Recent publications

2017

Hepperla AJ, Davis IJ as part of the Cancer Genome Atlas Research Network. Comprehensive and integrated genomic characterization of adult soft tissue sarcoma. Cell. 171:950-965.e28. doi: 10.1016/j.cell.2017.10.014. (2017)

McDaniel SL, Hepperla AJ, Huang J, Dronamraju R, Adams AT, Kulkarni VG, Davis IJ, Strahl BD.  H3K36 methylation regulates nutrient stress response in Saccharomyces cerevisiae by enforcing transcriptional fidelity. Cell Reports. 19:2371-2382. doi: 10.1016/j.celrep.2017.05.057. (2017)

Fahey CC, Davis IJ. SETting the stage for cancer development: SETD2 and the consequences of lost methylation. Cold Spring Harb Perspect Med. 7(5). pii: a026468. doi: 10.1101/cshperspect.a026468. (2017)

2016

Gomez NC, Hepperla AJ, Dumitru R, Simon JM, Fang F, Davis IJ.Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer. Cell Reports. 17:1607-1620. doi: 10.1016/j.celrep.2016.10.011. (2016).

Hacker KE, Fahey CC, Shinsky SA, Chiang YJ, DiFiore JV, Jha DK, Vo AH, Shavit JA, Davis IJ, Strahl BD, Rathmell WK. Structure/function analysis of recurrent mutations in SETD2 reveals a critical and conserved role for a SET domain residue in maintaining protein stability and H3K36 trimethylation. J. Biological Chemistry. pii: jbc.M116.739375. (2016)

Park IY, Powell RT, Tripathi DN, Dere R, Ho TH, Blasius TL, Chiang YC, Davis IJ, Fahey CC, Hacker KE, Verhey KJ, Bedford MT, Jonasch E, Rathmell WK, Walker CL. Dual chromatin and cytoskeletal remodeling by SETD2. Cell. 166:950-62. (2016)

Dominguez D, Tsai YH, Gomez N, Jha DK, Davis I, Wang Z. A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer. Cell Research. 26:946-62. (2016)

Crowther AJ, Ocasio JK, Fang F, Meidinger J, Wu J, Deal AM, Chang SX, Yuan H, Schmid R, Davis I, Gershon TR. Radiation Sensitivity in a Preclinical Mouse Model of Medulloblastoma Relies on the Function of the Intrinsic Apoptotic Pathway. Cancer Research. 76:3211-32. (2016)

O’Neill AF, Adil EA, Irace AL, Neff L, Davis IJ, Perez-Atayde AR, Voss SD, Weinberg O, Rahbar R Post-transplant lymphoproliferative disorder of the pediatric airway: Presentation and management.  International Journal of Pediatric Otorhinolaryngology. 86:218-223. (2016).

Scelo G, Hofmann JN, Banks RE, Bigot P, Bhatt RS, Cancel-Tassin G, Chew SK, Creighton CJ, Cussenot O, Davis IJ, Escudier B, Frayling TM, Häggström C, Hildebrandt MA, Holcatova I, Johansson M, Linehan WM, McDermott DF, Nathanson KL, Ogawa S, Perlman EJ, Purdue MP, Stattin P, Swanton C, Vasudev NS, Wu X, Znaor A, Brennan P, Chanock SJ. International cancer seminars – A focus on kidney cancer. Annals of Oncology. Apr 29. pii: mdw186 (2016)

Pattenden SG, Simon JM, Wali A, Jayakody CM, Troutman J, McFadden AW, Wooten J, Wood CC, Frye SV, Janzen WP, Davis IJ. High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility. Proc. Natl. Acad. Sci. USA. (2016)

Waldron L, Steimle JD, Greco TM, Gomez NC, Dorr KM, Kweon J, Temple B, Yang XH, Wilczewski CM, Davis IJ, Cristea IM, Moskowitz IP, Conlon FL.The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation. Developmental Cell. 36:262-75. (2016)

Roode LE, Brighton H, Bo T, Perry JL, Parrott MC, Kersey F, Luft JC, Bear JE, DeSimone JM, Davis IJ. Subtumoral analysis of PRINT nanoparticle distribution reveals targeting variation based on cellular and particle properties. Nanomedicine. doi:10.1016/j.nano.2015.12.382. (2016)

 

2015

Simon JM, Parker JS, Liu F, Rothbart SB, Ait-Si-Ali S, Strahl BD, Jin J, Davis IJ, Mosley AL, Pattenden SG. A role for Widely Interspaced Zinc Finger (WIZ) in retention of the G9A methyltransferase on chromatin. Journal of Biological Chemistry. 290:26088-102. (2015)

Gomez NC, Davis IJ. Linking germline and somatic variation in Ewing sarcoma. Nature Genetics. 47:964-5. (2015)

Walker MP, Stopford CM, Cederlund M, Fang F, Jahn C, Rabinowitz AD, Goldfarb D, Graham DM, Yan F, Deal AM, Fedoriw Y, Richards KL, Davis IJ, Weidinger G, Damania B, Major MB. FOXP1 potentiates Wnt/β-catenin signaling in diffuse large B cell lymphoma. Science Signaling. 8:ra12. (2015)

 

2014

Orvis T, Hepperla A, Walter V, Song S, Simon JM, Parker JS, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman BE. BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. Cancer Research. 74:6486-98. (2014)

Chan KT, Asokan SB, King SJ, Bo T, Dubose ES, Liu W, Berginski ME, Simon JM, Davis IJ, Gomez SM, Sharpless NE, Bear JE. LKB 1 loss in melanoma disrupts directional migration towards extracellular matrix cues. Journal of Cell Biology, 207:299-315. (2014)

Patel M, Gomez NC, McFadden AW, Moats-Staats BM, Wu S, Rojas A, Sapp T, Simon JM, Smith SV, Kaiser-Rogers K, Davis IJ. PTEN deficiency mediates a reciprocal response to IGF-1 and mTOR inhibition. Molecular Cancer Research. 12:1610-20. (2014)

Konze KD, Pattenden SG, Liu F, Barstye-Lovejoy D, Li F, Simon JM, Davis IJ, Vedadi M, Jin J. A chemical tool for in vitro and in vivo precipitation of lysine methyltransferase G9a. ChemMedChem 9:549-53. (2014)

Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ. Variation in  chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Research. 24:241-50. (2014)

 

2013

Wu C, Haynes EM, Asokan SB, Simon JM, Sharpless NE, Baldwin AS, Davis IJ, Johnson GL, Bear JE. Loss of Arp2/3 induces and NF-kB-dependent, nonautonomous effect on chemotactic signaling. J Cell Biol. 203:907-16. (2013)

Sankar S, Gomez NC, Bell R, Patel M, Davis IJ, Lessnick SL, Luo W. EWS and RE1-silencing transcription factor inhibit neuronal phenotype development and oncogenic transformation in Ewing sarcoma. Genes Cancer. 4:241-50. (2013)

Hilton IB, Simon JM, Lieb JD, Davis IJ, Damania B, Dittmer DP. The open chromatin landscape of Kaposi’s sarcoma-associate herpesvirus. J. Virol. 87:11831-42. (2013)

Shukla N, Schiffman J, Reed D, Davis IJ, Womer RB, Lessnick SL, Lawlor ER; COG Ewing Sarcoma Biology Committee. Biomarkers in Ewing Sarcoma: The Promise and Challenge of Personalized Medicine. A Report from the Children’s Oncology Group. Front Oncology. Jun 6;3:141 (2013).

Simon JM, Giresi PG, Davis IJ, Lieb JD. A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE). Curr Protoc Mol Biol. Chapter 21: Unit 21.26 (2013).

Coulter DW, Walko C, Patel J, Moats-Staats BM, McFadden A, Smith SV, Khan WA, Bridges AS, Deal AM, Oesterheld J, Davis IJ, Blatt J. Valproic acid reduces the tolerability of temsirolimus in children and adolescents with solid tumors. Anticancer Drugs. 24,415-21 (2013).

 

2012

Jonasch E, Futreal PA, Davis IJ, Bailey ST, Kim WY, Brugarolas J, Giaccia AJ, Kurban G, Pause A, Frydman J, Zurita AJ, Rini BI, Sharma P, Atkins MB, Walker CL, Rathmell WK. State of the science: an update on renal cell carcinoma. Molecular Cancer Research 10, 859-80 (2012).

Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 488, 75–82 (2012).

Wagner AJ, Goldberg JM, Dubois SG, Choy E, Rosen L, Pappo A, Geller J, Judson I, Hogg D, Senzer N, Davis IJ, Chai F, Waghorne C, Schwartz B, Demetri GD. Tivantinib (ARQ197), a selective inhibitor of MET, in patients with microphthalmia transcription factor-associated  tumors: Results of a multicenter phase 2 trial. Cancer May 17 (2012).

Patel M, Simon JM, Iglesia MD, Wu SB, McFadden AW, Lieb JD, and Davis IJ. Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription. Genome Research 22, 259–270 (2012).

Simon JM, Giresi PG, Davis IJ, and Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature Protocols 7, 256–267 (2012).

 

2011

Song L, Zhang Z, Grasfeder LL, Boyle AP, 
Giresi PG, Lee B-K, Sheffield NC, Graf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y,  Showers KA, Simon JM, Vales T, Wang T
, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, and Furey TS. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research 21, 1757-67 (2011).

Mosquera JM, Dal Cin P, Mertz KD, Perner S, Davis IJ, Fisher DE, Rubin MA, Hirsch MS. Validation of a TFE3 break-apart FISH assay for Xp11.2 translocation renal cell carcinomas. Diagnostic Molecular Pathology 20, 129-37 (2011).

Resseguie ME, da Costa KA, Galanko JA, Patel M, Davis IJ, Zeisel SH. Aberrant estrogen regulation of PEMT results in choline deficiency-associated liver dysfunction. Journal of Biological Chemistry 286, 1649-58 (2011).

 

2010

Gaulton, K. J., Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, Berney T, Montanya E, Mohlke KL, Lieb JD, Ferrer J. A map of open chromatin in human pancreatic islets. Nature Genetics 42, 255–259 (2010).

Davis IJ, McFadden AW, Zhang Y, Coxon A, Burgess TL, Wagner AJ, Fisher DE. Identification of the receptor tyrosine kinase c-Met and its ligand, hepatocyte growth factor, as therapeutic targets for clear cell sarcoma. Cancer Research 70, 639-45 (2010).

 

Earlier

Sun W, Buck MJ, Patel M, Davis IJ. Improved ChIP-chip analysis by a mixture model approach. BMC Bioinformatics. 10, 173 (2009).

Davis IJ, Fisher DE. MiT transcription factor associated malignancies in man. Cell Cycle. 6:1724-9 (2007).

Tsuda M, Davis IJ, Argani P, Shukla N, McGill GG, Nagai M, Saito T, Laé M, Fisher DE, Ladanyi M. TFE3 fusions activate MET signaling by transcriptional up-regulation, defining another class of tumors as candidates for therapeutic MET inhibition. Cancer Research. 67, 919-29 (2007).

Davis IJ, Kim JJ, Ozsolak F, Widlund HR, Rozenblatt-Rosen O, Granter SR, Du J, Fletcher JA, Denny CT, Lessnick SL, Linehan WM, Kung AL, Fisher DE. Oncogenic MITF dysregulation in clear cell sarcoma: defining the MiT family of human cancers. Cancer Cell. 9, 473-84 (2006).

Argani P, Laé M, Hutchinson B, Reuter VE, Collins MH, Perentesis J, Tomaszewski JE, Brooks JS, Acs G, Bridge JA, Vargas SO, Davis IJ, Fisher DE, Ladanyi M. Renal carcinomas with the t(6;11)(p21;q12): clinicopathologic features and demonstration of the specific alpha-TFEB gene fusion by immunohistochemistry, RT-PCR, and DNA PCR. American Journal of Surgical Pathology. 29, 230-40 (2005).

Miller AJ, Levy C, Davis IJ, Razin E, Fisher DE. Sumoylation of MITF and its related family members TFE3 and TFEB. Journal of Biological Chemistry. 280, 146-55 (2005).

Mukohara T, Civiello G, Davis IJ, Taffaro ML, Christensen J, Fisher DE, Johnson BE, Janne PA. Inhibition of the met receptor in mesothelioma. Clin. Cancer Research. 11:8122-30. (2005)

Miller AJ, Levy C, Davis IJ, Razin E, Fisher DE. Sumoylation of MITF and its related family members TFE3 and TFEB. Journal of Biological Chemistry. 280:146-55. (2005)

Davis IJ, Hsi BL, Arroyo JD, Vargas SO, Yeh YA, Motyckova G, Valencia P, Perez-Atayde AR, Argani P, Ladanyi M, Fletcher JA, Fisher DE. Cloning of an Alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation. Proceedings of the National Academy of Sciences U S A. 100, 6051-6 (2003).

Vargas SO, French CA, Faul PN, Fletcher JA, Davis IJ, Dal Cin P, Perez-Atayde AR. Upper respiratory tract carcinoma with chromosomal translocation 15;19; evidence for a distinct entity of young patients with a rapidly fatal course. Cancer. 92:1195-203. (2001)