DNA

Publications

In recent years, the Costello Lab has published research in a variety of academic journals, including Science, Nature, Nature Communications, and Cancer Cell. Below includes a featured selection of recent publications.

 

Intermediate DNA methylation is a conserved signature of genome regulation

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.

Nat Commun. 2015 Feb 15; (6): 6363. doi: doi: 10.1038/ncomms7363.
PubMed Link >

Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser

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

Nat Biotechnol. 2015; 33 (4): 345-6.
PubMed Link >

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

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.

Nat Commun. 2014 Nov 25; 5: 5442. doi: 10.1038/ncomms6442.
PubMed Link >

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

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.

Cell Rep. 2014 Nov 20; 9 (4): 1228-34. doi: 10.1016/j.celrep.2014.10.031. Epub 2014 Nov 20.
PubMed Link >

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

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

Bioinformatics. 2014 Aug 1; 30 (15): 2206-7. doi: 10.1093/bioinformatics/btu191. Epub 2014 Apr 10.
PubMed Link >

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

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

Neuro Oncol. 2014; 16 (7): 984-90.
PubMed Link >

Early epigenetic downregulation of WNK2 kinase during pancreatic ductal adenocarcinoma development

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

Oncogene. 2014 Jun 26; 33 (26): 3401-10. doi: 10.1038/onc.2013.312. Epub 2013 Aug 5.
PubMed Link >

Recurrent epimutations activate gene body promoters in primary glioblastoma

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.

Genome Res. 2014 Jul 30; 24 (5): 761-74. doi: 10.1101/gr.164707.113. Epub 2014 Apr 7.
PubMed Link >

Response of primary glioblastoma cells to therapy is patient specific and independent of cancer stem cell phenotype

Fouse SD, Nakamura JL, James CD, Chang S, Costello JF.

Neuro Oncol. 2014; 16 (3): 173-8. doi: 10.1093/neuonc/not229. Epub 2013 Dec 4.
PubMed Link >

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

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.

Nat Rev Cancer. 2014; 14 (2): 92-107. doi: 10.1038/nrc3655.
PubMed Link >

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

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 SJ, Hirst M, Marra MA, Saito N, Aburatani H, Mukasa A, Berger MS, Chang SM, Taylor BS, Costello JF.

Science. 2014 Jan 10; 343 (6167): 189-193. doi: 10.1126/science.1239947. Epub 2013 Dec 12.
PubMed Link >

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

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.

Neuro Oncol. 2014; 16 (2): 173-8. doi: 10.1093/neuonc/not229. Epub 2013 Dec 4.
PubMed Link >