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Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations.

Grant AD, Vail P, Padi M, Witkiewicz AK, Knudsen ES.

Sci Rep. 2019 Sep 4;9(1):12766. doi: 10.1038/s41598-019-48967-8.


Cell Cycle and Beyond: Exploiting New RB1 Controlled Mechanisms for Cancer Therapy.

Knudsen ES, Pruitt SC, Hershberger PA, Witkiewicz AK, Goodrich DW.

Trends Cancer. 2019 May;5(5):308-324. doi: 10.1016/j.trecan.2019.03.005. Epub 2019 Apr 30. Review.


Combination of ERK and autophagy inhibition as a treatment approach for pancreatic cancer.

Bryant KL, Stalnecker CA, Zeitouni D, Klomp JE, Peng S, Tikunov AP, Gunda V, Pierobon M, Waters AM, George SD, Tomar G, Papke B, Hobbs GA, Yan L, Hayes TK, Diehl JN, Goode GD, Chaika NV, Wang Y, Zhang GF, Witkiewicz AK, Knudsen ES, Petricoin EF 3rd, Singh PK, Macdonald JM, Tran NL, Lyssiotis CA, Ying H, Kimmelman AC, Cox AD, Der CJ.

Nat Med. 2019 Apr;25(4):628-640. doi: 10.1038/s41591-019-0368-8. Epub 2019 Mar 4.


Correction: Kinome-Wide RNA Interference Screen Reveals a Role for PDK1 in Acquired Resistance to CDK4/6 Inhibition in ER-Positive Breast Cancer.

Jansen VM, Bhola NE, Bauer JA, Formisano L, Lee KM, Hutchinson KE, Witkiewicz AK, Moore PD, Estrada MV, Sánchez V, Ericsson PG, Sanders ME, Pohlmann PR, Pishvaian MJ, Riddle DA, Dugger TC, Wei W, Knudsen ES, Arteaga CL.

Cancer Res. 2019 Feb 15;79(4):874. doi: 10.1158/0008-5472.CAN-18-4086. No abstract available.


Cell cycle plasticity driven by MTOR signaling: integral resistance to CDK4/6 inhibition in patient-derived models of pancreatic cancer.

Knudsen ES, Kumarasamy V, Ruiz A, Sivinski J, Chung S, Grant A, Vail P, Chauhan SS, Jie T, Riall TS, Witkiewicz AK.

Oncogene. 2019 May;38(18):3355-3370. doi: 10.1038/s41388-018-0650-0. Epub 2019 Jan 29.


Coordinately Targeting Cell-Cycle Checkpoint Functions in Integrated Models of Pancreatic Cancer.

Chung S, Vail P, Witkiewicz AK, Knudsen ES.

Clin Cancer Res. 2019 Apr 1;25(7):2290-2304. doi: 10.1158/1078-0432.CCR-18-1620. Epub 2018 Dec 11.


KRAS Suppression-Induced Degradation of MYC Is Antagonized by a MEK5-ERK5 Compensatory Mechanism.

Vaseva AV, Blake DR, Gilbert TSK, Ng S, Hostetter G, Azam SH, Ozkan-Dagliyan I, Gautam P, Bryant KL, Pearce KH, Herring LE, Han H, Graves LM, Witkiewicz AK, Knudsen ES, Pecot CV, Rashid N, Houghton PJ, Wennerberg K, Cox AD, Der CJ.

Cancer Cell. 2018 Nov 12;34(5):807-822.e7. doi: 10.1016/j.ccell.2018.10.001.


Targeting the Vulnerability of RB Tumor Suppressor Loss in Triple-Negative Breast Cancer.

Witkiewicz AK, Chung S, Brough R, Vail P, Franco J, Lord CJ, Knudsen ES.

Cell Rep. 2018 Jan 30;22(5):1185-1199. doi: 10.1016/j.celrep.2018.01.022.


Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors.

Mannakee BK, Balaji U, Witkiewicz AK, Gutenkunst RN, Knudsen ES.

Bioinformatics. 2018 May 15;34(10):1713-1718. doi: 10.1093/bioinformatics/bty010.


Composite analysis of immunological and metabolic markers defines novel subtypes of triple negative breast cancer.

Adams TA, Vail PJ, Ruiz A, Mollaee M, McCue PA, Knudsen ES, Witkiewicz AK.

Mod Pathol. 2018 Feb;31(2):288-298. doi: 10.1038/modpathol.2017.126. Epub 2017 Oct 6.


Sampling strategies to capture single-cell heterogeneity.

Rajaram S, Heinrich LE, Gordan JD, Avva J, Bonness KM, Witkiewicz AK, Malter JS, Atreya CE, Warren RS, Wu LF, Altschuler SJ.

Nat Methods. 2017 Oct;14(10):967-970. doi: 10.1038/nmeth.4427. Epub 2017 Sep 4.


The transcriptome of CDK4/6 inhibition.

Knudsen ES, Witkiewicz AK.

Aging (Albany NY). 2017 Aug 30;9(8):1859-1860. doi: 10.18632/aging.101285. No abstract available.


Biological specificity of CDK4/6 inhibitors: dose response relationship, in vivo signaling, and composite response signature.

Knudsen ES, Hutcheson J, Vail P, Witkiewicz AK.

Oncotarget. 2017 Jul 4;8(27):43678-43691. doi: 10.18632/oncotarget.18435.


Stratification of Pancreatic Ductal Adenocarcinoma: Combinatorial Genetic, Stromal, and Immunologic Markers.

Knudsen ES, Vail P, Balaji U, Ngo H, Botros IW, Makarov V, Riaz N, Balachandran V, Leach S, Thompson DM, Chan TA, Witkiewicz AK.

Clin Cancer Res. 2017 Aug 1;23(15):4429-4440. doi: 10.1158/1078-0432.CCR-17-0162. Epub 2017 Mar 27.


The Strange Case of CDK4/6 Inhibitors: Mechanisms, Resistance, and Combination Strategies.

Knudsen ES, Witkiewicz AK.

Trends Cancer. 2017 Jan;3(1):39-55. doi: 10.1016/j.trecan.2016.11.006. Review.


Kinome-Wide RNA Interference Screen Reveals a Role for PDK1 in Acquired Resistance to CDK4/6 Inhibition in ER-Positive Breast Cancer.

Jansen VM, Bhola NE, Bauer JA, Formisano L, Lee KM, Hutchinson KE, Witkiewicz AK, Moore PD, Estrada MV, Sánchez V, Ericsson PG, Sanders ME, Pohlmann PR, Pishvaian MJ, Riddle DA, Dugger TC, Wei W, Knudsen ES, Arteaga CL.

Cancer Res. 2017 May 1;77(9):2488-2499. doi: 10.1158/0008-5472.CAN-16-2653. Epub 2017 Mar 1. Erratum in: Cancer Res. 2019 Feb 15;79(4):874.


Pancreatic cancer cell lines as patient-derived avatars: genetic characterisation and functional utility.

Knudsen ES, Balaji U, Mannakee B, Vail P, Eslinger C, Moxom C, Mansour J, Witkiewicz AK.

Gut. 2018 Mar;67(3):508-520. doi: 10.1136/gutjnl-2016-313133. Epub 2017 Jan 10.


Erratum: Pancreatic stellate cells support tumour metabolism through autophagic alanine secretion.

Sousa CM, Biancur DE, Wang X, Halbrook CJ, Sherman MH, Zhang L, Kremer D, Hwang RF, Witkiewicz AK, Ying H, Asara JM, Evans RM, Cantley LC, Lyssiotis CA, Kimmelman AC.

Nature. 2016 Dec 1;540(7631):150. doi: 10.1038/nature19851. Epub 2016 Oct 5. No abstract available.


Unique metabolic features of pancreatic cancer stroma: relevance to the tumor compartment, prognosis, and invasive potential.

Knudsen ES, Balaji U, Freinkman E, McCue P, Witkiewicz AK.

Oncotarget. 2016 Nov 29;7(48):78396-78411. doi: 10.18632/oncotarget.11893.


Defining the transcriptional and biological response to CDK4/6 inhibition in relation to ER+/HER2- breast cancer.

Knudsen ES, Witkiewicz AK.

Oncotarget. 2016 Oct 25;7(43):69111-69123. doi: 10.18632/oncotarget.11588.


Pancreatic stellate cells support tumour metabolism through autophagic alanine secretion.

Sousa CM, Biancur DE, Wang X, Halbrook CJ, Sherman MH, Zhang L, Kremer D, Hwang RF, Witkiewicz AK, Ying H, Asara JM, Evans RM, Cantley LC, Lyssiotis CA, Kimmelman AC.

Nature. 2016 Aug 25;536(7617):479-83. doi: 10.1038/nature19084. Epub 2016 Aug 10. Erratum in: Nature. 2016 Dec 1;540(7631):150.


Integrated Patient-Derived Models Delineate Individualized Therapeutic Vulnerabilities of Pancreatic Cancer.

Witkiewicz AK, Balaji U, Eslinger C, McMillan E, Conway W, Posner B, Mills GB, O'Reilly EM, Knudsen ES.

Cell Rep. 2016 Aug 16;16(7):2017-31. doi: 10.1016/j.celrep.2016.07.023. Epub 2016 Aug 4.


Paracrine Induction of HIF by Glutamate in Breast Cancer: EglN1 Senses Cysteine.

Briggs KJ, Koivunen P, Cao S, Backus KM, Olenchock BA, Patel H, Zhang Q, Signoretti S, Gerfen GJ, Richardson AL, Witkiewicz AK, Cravatt BF, Clardy J, Kaelin WG Jr.

Cell. 2016 Jun 30;166(1):126-39. doi: 10.1016/j.cell.2016.05.042.


Immunologic and Metabolic Features of Pancreatic Ductal Adenocarcinoma Define Prognostic Subtypes of Disease.

Hutcheson J, Balaji U, Porembka MR, Wachsmann MB, McCue PA, Knudsen ES, Witkiewicz AK.

Clin Cancer Res. 2016 Jul 15;22(14):3606-17. doi: 10.1158/1078-0432.CCR-15-1883. Epub 2016 Feb 8.


Metabolic Reprogramming of Pancreatic Cancer Mediated by CDK4/6 Inhibition Elicits Unique Vulnerabilities.

Franco J, Balaji U, Freinkman E, Witkiewicz AK, Knudsen ES.

Cell Rep. 2016 Feb 9;14(5):979-990. doi: 10.1016/j.celrep.2015.12.094. Epub 2016 Jan 21.


The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells.

Blanco FF, Jimbo M, Wulfkuhle J, Gallagher I, Deng J, Enyenihi L, Meisner-Kober N, Londin E, Rigoutsos I, Sawicki JA, Risbud MV, Witkiewicz AK, McCue PA, Jiang W, Rui H, Yeo CJ, Petricoin E, Winter JM, Brody JR.

Oncogene. 2016 May;35(19):2529-41. doi: 10.1038/onc.2015.325. Epub 2015 Sep 21.


Genetic Diversity of Pancreatic Ductal Adenocarcinoma and Opportunities for Precision Medicine.

Knudsen ES, O'Reilly EM, Brody JR, Witkiewicz AK.

Gastroenterology. 2016 Jan;150(1):48-63. doi: 10.1053/j.gastro.2015.08.056. Epub 2015 Sep 15. Review.


Selective impact of CDK4/6 suppression on patient-derived models of pancreatic cancer.

Witkiewicz AK, Borja NA, Franco J, Brody JR, Yeo CJ, Mansour J, Choti MA, McCue P, Knudsen ES.

Oncotarget. 2015 Jun 30;6(18):15788-801.


Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets.

Witkiewicz AK, McMillan EA, Balaji U, Baek G, Lin WC, Mansour J, Mollaee M, Wagner KU, Koduru P, Yopp A, Choti MA, Yeo CJ, McCue P, White MA, Knudsen ES.

Nat Commun. 2015 Apr 9;6:6744. doi: 10.1038/ncomms7744.


The RB tumor suppressor at the intersection of proliferation and immunity: relevance to disease immune evasion and immunotherapy.

Hutcheson J, Witkiewicz AK, Knudsen ES.

Cell Cycle. 2015;14(24):3812-9. doi: 10.1080/15384101.2015.1010922. Review.


The history and future of targeting cyclin-dependent kinases in cancer therapy.

Asghar U, Witkiewicz AK, Turner NC, Knudsen ES.

Nat Rev Drug Discov. 2015 Feb;14(2):130-46. doi: 10.1038/nrd4504. Review.


RB loss contributes to aggressive tumor phenotypes in MYC-driven triple negative breast cancer.

Knudsen ES, McClendon AK, Franco J, Ertel A, Fortina P, Witkiewicz AK.

Cell Cycle. 2015;14(1):109-22. doi: 10.4161/15384101.2014.967118.


Acetate dependence of tumors.

Comerford SA, Huang Z, Du X, Wang Y, Cai L, Witkiewicz AK, Walters H, Tantawy MN, Fu A, Manning HC, Horton JD, Hammer RE, McKnight SL, Tu BP.

Cell. 2014 Dec 18;159(7):1591-602. doi: 10.1016/j.cell.2014.11.020.


MCT4 defines a glycolytic subtype of pancreatic cancer with poor prognosis and unique metabolic dependencies.

Baek G, Tse YF, Hu Z, Cox D, Buboltz N, McCue P, Yeo CJ, White MA, DeBerardinis RJ, Knudsen ES, Witkiewicz AK.

Cell Rep. 2014 Dec 24;9(6):2233-49. doi: 10.1016/j.celrep.2014.11.025. Epub 2014 Dec 11.


MUC1 Promoter-Driven DTA as a Targeted Therapeutic Strategy against Pancreatic Cancer.

Tholey RM, Lal S, Jimbo M, Burkhart RA, Blanco FF, Cozzitorto JA, Eisenberg JD, Jiang W, Iacobuzio-Donahue CA, Witkiewicz AK, Glbert M, Yeo CJ, Brody JR, Sawicki JA, Winter JM.

Mol Cancer Res. 2015 Mar;13(3):439-48. doi: 10.1158/1541-7786.MCR-14-0199. Epub 2014 Oct 21.


Retinoblastoma tumor suppressor pathway in breast cancer: prognosis, precision medicine, and therapeutic interventions.

Witkiewicz AK, Knudsen ES.

Breast Cancer Res. 2014 May 7;16(3):207. doi: 10.1186/bcr3652. Review.


Systematically defining single-gene determinants of response to neoadjuvant chemotherapy reveals specific biomarkers.

Witkiewicz AK, Balaji U, Knudsen ES.

Clin Cancer Res. 2014 Sep 15;20(18):4837-48. doi: 10.1158/1078-0432.CCR-14-0885. Epub 2014 Jul 21.


Retinoblastoma protein potentiates the innate immune response in hepatocytes: significance for hepatocellular carcinoma.

Hutcheson J, Bourgo RJ, Balaji U, Ertel A, Witkiewicz AK, Knudsen ES.

Hepatology. 2014 Oct;60(4):1231-40. doi: 10.1002/hep.27217. Epub 2014 Aug 28.


RB tumor suppressive function in response to xenobiotic hepatocarcinogens.

Reed C, Hutcheson J, Mayhew CN, Witkiewicz AK, Knudsen ES.

Am J Pathol. 2014 Jun;184(6):1853-9. doi: 10.1016/j.ajpath.2014.02.025. Epub 2014 Apr 13.


dCK expression correlates with 5-fluorouracil efficacy and HuR cytoplasmic expression in pancreatic cancer: a dual-institutional follow-up with the RTOG 9704 trial.

McAllister F, Pineda DM, Jimbo M, Lal S, Burkhart RA, Moughan J, Winter KA, Abdelmohsen K, Gorospe M, Acosta Ade J, Lankapalli RH, Winter JM, Yeo CJ, Witkiewicz AK, Iacobuzio-Donahue CA, Laheru D, Brody JR.

Cancer Biol Ther. 2014 Jun 1;15(6):688-98. doi: 10.4161/cbt.28413. Epub 2014 Mar 11.


The retinoblastoma tumor suppressor pathway modulates the invasiveness of ErbB2-positive breast cancer.

Witkiewicz AK, Cox DW, Rivadeneira D, Ertel AE, Fortina P, Schwartz GF, Knudsen ES.

Oncogene. 2014 Jul 24;33(30):3980-91. doi: 10.1038/onc.2013.367. Epub 2013 Oct 14.


EZH2 and ALDH1 expression in ductal carcinoma in situ: complex association with recurrence and progression to invasive breast cancer.

Knudsen ES, Dervishaj O, Kleer CG, Pajak T, Schwartz GF, Witkiewicz AK.

Cell Cycle. 2013 Jul 1;12(13):2042-50. doi: 10.4161/cc.25065. Epub 2013 Jun 6.


Mitoxantrone targets human ubiquitin-specific peptidase 11 (USP11) and is a potent inhibitor of pancreatic cancer cell survival.

Burkhart RA, Peng Y, Norris ZA, Tholey RM, Talbott VA, Liang Q, Ai Y, Miller K, Lal S, Cozzitorto JA, Witkiewicz AK, Yeo CJ, Gehrmann M, Napper A, Winter JM, Sawicki JA, Zhuang Z, Brody JR.

Mol Cancer Res. 2013 Aug;11(8):901-11. doi: 10.1158/1541-7786.MCR-12-0699. Epub 2013 May 21.


Melanoma adapts to RAF/MEK inhibitors through FOXD3-mediated upregulation of ERBB3.

Abel EV, Basile KJ, Kugel CH 3rd, Witkiewicz AK, Le K, Amaravadi RK, Karakousis GC, Xu X, Xu W, Schuchter LM, Lee JB, Ertel A, Fortina P, Aplin AE.

J Clin Invest. 2013 May;123(5):2155-68. doi: 10.1172/JCI65780. Epub 2013 Apr 1.


Dormant cancer cells contribute to residual disease in a model of reversible pancreatic cancer.

Lin WC, Rajbhandari N, Liu C, Sakamoto K, Zhang Q, Triplett AA, Batra SK, Opavsky R, Felsher DW, DiMaio DJ, Hollingsworth MA, Morris JP 4th, Hebrok M, Witkiewicz AK, Brody JR, Rui H, Wagner KU.

Cancer Res. 2013 Mar 15;73(6):1821-30. doi: 10.1158/0008-5472.CAN-12-2067. Epub 2013 Mar 6.


Regulation of miR106b cluster through the RB pathway: mechanism and functional targets.

Thangavel C, Boopathi E, Ertel A, Lim M, Addya S, Fortina P, Witkiewicz AK, Knudsen ES.

Cell Cycle. 2013 Jan 1;12(1):98-111. doi: 10.4161/cc.23029. Epub 2012 Dec 19.


Retinoblastoma and phosphate and tensin homolog tumor suppressors: impact on ductal carcinoma in situ progression.

Knudsen ES, Pajak TF, Qeenan M, McClendon AK, Armon BD, Schwartz GF, Witkiewicz AK.

J Natl Cancer Inst. 2012 Dec 5;104(23):1825-36. doi: 10.1093/jnci/djs446. Epub 2012 Nov 28.


Somatostatin receptor scintigraphy in patients with metastatic uveal melanoma.

Valsecchi ME, Coronel M, Intenzo CM, Kim SM, Witkiewicz AK, Sato T.

Melanoma Res. 2013 Feb;23(1):33-9. doi: 10.1097/CMR.0b013e32835b70e9.


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