Jason Gertz, PhD

Research Interests

  • Breast Cancer
  • Gene Expression Regulation
  • Transcription Factors
  • Endometrial Cancer
  • Estrogen Receptors


Lab Website


  • English

Academic Information

  • Departments: Oncological Sciences - Assistant Professor
  • Cancer Center Programs: Nuclear Control of Cell Growth & Differentiation

Academic Office Information

  • 801-213-5662
  • Huntsman Cancer Institute
    2000 Circle of Hope, Room: 3717
    Salt Lake City, UT 84112

Academic Bio

Jason Gertz, PhD, is an investigator at Huntsman Cancer Institute (HCI) and an assistant professor in the Department of Oncological Sciences at the University of Utah. He is also a member of the Nuclear Control of Cell Growth and Differentiation Program. Dr. Gertz studies the role of transcription factors in cancer.

The inappropriate expression of genes is a common defect across different types of cancer. Transcription factors, which orchestrate gene expression patterns by interacting with specific loci throughout the genome, play a key role in the growth and development of tumors. Dr. Gertz’s research goal is to understand how transcription factors choose their genomic binding sites, how binding events lead to gene expression changes, and how the actions of transcription factors are altered in cancer. To determine the roles that transcription factors play in gene regulation, his lab uses and develops experimental methods that take advantage of next-generation sequencing to create high-resolution maps of gene regulatory networks. The Gertz lab also utilizes cutting edge computational approaches to take full advantage of these rich genomic datasets. The study of transcription factors in cancer promises to lead to new therapeutic targets and an understanding of key events that occur during tumorigenesis.

Dr. Gertz received a BA in Mathematics with concentrations in Computer Science and Economics from Cornell University in 2003. In 2008, he received a PhD in Computational Biology from Washington University School of Medicine. He was a postdoctoral fellow in Richard M. Myers’ laboratory at the HudsonAlpha Institute for Biotechnology, where he was funded in part by the American Cancer Society. To learn more about the Gertz lab, please visit http://www.huntsmancancer.org/gertzlab.

Education History

Type School Degree
Postdoctoral Fellowship HudsonAlpha Institute for Biotechnology
Postdoctoral Fellow
Doctoral Training Washington University School of Medicine
Computational Biology
Undergraduate Cornell University

Selected Publications

Journal Article

  1. Blanchard Z, Vahrenkamp JM, Berrett KC, Arnesen S, Gertz J ().

    Estrogen-independent molecular actions of mutant estrogen receptor alpha in endometrial cancer

    . Genome Res.
  2. Chalishazar MD, Wait SJ, Huang F, Ireland AS, Mukhopadhyay A, Lee Y, Schuman S, Guthrie MR, Berrett K, Vahrenkamp J, Hu Z, Kudla M, Modzelewska K, Wang G, Ingolia NT, Gertz J, Lum DH, Cosulich SC, Bomalaski JS, DeBerardinis RJ, Oliver TG (2019). MYC-driven small cell lung cancer is metabolically distinct and vulnerable to arginine depletion. (Epub ahead of print) Clin Cancer Res.
  3. Rodriguez AC, Blanchard Z, Maurer KA, Gertz J (2019 Feb 2). Estrogen Signaling in Endometrial Cancer: a Key Oncogenic Pathway with Several Open Questions. Horm Cancer, 10(2-3), 51-63.
  4. Farhang N, Ginley-Hidinger M, Berrett K, Gertz J, Lawrence B, Bowles R (2019). Lentiviral CRISPR Epigenome Editing of Inflammatory Receptors as a Gene Therapy Strategy for Disc Degeneration. (Epub ahead of print) Hum Gene Ther.
  5. Mollaoglu G, Jones A, Wait SJ, Mukhopadhyay A, Jeong S, Arya R, Camolotto SA, Mosbruger TL, Stubben CJ, Conley CJ, Bhutkar A, Vahrenkamp JM, Berrett KC, Cessna MH, Lane TE, Witt BL, Salama ME, Gertz J, Jones KB, Snyder EL, Oliver TG (2018 Oct 16). The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment. Immunity, 49(4), 764-779.e9.
  6. Carleton JB, Berrett KC, Gertz J (2018 Jun 2). Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines. J Vis Exp, (136).
  7. Vahrenkamp JM, Yang CH, Rodriguez AC, Almomen A, Berrett KC, Trujillo AN, Guillen KP, Welm BE, Jarboe EA, Janat-Amsbury MM, Gertz J (2018 Mar 13). Clinical and Genomic Crosstalk between Glucocorticoid Receptor and Estrogen Receptor α In Endometrial Cancer. Cell Rep, 22(11), 2995-3005.
  8. Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR (2018 Feb). GIGGLE: a search engine for large-scale integrated genome analysis. Nat Methods, 15(2), 123-126.
  9. Carleton JB, Berrett KC, Gertz J (2017 Oct 25). Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers. Cell Syst, 5(4), 333-344.e5.
  10. Stover JD, Farhang N, Berrett KC, Gertz J, Lawrence B, Bowles RD (2017 Jul 01). CRISPR Epigenome Editing of AKAP150 in DRG Neurons Abolishes Degenerative IVD-Induced Neuronal Activation. Mol Ther, 25(9), 2014-2027.
  11. Ramaker RC, Bowling KM, Lasseigne BN, Hagenauer MH, Hardigan AA, Davis NS, Gertz J, Cartagena PM, Walsh DM, Vawter MP, Jones EG, Schatzberg AF, Barchas JD, Watson SJ, Bunney BG, Akil H, Bunney WE, Li JZ, Cooper SJ, Myers RM (2017 Jul 28). Post-mortem molecular profiling of three psychiatric disorders. Genome Medicine, 9(1), 72.
  12. Mollaoglu G, Guthrie MR, Bhm S, Brgelmann J, Can I, Ballieu PM, Marx A, George J, Heinen C, Chalishazar MD, Cheng H, Ireland AS, Denning KE, Mukhopadhyay A, Vahrenkamp JM, Berrett KC, Mosbruger TL, Wang J, Kohan JL, Salama ME, Witt BL, Peifer M, Thomas RK, Gertz J, Johnson JE, Gazdar AF, Wechsler-Reya RJ, Sos ML, Oliver TG (2016 Dec 31). MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition. Cancer Cell, 31(2), 270-285.
  13. McDaniel JM, Varley KE, Gertz J, Savic DS, Roberts BS, Bailey SK, Shevde LA, Ramaker RC, Lasseigne BN, Kirby MK, Newberry KM, Partridge EC, Jones AL, Boone B, Levy SE, Oliver PG, Sexton KC, Grizzle WE, Forero A, Buchsbaum DJ, Cooper SJ, Myers RM (2016 Dec 24). Genomic regulation of invasion by STAT3 in triple negative breast cancer. Oncotarget, 8(5), 8226-8238.
  14. DAmato NC, Gordon MA, Babbs B, Spoelstra NS, Carson Butterfield KT, Torkko KC, Phan VT, Barton VN, Rogers TJ, Sartorius CA, Elias A, Gertz J, Jacobsen BM, Richer JK (2016 Nov). Cooperative Dynamics of AR and ER Activity in Breast Cancer. Mol Cancer Res, 14(11), 1054-1067.
  15. Savic D, Ramaker RC, Roberts BS, Dean EC, Burwell TC, Meadows SK, Cooper SJ, Garabedian MJ, Gertz J, Myers RM (2016). Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation. Genome Medicine, 8(1), 74.
  16. Young EL, Feng BJ, Stark AW, Damiola F, Durand G, Forey N, Francy TC, Gammon A, Kohlmann WK, Kaphingst KA, McKay-Chopin S, Nguyen-Dumont T, Oliver J, Paquette AM, Pertesi M, Robinot N, Rosenthal JS, Vallee M, Voegele C, Hopper JL, Southey MC, Andrulis IL, John EM, Hashibe M, Gertz J, Breast Cancer Family Registry, Le Calvez-Kelm F, Lesueur F, Goldgar DE, Tavtigian SV (2016 Jun). Multigene testing of moderate-risk genes: be mindful of the missense. J Med Genet, 53(6), 366-76.
  17. Kirby MK, Ramaker RC, Gertz J, Davis NS, Johnston BE, Oliver PG, Sexton KC, Greeno EW, Christein JD, Heslin MJ, Posey JA, Grizzle WE, Vickers SM, Buchsbaum DJ, Cooper SJ, Myers RM (2016 May 26). RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4.LID - S1574-7891(16)30040-0 [pii]LID - 10.1016/j.molonc.2016.05.004 [doi]. (Epub ahead of print) Mol Oncol.
  18. Camp NJ, Lin WY, Bigelow A, Burghel GJ, Mosbruger TL, Parry MA, Waller RG, Rigas SH, Tai PY, Berrett K, Rajamanickam V, Cosby R, Brock IW, Jones B, Connley D, Sargent R, Wang G, Factor RE, Bernard PS, Cannon-Albright L, Knight S, Abo R, Werner TL, Reed MW, Gertz J, Cox A (2016 Apr 1). Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus. Cancer Res, 76(7), 1916-25.
  19. Savic D, Roberts BS, Carleton JB, Partridge EC, White MA, Cohen BA, Cooper GM, Gertz J, Myers RM (2015 Dec). Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites. Genome Res, 25(12), 1791-800.
  20. Slattery ML, Herrick JS, Mullany LE, Gertz J, Wolff RK (2015). Improved survival among colon cancer patients with increased differentially expressed pathways. BMC Medicine, 13, 75.
  21. Varley KE, Gertz J, Roberts BS, Davis NS, Bowling KM, Kirby MK, Nesmith AS, Oliver PG, Grizzle WE, Forero A, Buchsbaum DJ, LoBuglio AF, Myers RM (2014 Jul). Recurrent read-through fusion transcripts in breast cancer. Breast Cancer Res Treat, 146(2), 287-97.
  22. Marinov, G K, Williams, B A, McCue, K, Schroth, G P, Gertz, J, Myers, R M, amp Wold, B J (). From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing. Genome Res, Mar 24(3), 496-510.
  23. Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM (2013 Oct 10). Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell, 52(1), 25-36.
  24. Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M (2013 Mar). Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics, 8(3), 317-32.
  25. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM (2013 Mar). Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res, 23(3), 555-67.
  26. Savic D, Gertz J, Jain P, Cooper GM, Myers RM (2013). Mapping genome-wide transcription factor binding sites in frozen tissues. Epigenetics Chromatin, 6(1), 30.
  27. Guo Y, Monahan K, Wu H, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q (2012 Dec 18). CTCF/cohesin-mediated DNA looping is required for protocadherin alpha promoter choice. Proc Natl Acad Sci U S A, 109(51), 21081-6.
  28. Gertz J, Reddy TE, Varley KE, Garabedian MJ, Myers RM (2012 Nov). Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner. Genome Res, 22(11), 2153-62.
  29. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, OGeen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M (2012 Sep 6). Architecture of the human regulatory network derived from ENCODE data. Nature, 489(7414), 91-100.
  30. The ENCODE Project Consortium (). ) An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74.
  31. Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA (2012 Sep). Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res, 22(9), 1680-8.
  32. Reddy TE, Gertz J, Crawford GE, Garabedian MJ, Myers RM (2012 Sep). The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes. Mol Cell Biol, 32(18), 3756-67.
  33. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M (2012 Sep). ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res, 22(9), 1813-31.
  34. Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM (2012 May). Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res, 22(5), 860-9.
  35. Simpson NE, Gertz J, Imberg K, Myers RM, Garabedian MJ (2012 Jan). Research resource: enhanced genome-wide occupancy of estrogen receptor alpha by the cochaperone p23 in breast cancer cells. Mol Endocrinol, 26(1), 194-202.
  36. Gertz J, Varley KE, Davis NS, Baas BJ, Goryshin IY, Vaidyanathan R, Kuersten S, Myers RM (2012 Jan). Transposase mediated construction of RNA-seq libraries. Genome Res, 22(1), 134-41.
  37. Ng SL, Friedman BA, Schmid S, Gertz J, Myers RM, Tenoever BR, Maniatis T (2011 Dec 27). IkappaB kinase epsilon (IKK(epsilon)) regulates the balance between type I and type II interferon responses. Proc Natl Acad Sci U S A, 108(52), 21170-5.
  38. Kucera KS, Reddy TE, Pauli F, Gertz J, Logan JE, Myers RM, Willard HF (2011 Oct 15). Allele-specific distribution of RNA polymerase II on female X chromosomes. Hum Mol Genet, 20(20), 3964-73.
  39. Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM (2011 Aug). Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet, 7(8), e1002228.
  40. The ENCODE Project Consortium (). A user's guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol, 9, e1001046.
  41. Gertz J, Gerke JP, Cohen BA (2010 Feb). Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions. Theor Popul Biol, 77(1), 1-5.
  42. Gertz J, Siggia ED, Cohen BA (2009 Jan 8). Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature, 457(7226), 215-8.
  43. Gertz J, Cohen BA (2009). Environment-specific combinatorial cis-regulation in synthetic promoters. Mol Syst Biol, 5, 244.
  44. Zeigler RD, Gertz J, Cohen BA (2007). A cis-regulatory logic simulator. BMC Bioinformatics, 8, 272.
  45. Gertz J, Fay JC, Cohen BA (2006). Phylogeny based discovery of regulatory elements. BMC Bioinformatics, 7, 266.
  46. Gertz J, Riles L, Turnbaugh P, Ho SW, Cohen BA (2005 Aug). Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics. Genome Res, 15(8), 1145-52.
  47. Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, Cokus S, Rothschild B (2003 Nov 1). Inferring protein interactions from phylogenetic distance matrices. Bioinformatics, 19(16), 2039-45.
  48. Ginley-Hidinger M, Carleton JB, Rodriguez AC, Berrett KC, Gertz J ().

    Sufficiency analysis of estrogen responsive enhancers using synthetic activators

    . Mol Syst Biol.
  49. Rodriguez AC, Vahrenkamp JM, Berrett KC, Clark KA, Guillen KP, Scherer SD, Yang CH, Welm BE, Janat-Amsbury MM, Graves BJ, Gertz J ().

    ETV4 is necessary for estrogen signaling and growth in endometrial cancer cells

    . Cancer Res.
  50. Vahrenkamp JM and Gertz J ().

    FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples

    . Genome Res.