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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.


The vulnerability of RB loss in breast cancer: Targeting a void in cell cycle control.

Knudsen ES, Zacksenhaus E.

Oncotarget. 2018 Jul 24;9(57):30940-30941. doi: 10.18632/oncotarget.25797. eCollection 2018 Jul 24. No abstract available.


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.


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.


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.


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.


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.


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.


Kinase-independent role of cyclin D1 in chromosomal instability and mammary tumorigenesis.

Casimiro MC, Di Sante G, Crosariol M, Loro E, Dampier W, Ertel A, Yu Z, Saria EA, Papanikolaou A, Li Z, Wang C, Addya S, Lisanti MP, Fortina P, Cardiff RD, Tozeren A, Knudsen ES, Arnold A, Pestell RG.

Oncotarget. 2015 Apr 20;6(11):8525-38.


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.


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.


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.


The changing landscape of hepatocellular carcinoma: etiology, genetics, and therapy.

Knudsen ES, Gopal P, Singal AG.

Am J Pathol. 2014 Mar;184(3):574-83. doi: 10.1016/j.ajpath.2013.10.028. Epub 2013 Dec 31. Review.


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.


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.


Expression of cyclin D1a and D1b as predictive factors for treatment response in colorectal cancer.

Myklebust MP, Li Z, Tran TH, Rui H, Knudsen ES, Elsaleh H, Fluge Ø, Vonen B, Myrvold HE, Leh S, Tveit KM, Pestell RG, Dahl O.

Br J Cancer. 2012 Nov 6;107(10):1684-91. doi: 10.1038/bjc.2012.463. Epub 2012 Oct 25.


RB-pathway disruption is associated with improved response to neoadjuvant chemotherapy in breast cancer.

Witkiewicz AK, Ertel A, McFalls J, Valsecchi ME, Schwartz G, Knudsen ES.

Clin Cancer Res. 2012 Sep 15;18(18):5110-22. doi: 10.1158/1078-0432.CCR-12-0903. Epub 2012 Jul 18.


Therapeutic response to CDK4/6 inhibition in breast cancer defined by ex vivo analyses of human tumors.

Dean JL, McClendon AK, Hickey TE, Butler LM, Tilley WD, Witkiewicz AK, Knudsen ES.

Cell Cycle. 2012 Jul 15;11(14):2756-61. doi: 10.4161/cc.21195. Epub 2012 Jul 15.


CDK4/6 inhibition antagonizes the cytotoxic response to anthracycline therapy.

McClendon AK, Dean JL, Rivadeneira DB, Yu JE, Reed CA, Gao E, Farber JL, Force T, Koch WJ, Knudsen ES.

Cell Cycle. 2012 Jul 15;11(14):2747-55. doi: 10.4161/cc.21127. Epub 2012 Jul 15.


Modification of the DNA damage response by therapeutic CDK4/6 inhibition.

Dean JL, McClendon AK, Knudsen ES.

J Biol Chem. 2012 Aug 17;287(34):29075-87. doi: 10.1074/jbc.M112.365494. Epub 2012 Jun 25.


ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice.

Casimiro MC, Crosariol M, Loro E, Ertel A, Yu Z, Dampier W, Saria EA, Papanikolaou A, Stanek TJ, Li Z, Wang C, Fortina P, Addya S, Tozeren A, Knudsen ES, Arnold A, Pestell RG.

J Clin Invest. 2012 Mar;122(3):833-43. doi: 10.1172/JCI60256. Epub 2012 Feb 6. Erratum in: J Clin Invest. 2013 May 1;123(5):2332.


Identification of a core member of the SWI/SNF complex, BAF155/SMARCC1, as a human tumor suppressor gene.

DelBove J, Rosson G, Strobeck M, Chen J, Archer TK, Wang W, Knudsen ES, Weissman BE.

Epigenetics. 2011 Dec;6(12):1444-53. doi: 10.4161/epi.6.12.18492.


Progression of ductal carcinoma in situ to invasive breast cancer is associated with gene expression programs of EMT and myoepithelia.

Knudsen ES, Ertel A, Davicioni E, Kline J, Schwartz GF, Witkiewicz AK.

Breast Cancer Res Treat. 2012 Jun;133(3):1009-24. doi: 10.1007/s10549-011-1894-3. Epub 2011 Dec 2.


RB restricts DNA damage-initiated tumorigenesis through an LXCXE-dependent mechanism of transcriptional control.

Bourgo RJ, Thangavel C, Ertel A, Bergseid J, McClendon AK, Wilkens L, Witkiewicz AK, Wang JY, Knudsen ES.

Mol Cell. 2011 Aug 19;43(4):663-72. doi: 10.1016/j.molcel.2011.06.029.

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