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View all Varley KE publications in the National Institutes of Health PubMed website

Selected Publications

A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncologyKatrin P. Guillen, Maihi Fujita, Andrew J. Butterfield, Sandra D. Scherer, Matthew H. Bailey, Zhengtao Chu, Yoko S. DeRose, Ling Zhao, Emilio Cortes-Sanchez, Chieh-Hsiang Yang, Jennifer Toner, Guoying Wang, Yi Qiao, Xiaomeng Huang, Jeffery A. Greenland, Jeffery M. Vahrenkamp, David H. Lum, Rachel E. Factor, Edward W. Nelson, Cindy B. Matsen, Jane M. Poretta, Regina Rosenthal, Anna C. Beck, Saundra S. Buys, Christos Vaklavas, John H. Ward, Randy L. Jensen, Kevin B. Jones, Zheqi Li, Steffi Oesterreich, Lacey E. Dobrolecki, Satya S. Pathi, Xing Yi Woo, Kristofer C. Berrett, Mark E. Wadsworth, Jeffrey H. Chuang, Michael T. Lewis, Gabor T. Marth, Jason Gertz, Katherine E. Varley, Bryan E. Welm, Alana L. Welm
bioRxiv 2021.02.28.433268; doi: https://doi.org/10.1101/2021.02.28.433268


A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer.
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.
Nat Commun. 2021 Dec 8;12(1):7139. doi: 10.1038/s41467-021-27055-4.PMID: 34880227


MS4A3 Promotes Differentiation in Chronic Myeloid Leukemia by Enhancing Common β Chain Cytokine Receptor Endocytosis.
Zhao H, Pomicter AD, Eiring AM, Franzini A, Ahmann J, Hwang JY, Senina AV, Helton B, Iyer SM, 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 J, Deininger MW.
Blood. 2021 Nov 15:blood.2021011802. doi: 10.1182/blood.2021011802. Online ahead of print.PMID: 34780648


CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing.
Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR.
PLoS One. 2021 Apr 8;16(4):e0241253. doi: 10.1371/journal.pone.0241253. eCollection 2021.PMID: 33830997


The lingering mysteries of metastatic recurrence in breast cancer.
Riggio AI, Varley KE, Welm AL.
Br J Cancer. 2021 Jan;124(1):13-26. doi: 10.1038/s41416-020-01161-4. Epub 2020 Nov 26.PMID: 33239679 Review.


STAT3 and GR Cooperate to Drive Gene Expression and Growth of Basal-Like Triple-Negative Breast Cancer.
Conway ME, McDaniel JM, Graham JM, Guillen KP, Oliver PG, Parker SL, Yue P, Turkson J, Buchsbaum DJ, Welm BE, Myers RM, Varley KE.
Cancer Res. 2020 Oct 15;80(20):4355-4370. doi: 10.1158/0008-5472.CAN-20-1379. Epub 2020 Aug 19.PMID: 32816914


Spatially-resolved quantification of proteins in triple negative breast cancers reveals differences in the immune microenvironment associated with prognosis.
Stewart RL, Matynia AP, Factor RE, Varley KE.
Sci Rep. 2020 Apr 20;10(1):6598. doi: 10.1038/s41598-020-63539-x.PMID: 32313087


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.
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).
Breast Cancer Res. 2020 Feb 18;22(1):22. doi: 10.1186/s13058-020-01258-x.PMID: 32070401 Clinical Trial.


A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer.
Stewart RL, Updike KL, Factor RE, Henry NL, Boucher KM, Bernard PS, Varley KE.
Cancer Res. 2019 Jul 1;79(13):3466-3478. doi: 10.1158/0008-5472.CAN-18-3014. Epub 2019 May 2.PMID: 31048497


Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development.
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.
Cell Rep. 2018 Aug 7;24(6):1653-1666.e7. doi: 10.1016/j.celrep.2018.07.025.PMID: 30089273


Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes.
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.
Cancer Immunol Res. 2016 May;4(5):390-9. doi: 10.1158/2326-6066.CIR-15-0243. Epub 2016 Mar 15.PMID: 26980599


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.
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; Translational Breast Cancer Research Consortium (TBCRC).
Clin Cancer Res. 2015 Jun 15;21(12):2722-9. doi: 10.1158/1078-0432.CCR-14-2780. Epub 2015 Mar 16.PMID: 25779953 Clinical Trial.


Recurrent read-through fusion transcripts in breast cancer.
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.
Breast Cancer Res Treat. 2014 Jul;146(2):287-97. doi: 10.1007/s10549-014-3019-2. Epub 2014 Jun 15.PMID: 24929677


Dynamic DNA methylation across diverse human cell lines and tissues.
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.
Genome Res. 2013 Mar;23(3):555-67. doi: 10.1101/gr.147942.112. Epub 2013 Jan 16.PMID: 23325432


Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.
Varley KE, Mitra RD.
Genome Res. 2010 Sep;20(9):1279-87. doi: 10.1101/gr.101212.109. Epub 2010 Jul 13.PMID: 20627893