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Daniel Savic, PhD
Daniel Savic, PhD


PhD – The University of Chicago, Chicago, Illinois (2012)

Research Interests

My primary research focus involves studying genome function and gene regulation in the context of pediatric leukemia in order to address a fundamental and critical question: how does the noncoding portion of the human genome impact chemotherapy response, chemotherapy resistance and relapse? The long-term goal of my research effort is to gain a better understanding of genome function, gene regulation and the underlying genetic factors impacting chemotherapeutic drug resistance and relapse in pediatric leukemia. Our laboratory is involved in three related areas of research:

  • Role of cis-regulatory elements in antileukemic drug resistance, drug response and disease relapse in pediatric leukemia
  • Functional characterization of non-coding DNA sequence variants associated with chemotherapeutic drug resistance and treatment outcome in pediatric leukemia
  • Development of novel pharmacogenomic assays

Selected Publications

Diedrich JD, Dong Q, Ferguson DC, Bergeron BP, Autry RJ, Qian M, Yang W, Smith C, Papizan JB, Connelly JP, Hagiwara K, Crews KR, Pruett-Miller SM, Pui CH, Yang JJ, Relling MV, Evans WE and Savic D. Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks. Leukemia 24 February, 2021.

Lee SH, Qian M, Yang W, Diedrich JD, Raetz E, Yang W, Dong Q, Devidas M, Pei D, Yeoh A, Cheng C, Pui CH, Evans WE, Mullighan CG, Hunger SP, Savic D, Relling MV, Loh M, Yang JJ. Genome-wide association study of susceptibility loci for TCF3-PBX1 acute lymphoblastic leukemia. J Natl Cancer Inst 3 Sept, 2020. doi:10.1093/jnci/djaa133

Partridge EC, Chhetri SB, Prokop JW, Ramaker RC, Jansen CS, Goh ST, Mackiewicz M, Newberry KM, Brandsmeier LA, Meadows SK, Messer CL,  Hardigan AA, Dean EC, Jian S, Savic D, Mortazavi A, Wold BJ, Myers RM, Mendenhall EM. Occupancy patterns of 208 chromatin-associated proteins in a single human cell type. Nature 583(7818):720-728, 2020.

ENCODE Project Consortium. Expanded encyclopedias of DNA elements in the human and mouse genomes. Nature 583(7818):699-710, 2020.

Autry RJ, Paugh SW, Carter R, Shi L, Liu J, Ferguson DC, Lau CE, Bonten EJ, Yang W, McCorkle JR, Beard JA, Panetta JC, Diedrich JD, Crews KR, Pei D, Coke CJ, Natarajan S, Khatamian A, Karol SE, Lopez-Lopez E, Diouf B, Smith C, Gocho Y, Hagiwara K, Roberts KG, Pounds S, Kornblau SM, Stock W, Paietta EM, Litzow MR, Inaba H, Mullighan CG, Jeha S, Pui CH, Cheng C, Savic D, Yu J, Gawad C, Relling MV, Yang JJ, Evans WE.  Integrative genomic analyses reveal mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia. Nature Cancer 9(8):2918-2929, 2020. 

Slavish P, Chi L, Yun MK, Tsurkan L, Martinez N, Jonchere B, Chai S, Connelly M, Waddell B, Das S, Neale G, Li Z, Shadrick W, Olsen R, Freeman K, Low J, Price J, Young B, Bharatham N, Boyd V, Lee R, Morfouace M, Roussel M, Chen T, Savic D, Guy RK, White S, Shelat A, Potter P. Bromodomain-selective BETi are potent antitumor agents against MYC-driven pediatric cancer. Cancer Research canres.3934.2019. 10 Jul, 2020. doi:10.1158/0008-5472.CAN-19-3934

Ramaker RC*, Savic D*, Hardigan AA, Newberry K, Cooper GM, Myers RM, Cooper SJ.  A genome-wide interactome of DNA-associated proteins in the human liver. Genome Research Nov;27(11):1950-1960, 2017. *equal contributions

Agee JM, Varley KE, Gertz J, Savic D, Roberts BS, Bailey SK, Shevde LA, Ramaker R, Lasseigne BN, Kirby MK, Newberry K, Partridge EC, Oliver PG, Sexton KG, Grizzle WE, Forero A, Buchsbaum DJ, Myers RM.  Genomic regulation of invasion by STAT3 in triple negative breast cancer.  Oncotarget Jan 31;8(5):8226-8238, 2017. 

Savic D, Ramaker RC, Roberts BS, Burwell TC, Dean EC, Meadows SK, Cooper SJ, Garabedian MJ, Gertz J, Myers RM. Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation. Genome Medicine Jul 11;8(1):74, 2016.

Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolution from annotation to functional interpretation. Seminars in Cellular and Developmental Biology Sep;57:40-50, 2016.

Savic D, Roberts BS, Carleston JB, Partridge EC, White MA, Cohen BA, Cooper GM, Gertz J, Myers RM. Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein beta binding sites. Genome Research Dec;25(12):1791-800, 2015.

Savic D, Partridge EC, Newberry K, Smith S, Meadows S, Roberts BS, Mackiewicz M, Mendenhall E, Myers RM. CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins. Genome Research Oct;25(10):1581-9,2015.

Paugh SW, Bonten EJ, Savic D, Ramsey LB, Thierfelder WE, Gurung P, Malireddi RKS, Actis M, Mayasundari A, Min J, Coss DR, Laudermilk LT, Panetta JC, McCorkle JR, Fan Y, Crews KR, Stocco G, Wilkinson MR, Ferreira AM, Cheng C, Yang W, Karol SE, Fernandez CA, Diouf B, Smith C, Hicks JK, Zanut A, Giordanengo A, Crona D, Bianchi JJ, Holmfeldt L, Mullighan CG, den Boer ML, Pieters R, Jeha S, Dunwell TL, Latif F, Bhojwani D, Carroll WL, Pui CH, Myers RM, Guy RK, Kanneganti TD, Relling MV, Evans WE. NALP3 inflammasome upregulation and CASP1 cleavage of the glucocorticoid receptor cause glucocorticoid resistance in leukemia cells. Nature Genetics Jun;47(6):607-14, 2015.

Savic D, Gertz J, Jain P, Copper GM, Myers RM. Mapping genome-wide transcription factor binding sites in frozen tissues. Epigenetics & Chromatin 6(1):30, 2013.

Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM. Distinct properties of cell type-specific and shared transcription factor binding sites. Molecular Cell 52(1):25-36, 2013. Recommended by Faculty 1000.

Sakabe NJ**, Savic D**, Nobrega MA. Transcriptional enhancers in development and disease. Genome Biology 13(1):238, 2012. **equal contributions and corresponding authors

Last update: March 2021