (New York, N.Y.)

Bell RJ, Rube HT, Kreig A, Mancini A, Fouse SD, Nagarajan RP, Choi S, Hong C, He D, Pekmezci M, Wiencke JK, Wrensch MR, Chang SM, Walsh KM, Myong S, Song JS, Costello JF

Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser.

Nature biotechnology

Zhou X, Li D, Zhang B, Lowdon RF, Rockweiler NB, Sears RL, Madden PA, Smirnov I, Costello JF, Wang T

Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment.

Acta neuropathologica

van Thuijl HF, Mazor T, Johnson BE, Fouse SD, Aihara K, Hong C, Malmstr?m A, Hallbeck M, Heimans JJ, Kloezeman JJ, Stenmark-Askmalm M, Lamfers ML, Saito N, Aburatani H, Mukasa A, Berger MS, S?derkvist P, Taylor BS, Molinaro AM, Wesseling P, Reijneveld JC, Chang SM, Ylstra B, Costello JF

Integrative analysis of 111 reference human epigenomes.

Nature

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M

Epigenetic and transcriptional determinants of the human breast.

Nature communications

Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M

Intermediate DNA methylation is a conserved signature of genome regulation.

Nature communications

Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF

HIGD1A Regulates Oxygen Consumption, ROS Production, and AMPK Activity during Glucose Deprivation to Modulate Cell Survival and Tumor Growth.

Cell reports

Ameri K, Jahangiri A, Rajah AM, Tormos KV, Nagarajan R, Pekmezci M, Nguyen V, Wheeler ML, Murphy MP, Sanders TA, Jeffrey SS, Yeghiazarians Y, Rinaudo PF, Costello JF, Aghi MK, Maltepe E

The genetics of splicing in neuroblastoma.

Cancer discovery

Chen J, Hackett CS, Zhang S, Song YK, Bell RJ, Molinaro AM, Quigley DA, Balmain A, Song JS, Costello JF, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA

Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.

Nature communications

Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB

Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes.

Cell reports

Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, Liao W, Oh DH, Cleaver JE, LeBoit PE, Costello JF, Lehmann AR, Gray JW, Spellman PT, Arron ST, Huh N, Purdom E, Cho RJ

A single-institution phase II trial of radiation, temozolomide, erlotinib, and bevacizumab for initial treatment of glioblastoma.

Neuro-oncology

Clarke JL, Molinaro AM, Phillips JJ, Butowski NA, Chang SM, Perry A, Costello JF, DeSilva AA, Rabbitt JE, Prados MD

methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser.

Bioinformatics (Oxford, England)

Zhou X, Li D, Lowdon RF, Costello JF, Wang T

Recurrent epimutations activate gene body promoters in primary glioblastoma.

Genome research

Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF

Whole-body cryotherapy: empirical evidence and theoretical perspectives.

Open access journal of sports medicine

Bleakley CM, Bieuzen F, Davison GW, Costello JT

Paediatric and adult glioblastoma: multiform (epi)genomic culprits emerge.

Nature reviews. Cancer

Sturm D, Bender S, Jones DT, Lichter P, Grill J, Becher O, Hawkins C, Majewski J, Jones C, Costello JF, Iavarone A, Aldape K, Brennan CW, Jabado N, Pfister SM

ALEA: a toolbox for allele-specific epigenomics analysis.

Bioinformatics (Oxford, England)

Younesy H, M?ller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJ

Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma.

Science (New York, N.Y.)

Johnson BE, Mazor T, Hong C, Barnes M, Aihara K, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao Y, Moore RA, Mungall AJ, Jones SJM, Hirst M, Marra MA, Saito N, Aburatani H, Mukasa A, Berger MS, Chang SM, Taylor BS, Costello JF

Where are we now? And where are we going? A report from the Accelerate Brain Cancer Cure (ABC2) low-grade glioma research workshop.

Neuro-oncology

Huse JT, Wallace M, Aldape KD, Berger MS, Bettegowda C, Brat DJ, Cahill DP, Cloughesy T, Haas-Kogan DA, Marra M, Miller CR, Nelson SJ, Salama SR, Soffietti R, Wen PY, Yip S, Yen K, Costello JF, Chang S

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

Nature biotechnology

Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK

Early epigenetic downregulation of WNK2 kinase during pancreatic ductal adenocarcinoma development.

Oncogene

Dutruel C, Bergmann F, Rooman I, Zucknick M, Weichenhan D, Geiselhart L, Kaffenberger T, Rachakonda PS, Bauer A, Giese N, Hong C, Xie H, Costello JF, Hoheisel J, Kumar R, Rehli M, Schirmacher P, Werner J, Plass C, Popanda O, Schmezer P

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.

Genome research

Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.

Genome research

Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Maire CL, Ligon KL, Madden PA, Tam A, Moore R, Hirst M, Marra MA, Zhang B, Costello JF, Wang T

Cancer Stem Cells Activate STAT3 the EZ Way.

Cancer cell

Fouse SD, Costello JF

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.

Nature genetics

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

Exploring long-range genome interactions using the WashU Epigenome Browser.

Nature methods

Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello JF, Wang T

Methods for cancer epigenome analysis.

Advances in experimental medicine and biology

Nagarajan RP, Fouse SD, Bell RJ, Costello JF

A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.

Cancer research

Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA, AACR Cancer Epigenome Task Force

Loss of WNK2 expression by promoter gene methylation occurs in adult gliomas and triggers Rac1-mediated tumour cell invasiveness.

Human molecular genetics

Moniz S, Martinho O, Pinto F, Sousa B, Loureiro C, Oliveira MJ, Moita LF, Honavar M, Pinheiro C, Pires M, Lopes JM, Jones C, Costello JF, Paredes J, Reis RM, Jordan P

Spark: a navigational paradigm for genomic data exploration.

Genome research

Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Nature

Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S

Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3.

The pharmacogenomics journal

Chen L, Hong C, Chen EC, Yee SW, Xu L, Almof EU, Wen C, Fujii K, Johns SJ, Stryke D, Ferrin TE, Simko J, Chen X, Costello JF, Giacomini KM

The Human Epigenome Browser at Washington University.

Nature methods

Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PA, Costello JF, Wang T

Phase II and pharmacogenomics study of enzastaurin plus temozolomide during and following radiation therapy in patients with newly diagnosed glioblastoma multiforme and gliosarcoma.

Neuro-oncology

Butowski N, Chang SM, Lamborn KR, Polley MY, Pieper R, Costello JF, Vandenberg S, Parvataneni R, Nicole A, Sneed PK, Clarke J, Hsieh E, Costa BM, Reis RM, Hristova-Kazmierski M, Nicol SJ, Thornton DE, Prados MD

Epigenetic silencing of MIR203 in multiple myeloma.

British journal of haematology

Wong KY, Liang R, So CC, Jin DY, Costello JF, Chim CS

Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells.

Nature cell biology

Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M

The A/G allele of rs16906252 predicts for MGMT methylation and is selectively silenced in premalignant lesions from smokers and in lung adenocarcinomas.

Clinical cancer research : an official journal of the American Association for Cancer Research

Leng S, Bernauer AM, Hong C, Do KC, Yingling CM, Flores KG, Tessema M, Tellez CS, Willink RP, Burki EA, Picchi MA, Stidley CA, Prados MD, Costello JF, Gilliland FD, Crowell RE, Belinsky SA

Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.

PloS one

Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ

The NIH Roadmap Epigenomics Mapping Consortium.

Nature biotechnology

Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Nature biotechnology

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, 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 JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF

Conserved role of intragenic DNA methylation in regulating alternative promoters.

Nature

Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF

A hierarchy of self-renewing tumor-initiating cell types in glioblastoma.

Cancer cell

Chen R, Nishimura MC, Bumbaca SM, Kharbanda S, Forrest WF, Kasman IM, Greve JM, Soriano RH, Gilmour LL, Rivers CS, Modrusan Z, Nacu S, Guerrero S, Edgar KA, Wallin JJ, Lamszus K, Westphal M, Heim S, James CD, VandenBerg SR, Costello JF, Moorefield S, Cowdrey CJ, Prados M, Phillips HS

Genome-scale DNA methylation analysis.

Epigenomics

Fouse SD, Nagarajan RO, Costello JF

Epigenetic inactivation of the miR-34a in hematological malignancies.

Carcinogenesis

Chim CS, Wong KY, Qi Y, Loong F, Lam WL, Wong LG, Jin DY, Costello JF, Liang R

Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma.

Cancer research

Costa BM, Smith JS, Chen Y, Chen J, Phillips HS, Aldape KD, Zardo G, Nigro J, James CD, Fridlyand J, Reis RM, Costello JF

A first look at entire human methylomes.

Nature biotechnology

Costello JF, Krzywinski M, Marra MA

Epigenetics of neurological cancers.

Future oncology (London, England)

Fouse SD, Costello JF

Molecular epigenetics and genetics in neuro-oncology.

Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics

Nagarajan RP, Costello JF

Epigenetic mechanisms in glioblastoma multiforme.

Seminars in cancer biology

Nagarajan RP, Costello JF

Food allergy is associated with an increased risk of asthma.

Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology

Schroeder A, Kumar R, Pongracic JA, Sullivan CL, Caruso DM, Costello J, Meyer KE, Vucic Y, Gupta R, Kim JS, Fuleihan R, Wang X

Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis.

Methods in molecular biology (Clifton, N.J.)

Costello JF, Hong C, Plass C, Smiraglia DJ

Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific.

Neuro-oncology

Jun P, Hong C, Lal A, Wong JM, McDermott MW, Bollen AW, Plass C, Held WA, Smiraglia DJ, Costello JF

Familial aggregation of food allergy and sensitization to food allergens: a family-based study.

Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology

Tsai HJ, Kumar R, Pongracic J, Liu X, Story R, Yu Y, Caruso D, Costello J, Schroeder A, Fang Y, Demirtas H, Meyer KE, O'Gorman MR, Wang X

Abnormal DNA methylation of CD133 in colorectal and glioblastoma tumors.

Cancer research

Yi JM, Tsai HC, Glöckner SC, Lin S, Ohm JE, Easwaran H, James CD, Costello JF, Riggins G, Eberhart CG, Laterra J, Vescovi AL, Ahuja N, Herman JG, Schuebel KE, Baylin SB

miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells.

BMC medicine

Silber J, Lim DA, Petritsch C, Persson AI, Maunakea AK, Yu M, Vandenberg SR, Ginzinger DG, James CD, Costello JF, Bergers G, Weiss WA, Alvarez-Buylla A, Hodgson JG

A sequence-based survey of the complex structural organization of tumor genomes.

Genome biology

Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC

Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.

BMC genomics

Smiraglia DJ, Kazhiyur-Mannar R, Oakes CC, Wu YZ, Liang P, Ansari T, Su J, Rush LJ, Smith LT, Yu L, Liu C, Dai Z, Chen SS, Wang SH, Costello J, Ioshikhes I, Dawson DW, Hong JS, Teitell MA, Szafranek A, Camoriano M, Song F, Elliott R, Held W, Trasler JM, Plass C, Wenger R

Molecular signatures define two main classes of meningiomas.

Molecular cancer

Carvalho LH, Smirnov I, Baia GS, Modrusan Z, Smith JS, Jun P, Costello JF, McDermott MW, Vandenberg SR, Lal A

Identification of DNA methylation in 3' genomic regions that are associated with upregulation of gene expression in colorectal cancer.

Epigenetics

Smith JF, Mahmood S, Song F, Morrow A, Smiraglia D, Zhang X, Rajput A, Higgins MJ, Krumm A, Petrelli NJ, Costello JF, Nagase H, Plass C, Held WA

Epigenome scans and cancer genome sequencing converge on WNK2, a kinase-independent suppressor of cell growth.

Proceedings of the National Academy of Sciences of the United States of America

Hong C, Moorefield KS, Jun P, Aldape KD, Kharbanda S, Phillips HS, Costello JF

Genome-epigenome interactions in cancer.

Human molecular genetics

Brena RM, Costello JF

Mining methylation for early detection of common cancers.

PLoS medicine

Brena RM, Plass C, Costello JF

Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells.

The Journal of biological chemistry

Reynolds PA, Sigaroudinia M, Zardo G, Wilson MB, Benton GM, Miller CJ, Hong C, Fridlyand J, Costello JF, Tlsty TD

A broad band of silence.

Nature genetics

Smith JS, Costello JF

DNA motifs associated with aberrant CpG island methylation.

Genomics

Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM

Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancer.

Genetic testing

Chen Y, Toland AE, McLennan J, Fridlyand J, Crawford B, Costello JF, Ziegler JL

Meningioma transcript profiles reveal deregulated Notch signaling pathway.

Cancer research

Cuevas IC, Slocum AL, Jun P, Costello JF, Bollen AW, Riggins GJ, McDermott MW, Lal A

Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3.

Nature genetics

Ching TT, Maunakea AK, Jun P, Hong C, Zardo G, Pinkel D, Albertson DG, Fridlyand J, Mao JH, Shchors K, Weiss WA, Costello JF

Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8.

Cancer research

Hong C, Maunakea A, Jun P, Bollen AW, Hodgson JG, Goldenberg DD, Weiss WA, Costello JF

Comparative epigenomics of leukemia.

Nature genetics

Costello JF

Phosphatase and tensin homologue growth suppression without phosphatase.

Proceedings of the National Academy of Sciences of the United States of America

Stokoe D, Costello JF

SOCS-3 is frequently silenced by hypermethylation and suppresses cell growth in human lung cancer.

Proceedings of the National Academy of Sciences of the United States of America

He B, You L, Uematsu K, Zang K, Xu Z, Lee AY, Costello JF, McCormick F, Jablons DM

Predicting aberrant CpG island methylation.

Proceedings of the National Academy of Sciences of the United States of America

Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM

DNA methylation in brain development and gliomagenesis.

Frontiers in bioscience : a journal and virtual library

Costello JF

Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors.

Nature genetics

Zardo G, Tiirikainen MI, Hong C, Misra A, Feuerstein BG, Volik S, Collins CC, Lamborn KR, Bollen A, Pinkel D, Albertson DG, Costello JF

Methylation matters: a new spin on maspin.

Nature genetics

Costello JF, Vertino PM

Restriction landmark genome scanning.

Methods (San Diego, Calif.)

Costello JF, Smiraglia DJ, Plass C

Restriction landmark genome scanning.

Methods in molecular biology (Clifton, N.J.)

Costello JF, Plass C, Cavenee WK

Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies.

Human molecular genetics

Smiraglia DJ, Rush LJ, Frühwald MC, Dai Z, Held WA, Costello JF, Lang JC, Eng C, Li B, Wright FA, Caligiuri MA, Plass C

Novel methylation targets in de novo acute myeloid leukemia with prevalence of chromosome 11 loci.

Blood

Rush LJ, Dai Z, Smiraglia DJ, Gao X, Wright FA, Frühwald M, Costello JF, Held WA, Yu L, Krahe R, Kolitz JE, Bloomfield CD, Caligiuri MA, Plass C

Methylation matters.

Journal of medical genetics

Costello JF, Plass C

Gene amplification in PNETs/medulloblastomas: mapping of a novel amplified gene within the MYCN amplicon.

Journal of medical genetics

Frühwald MC, O'Dorisio MS, Rush LJ, Reiter JL, Smiraglia DJ, Wenger G, Costello JF, White PS, Krahe R, Brodeur GM, Plass C

Aberrant CpG-island methylation has non-random and tumour-type-specific patterns.

Nature genetics

Costello JF, Frühwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X, Wright FA, Feramisco JD, Peltomäki P, Lang JC, Schuller DE, Yu L, Bloomfield CD, Caligiuri MA, Yates A, Nishikawa R, Su Huang H, Petrelli NJ, Zhang X, O'Dorisio MS, Held WA, Cavenee WK, Plass C

Aberrant methylation of genes in low-grade astrocytomas.

Brain tumor pathology

Costello JF, Plass C, Cavenee WK

A new tool for the rapid cloning of amplified and hypermethylated human DNA sequences from restriction landmark genome scanning gels.

Genomics

Smiraglia DJ, Frühwald MC, Costello JF, McCormick SP, Dai Z, Peltomäki P, O'Dorisio MS, Cavenee WK, Plass C

Methylation-associated silencing of the tissue inhibitor of metalloproteinase-3 gene suggest a suppressor role in kidney, brain, and other human cancers.

Cancer research

Bachman KE, Herman JG, Corn PG, Merlo A, Costello JF, Cavenee WK, Baylin SB, Graff JR

An arrayed human not I-EcoRV boundary library as a tool for RLGS spot analysis.

DNA research : an international journal for rapid publication of reports on genes and genomes

Plass C, Weichenhan D, Catanese J, Costello JF, Yu F, Yu L, Smiraglia D, Cavenee WK, Caligiuri MA, deJong P, Held WA

Cyclin-dependent kinase 6 (CDK6) amplification in human gliomas identified using two-dimensional separation of genomic DNA.

Cancer research

Costello JF, Plass C, Arap W, Chapman VM, Held WA, Berger MS, Su Huang HJ, Cavenee WK

Methylation of CpG island transcription factor binding sites is unnecessary for aberrant silencing of the human MGMT gene.

The Journal of biological chemistry

Pieper RO, Patel S, Ting SA, Futscher BW, Costello JF

Silencing of p16/CDKN2 expression in human gliomas by methylation and chromatin condensation.

Cancer research

Costello JF, Berger MS, Huang HS, Cavenee WK

O6-methylguanine-DNA methyltransferase in tumors and cells of the oligodendrocyte lineage.

The Canadian journal of neurological sciences. Le journal canadien des sciences neurologiques

Nutt CL, Costello JF, Bambrick LL, Yarosh DB, Swinnen LJ, Chambers AF, Cairncross JG

Direct correlation between methylation status and expression of the human O-6-methylguanine DNA methyltransferase gene.

Cancer communications

Pieper RO, Costello JF, Kroes RA, Futscher BW, Marathi U, Erickson LC

Metropolitan forensic anthropology team (MFAT) case studies in identification: 3. Identification of John J. Sullivan, the missing journalist.

Journal of forensic sciences

Zugibe FT, Taylor J, Weg N, DiBennerdo R, Costello JT, DeForest P

Glucose utilization and production by the dog kidney in vivo in metabolic acidosis and alkalosis.

The Journal of clinical investigation

Costello J, Scott JM, Wilson P, Bourke E