Katherine E. Varley

Katherine E. Varley, PhD

Languages spoken: English

Academic Information

Departments Primary - Oncological Sciences

Academic Office Information

Katherine.Varley@hci.utah.edu

Lab

Research Interests

  • Breast Cancer
  • Epigenetics
  • Gene Expression Regulation
  • Medical Diagnosis and Prognosis Using Biomarkers

Katherine (K-T) Varley, PhD, is an investigator at Huntsman Cancer Institute and an assistant professor in the Department of Oncological Sciences at the University of Utah. She is a member of the Nuclear Control of Cell Growth and Differentiation Program and her laboratory studies epigenetic gene regulation in breast cancer.

Genomic technology has revolutionized the ability to detect the molecular defects that occur in cancer. Dr. Varley’s research focuses on using next-generation sequencing assays and computational analysis to study the gene expression, transcription factor binding and DNA methylation patterns in breast cancer. Her goals are to answer fundamental questions about how epigenetic gene regulation is disrupted in cancer cells as well as to discover drug targets and biomarkers that may have a more immediate impact on breast cancer treatment. Research in her lab involves the development of new molecular methods and bioinformatics approaches to explore the cancer genome and to translate discoveries into clinical tools that improve patient care.

Dr. Varley received her BS in Biology with a concentration in Computational Biology from Cornell University in 2003. She received her PhD in Computational Biology in 2009 from Washington University School of Medicine where Dr. Robi Mitra was her thesis advisor. Her postdoctoral studies were conducted in Dr. Richard M. Myers’ laboratory at the HudsonAlpha Institute for Biotechnology and included collaborative studies with the ENCODE Project Consortium and researchers at the University of Alabama at Birmingham Comprehensive Cancer Center.

Education History

Postdoctoral Fellowship HudsonAlpha Institute for Biotechnology
 Postdoctoral Fellow
Doctoral Training Washington University School of Medicine
 PhD
Undergraduate Cornell University
 BS

Selected Publications

Journal Article

  1. Lim TY, Wilde BR, Thomas ML, Murphy KE, Vahrenkamp JM, Conway ME, Varley KE, Gertz J, Ayer DE (2023). TXNIP loss expands Myc-dependent transcriptional programs by increasing Myc genomic binding. PLoS Biol, 21(3), e3001778. (Read full article)
  2. Gonzalez MA, Olivas IM, Bencomo-Alvarez AE, Rubio AJ, Barreto-Vargas C, Lopez JL, Dang SK, Solecki JP, McCall E, Astudillo G, Velazquez VV, Schenkel K, Reffell K, Perkins M, Nguyen N, Apaflo JN, Alvidrez E, Young JE, Lara JJ, Yan D, Senina A, Ahmann J, Varley KE, Mason CC, Eide CA, Druker BJ, Nurunnabi M, Padilla O, Bajpeyi S, Eiring AM (2022). Loss of G0/G1 switch gene 2 (G0S2) promotes disease progression and drug resistance in chronic myeloid leukaemia (CML) by disrupting glycerophospholipid metabolism. Clin Transl Med, 12(12), e1146. (Read full article)
  3. Baessler A, Novis CL, Shen Z, Perovanovic J, Wadsworth M, Thiede KA, Sircy LM, Harrison-Chau M, Nguyen NX, Varley KE, Tantin D, Hale JS (2022). Tet2 coordinates with Foxo1 and Runx1 to balance T follicular helper cell and T helper 1 cell differentiation. Sci Adv, 8(24), eabm4982. (Read full article)
  4. Clark KA, Paquette A, Tao K, Bell R, Boyle JL, Rosenthal J, Snow AK, Stark AW, Thompson BA, Unger J, Gertz J, Varley KE, Boucher KM, Goldgar DE, Foulkes WD, Thomas A, Tavtigian SV (2021). Comprehensive evaluation and efficient classification of BRCA1 RING domain missense substitutions. Am J Hum Genet, 109(6), 1153-1174. (Read full article)
  5. Zhao H, Pomicter AD, Eiring AM, Franzini A, Ahmann J, Hwang JY, Senina A, Helton B, Iyer S, Yan D, Khorashad JS, Zabriskie MS, Agarwal A, Redwine HM, Bowler AD, Clair PM, McWeeney SK, Druker BJ, Tyner JW, Stirewalt DL, Oehler VG, Varambally S, Berrett KC, Vahrenkamp JM, Gertz J, Varley KE, Radich JP, Deininger MW (2021). MS4A3 promotes differentiation in chronic myeloid leukemia by enhancing common β-chain cytokine receptor endocytosis. Blood, 139(5), 761-778. (Read full article)
  6. Guillen KP, Fujita M, Butterfield AJ, Scherer SD, Bailey MH, Chu Z, DeRose YS, Zhao L, Cortes-Sanchez E, Yang CH, Toner J, Wang G, Qiao Y, Huang X, Greenland JA, Vahrenkamp JM, Lum DH, Factor RE, Nelson EW, Matsen CB, Poretta JM, Rosenthal R, Beck AC, Buys SS, Vaklavas C, Ward JH, Jensen RL, Jones KB, Li Z, Oesterreich S, Dobrolecki LE, Pathi SS, Woo XY, Berrett KC, Wadsworth ME, Chuang JH, Lewis MT, Marth GT, Gertz J, Varley KE, Welm BE, Welm AL (2022). A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. Nat Cancer, 3(2), 232-250. (Read full article)
  7. Liu Y, Wu Z, Zhou J, Ramadurai DKA, Mortenson KL, Aguilera-Jimenez E, Yan Y, Yang X, Taylor AM, Varley KE, Gertz J, Choi PS, Cherniack AD, Chen X, Bass AJ, Bailey SD, Zhang X (2021). A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. Nat Commun, 12(1), 7139. (Read full article)
  8. Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR (2021). CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. PLoS One, 16(4), e0241253. (Read full article)
  9. Riggio AI, Varley KE, Welm AL (2020). The lingering mysteries of metastatic recurrence in breast cancer. Br J Cancer, 124(1), 13-26. (Read full article)
  10. Conway ME, McDaniel JM, Graham JM, Guillen KP, Oliver PG, Parker SL, Yue P, Turkson J, Buchsbaum DJ, Welm BE, Myers RM, Varley KE (2020). STAT3 and GR Cooperate to Drive Gene Expression and Growth of Basal-Like Triple-Negative Breast Cancer. Cancer Res, 80(20), 4355-4370. (Read full article)
  11. Stewart RL, Matynia AP, Factor RE, Varley KE (2020). Spatially-resolved quantification of proteins in triple negative breast cancers reveals differences in the immune microenvironment associated with prognosis. Sci Rep, 10(1), 6598. (Read full article)
  12. Vaklavas C, Roberts BS, Varley KE, Lin NU, Liu MC, Rugo HS, Puhalla S, Nanda R, Storniolo AM, Carey LA, Saleh MN, Li Y, Delossantos JF, Grizzle WE, LoBuglio AF, Myers RM, Forero-Torres A, Translational Breast Cancer Research Consortium TBCRC (2020). TBCRC 002: a phase II, randomized, open-label trial of preoperative letrozole with or without bevacizumab in postmenopausal women with newly diagnosed stage 2/3 hormone receptor-positive and HER2-negative breast cancer. Breast Cancer Res, 22(1), 22. (Read full article)
  13. Stewart RL, Updike KL, Factor RE, Henry NL, Boucher KM, Bernard PS, Varley KE (2019). A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer. Cancer Res, 79(13), 3466-3478. (Read full article)
  14. Giraddi RR, Chung CY, Heinz RE, Balcioglu O, Novotny M, Trejo CL, Dravis C, Hagos BM, Mehrabad EM, Rodewald LW, Hwang JY, Fan C, Lasken R, Varley KE, Perou CM, Wahl GM, Spike BT (2018). Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development. Cell Rep, 24(6), 1653-1666.e7. (Read full article)
  15. Zabriskie MS, Antelope O, Verma AR, Draper LR, Eide CA, Pomicter AD, Tran TH, Druker BJ, Tyner JW, Miles RR, Graham JM, Hwang JY, Varley KE, Toydemir RM, Deininger MW, Raetz EA, OHare T (2017). A novel AGGF1-PDGFRb fusion in pediatric T-cell acute lymphoblastic leukemia. Haematologica, 103(2), e87-e91. (Read full article)
  16. 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 (2017). Genomic regulation of invasion by STAT3 in triple negative breast cancer. Oncotarget, 8(5), 8226-8238. (Read full article)
  17. Forero A, Li Y, Chen D, Grizzle WE, Updike KL, Merz ND, Downs-Kelly E, Burwell TC, Vaklavas C, Buchsbaum DJ, Myers RM, LoBuglio AF, Varley KE (2016). Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes. Cancer Immunol Res, 4(5), 390-9. (Read full article)
  18. Forero-Torres A, Varley KE, Abramson VG, Li Y, Vaklavas C, Lin NU, Liu MC, Rugo HS, Nanda R, Storniolo AM, Traina TA, Patil S, Van Poznak CH, Nangia JR, Irvin WJ Jr, Krontiras H, De Los Santos JF, Haluska P, Grizzle W, Myers RM, Wolff AC (2015). TBCRC 019: A Phase II Trial of Nanoparticle Albumin-Bound Paclitaxel with or without the Anti-Death Receptor 5 Monoclonal Antibody Tigatuzumab in Patients with Triple-Negative Breast Cancer. Clin Cancer Res, 21(12), 2722-9. (Read full article)
  19. 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). Recurrent read-through fusion transcripts in breast cancer. Breast Cancer Res Treat, 146(2), 287-97. (Read full article)
  20. Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM (2013). Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell, 52(1), 25-36. (Read full article)
  21. 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). Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics, 8(3), 317-32. (Read full article)
  22. 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). Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res, 23(3), 555-67. (Read full article)
  23. Guo Y, Monahan K, Wu H, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q (2012). CTCF/cohesin-mediated DNA looping is required for protocadherin alpha promoter choice. Proc Natl Acad Sci U S A, 109(51), 21081-6. (Read full article)
  24. Gertz J, Reddy TE, Varley KE, Garabedian MJ, Myers RM (2012). 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. (Read full article)
  25. 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). Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res, 22(9), 1680-8. (Read full article)
  26. 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). Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res, 22(5), 860-9. (Read full article)
  27. Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernandez-Neuta I, Samper S, Martin C, Garcia MJ, Ritacco V, Lopez L, Robledo J, Zambrano MM, Mitra RD, Del Portillo P (2012). IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. BMC Genomics, 13, 249. (Read full article)
  28. Gertz J, Varley KE, Davis NS, Baas BJ, Goryshin IY, Vaidyanathan R, Kuersten S, Myers RM (2012). Transposase mediated construction of RNA-seq libraries. Genome Res, 22(1), 134-41. (Read full article)
  29. ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74.
  30. Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM (2011). Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet, 7(8), e1002228. (Read full article)
  31. ENCODE Project Consortium (2011). A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol, 9(4), e1001046.
  32. Varley KE, Mitra RD (2010). Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res, 20(9), 1279-87. (Read full article)
  33. Varley KE, Mutch DG, Edmonston TB, Goodfellow PJ, Mitra RD (2009). Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing. Nucleic Acids Res, 37(14), 4603-12. (Read full article)
  34. Varley KE, Mitra RD (2009). Nested Patch PCR for highly multiplexed amplification of genomic loci. Cold Spring Harb Protoc, 2009(7), pdb.prot5252. (Read full article)
  35. Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD (2009). Quantification of rare allelic variants from pooled genomic DNA. Nat Methods, 6(4), 263-5. (Read full article)
  36. Varley KE, Mitra RD (2008). Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Res, 18(11), 1844-50. (Read full article)
  37. Zhao G, Chang KY, Varley K, Stormo GD (2007). Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach. PLoS One, 2(2), e262. (Read full article)

Patent

  1. Katherine E. Varley, Ryan H. Miller, Jeffrey Greenland (2019). Targeted sequencing to detect and quantify low levels of methylated DNA. In preparation.
  2. Katherine E. Varley, Rachel L. Stewart, Philip S. Bernard, and Katherine Updike (2019). Multigene assay to assess risk of recurrence of cancer. Provisional. U.S. Patent No. 62/829,440. Washington, D.C.:U.S. Patent and Trademark Office.
  3. Richard M. Myers, Albert F. Lobuglio, Katherine E. Varley, Andres Forero, Donald J. Buchsbaum (2014). Biomarkers for triple-negative breast cancer. U.S. Patent No. WO2016037009 A1. International Application Published Under the Patent Cooperation Treaty. World Intellectual Property Organization.. Washington, D.C.:U.S. Patent and Trademark Office.
  4. Katherine E. Varley, D. Troy Moore, Randall Bachmeyer, David Kloske (2014). Capture Methodologies for Circulating Cell Free DNA. U.S. Patent No. US 9,982,255 B2. Washington, D.C.:U.S. Patent and Trademark Office.
  5. Katherine E. Varley, Richard M. Myers, Brian S. Roberts, Jason Gertz, Donald J. Buchsbaum, Andres Forero-Torres, Albert F. LoBuglio (2012). Novel Read-Through Fusion Polynucleotides and Polypeptides and Uses Thereof. U.S. Patent No. 13/828,901. Publication No. US2017/0267733 A1. Washington, D.C.:U.S. Patent and Trademark Office.
  6. Robi M. Mitra, Katherine E. Varley (2008). Method for multiplexed nucleic acid patch polymerase chain reaction. U.S. Patent No. US 8,586,310 B2 and US 9,909,170 B2. Washington, D.C.:U.S. Patent and Trademark Office.

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