Publications

2023

  • Pitea A*, Turnham RE*, Eckhardt M, Jang GM, Xu Z, Lim HC, Choi A, Von Dollen J, Levin RS, Webber JT, McCarthy E, Hu J, Li X, Che L, Chan GKL, Kelley RK, Swaney DL, Zhang W, Bandyopadhyay S, Theis FJ, Chen X, Shokat KM, Ideker T, Krogan NJ, Gordan JD. HBV rewires liver cancer signaling by altering PP2A complexes. bioRxiv 2023.03.15.532845. doi: https://doi.org/10.1101/2023.03.15.532845 *equal contribution
  • Zack T, Losert KP, Maisel SM, Wild J, Yaqubie A, Herman M, Knox JJ, Mayer RJ, Venook AP, Butte A, O'Neill AF, Abou-Alfa GK, Gordan JD. Defining incidence and complications of fibrolamellar liver cancer through tiered computational analysis of clinical data. NPJ Precis Oncol. 2023 Mar 23;7(1):29. doi: 10.1038/s41698-023-00371-2. PMID: 36959495 PMCID: PMC10034241
  • Chan GKL, Maisel S, Hwang YC, Pascual BC, Wolber RRB, Vu P, Patra KC, Bouhaddou M, Kenerson HL, Lim HC, Long D, Yeung RS, Sethupathy P, Swaney DL, Krogan NJ, Turnham RE, Riehle KJ, Scott JD, Bardeesy N, Gordan JD. Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms. Elife. 2023 Jan 24;12. doi: 10.7554/eLife.69521. PMCID: PMC9925115.

2022

  • Qing T, Liu J, Liu F, Mitchell DC, Beresis RT, Gordan JD. Methods to assess small molecule allosteric modulators of the STRAD pseudokinase. Methods Enzymol. 2022;667:427-453. PMID: 35525550
  • Wu Q, Zhen Y, Shi L, Vu P, Greninger P, Adil R, Merritt J, Egan R, Wu MJ, Yin X, Ferrone CR, Deshpande V, Baiev I, Pinto CJ, McLoughlin DE, Walmsley CS, Stone JR, Gordan JD, Zhu AX, Juric D, Goyal L, Benes CH, Bardeesy N. EGFR Inhibition Potentiates FGFR Inhibitor Therapy and Overcomes Resistance in FGFR2 Fusion-Positive Cholangiocarcinoma. Cancer Discov. 2022 May 2;12(5):1378-1395. doi: 10.1158/2159-8290.CD-21-1168. PMID: 35420673
  • Melnyk JE, Steri V, Nguyen HG, Hwang YC, Gordan JD, Hann B, Feng FY, Shokat KM. Targeting a splicing-mediated drug resistance mechanism in prostate cancer by inhibiting transcriptional regulation by PKCβ1. Oncogene. 2022 Mar; 41(11):1536-1549. PMID: 35087237. PMCID: PMC8913362

2021

  • Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van 't Veer L, Ashworth A, Ideker T, Krogan NJ. A protein interaction landscape of breast cancer. Science. 2021 Oct 1; 374(6563):eabf3066. PMID: 34591612.
  • Lim HC, Gordan JD. Tumor hepatitis B virus RNA identifies a clinically and molecularly distinct subset of hepatocellular carcinoma. PLOS Computational Biology. 2021 Feb 9;17(2):e1008699. PMID: 33561166, PMCID: PMC7909678.

2020

  • Gordan JD, Kennedy EB, Abou-Alfa GK, Beg M, Goff L, Guy J, Gupta S, Harris WP, Iyer R, Jaiyesimi I, Jhawer M, Karippot A, Kaseb AO, Kelley RK, Knox J, Kortmansky J, Brower ST, Gade TP, Venepalli NK, Taddei TH, Leaf A, Wilson A,  Remak W,  Shroff R,  Sohal DPS, Zhu AX, Rose MG. Systemic Therapy for Advanced Hepatocellular Carcinoma: American Society of Clinical Oncology Clinical Practice Guideline. J Clin Oncol. 2020 Dec 20;38(36):4317-4345. PMID: 33197225. 
  • Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC,  Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le, Shue YT, Ko JH,  Lee MC,  Kong C, Nomura DK, Ohlmeyer M, Swaney DL, Krogan NK. Jackson PK,  Narla G, Gordan JD,  Shokat KM, Sage J. Unbiased proteomic profiling uncovers a targetable GNAS/PKA/PP2A axis in small cell lung cancer stem cells. 2020. Cancer Cell, Jul 13;38(1):129-143. PMID: 32531271.

2019

  • Wang J, Wang H, Peters M, Ding N, Ribback S, Utpatel K, Cigliano A, Dombrowski/> F, Xu M, Chen X, Song X, Che L, Evert M, Cossu A, Gordan J, Zeng Y, Chen X, Calvisi DF. Loss of Fbxw7 synergizes with activated Akt signaling to promote c-Myc dependent cholangiocarcinogenesis. J Hepatol. 2019 Oct;71(4):742-752. PubMed PMID: 31195063.
  • Lou K, Steri V, Ge AY, Hwang YC, Yogodzinski CH, Shkedi AR, Choi ALM, Mitchell DC, Swaney DL, Hann B, Gordan JD, Shokat KM, Gilbert LA. KRAS(G12C) inhibition produces a driver-limited state revealing collateral dependencies. Sci Signal. 2019 May 28;12(583). pii: eaaw9450. doi: 10.1126/scisignal.aaw9450. PMID: 31138768.
  • Frazier NM, Brand T, Gordan JD, Grandis J, Jura N. Overexpression-mediated activation of MET in the Golgi promotes HER3/ERBB3 phosphorylation. Oncogene. 2019 Mar;38(11):1936-1950. doi: 10.1038/s41388-018-0537-0. Epub 2018 Nov 2. PMID: 30390071; PMCID: PMC6417953.
  • Xu Y, Poggio M, Jin HY, Shi Z, Forester CM, Wang Y, Stumpf CR, Xue L, Devericks E, So L, Nguyen HG, Griselin A, Gordan JD, Umetsu SE, Reich SH, Worland ST, Asthana S, Barna M, Webster KR, Cunningham JT, Ruggero D. Translation control of the immune checkpoint in cancer and its therapeutic targeting. Nat Med. 2019 Feb;25(2):301-311. doi: 10.1038/s41591-018-0321-2. Epub 2019 Jan 14. PMID: 30643286; PMCID: PMC6613562.
  • Song X, Liu X, Wang H, Wang J, Qiao Y, Cigliano A, Utpatel K, Ribback S, Pilo MG, Serra M, Gordan JD, Che L, Zhang S, Cossu A, Porcu A, Pascale RM, Dombrowski F, Hu H, Calvisi DF, Evert M, Chen X. Combined CDK4/6 and Pan-mTOR Inhibition Is Synergistic Against Intrahepatic Cholangiocarcinoma. Clin Cancer Res. 2019 Jan 1;25(1):403-413. doi: 10.1158/1078-0432.CCR-18-0284. Epub 2018 Jul 3. PMID: 30084835; PMCID: PMC6423983.

2018

  • ​Lim HC, Montesion M, Botton T, Collisson EA, Umetsu SE, Behr SC, Gordan JD, Stephens PJ, Kelley RK. 2018. Hybrid Capture-Based Tumor Sequencing and Copy Number Analysis to Confirm Origin of Metachronous Metastases in BRCA1-Mutant Cholangiocarcinoma Harboring a Novel YWHAZ-BRAF Fusion. Oncologist. Sep;23(9):998- PMCID: PMC6192605.
  • Donnella HJ, Webber JT, Levin RS, Camarda R, Momcilovic O, Bayani N, Shah KN, Korkola JE, Shokat KM, Goga A, Gordan JD, Bandyopadhyay S. Kinome rewiring reveals AURKA limits PI3K-pathway inhibitor efficacy in breast cancer. Nat Chem Biol. 2018 Aug;14(8):768-777. doi: 10.1038/s41589-018-0081-9. Epub 2018 Jun 25. PMID: 29942081; PMCID: PMC6051919.
  • Wang J, Dong M, Xu Z, Song X, Zhang S, Qiao Y, Che L, Gordan J, Hu K, Liu Y, Calvisi DF, Chen X. Notch2 controls hepatocyte-derived cholangiocarcinoma formation in mice. Oncogene. 2018 Mar 16. PMID: 29545603.
  • Dong M, Liu X, Evert K, Utpatel K, Peters M, Zhang S, Xu Z, Che L, Cigliano A, Ribback S, Dombrowski F, Cossu A, Gordan J, Calvisi DF, Evert M, Liu Y, Chen X. Efficacy of MEK inhibition in a K-Ras-driven cholangiocarcinoma preclinical model. Cell Death Dis. 2018 Jan 18;9(2):31. PMID: 29348467.

2017

  • Rajaram S, Heinrich LE, Gordan JD, Avva J, Bonness KM, Witkiewicz AK, Malter JS, Atreya CE, Warren RS, Wu LF, Altschuler SJ. Sampling strategies to capture single-cell heterogeneity. Nat Methods. 2017 Sep 04. PMID: 28869755. PMCID: PMC5658002.
  • Zhang S, Song X, Cao D, Xu Z, Fan B, Che L, Hu J, Chen B, Dong M, Pilo MG, Cigliano A, Evert K, Ribback S, Dombrowski F, Pascale RM, Cossu A, Vidili G, Porcu A, Simile MM, Pes GM, Giannelli G, Gordan J, Wei L, Evert M, Cong W, Calvisi DF, Chen X. Pan-mTOR inhibitor MLN0128 is effective against intrahepatic cholangiocarcinoma in mice. J Hepatol. 2017 Dec;67(6):1194-1203. PMID: 28733220.

2016 

  • Urisman A, Levin RS, Gordan JD, Webber JT, Hernandez H, Ishihama Y, Shokat KM, Burlingame AL. An optimized chromatographic strategy for multiplexing in parallel reaction monitoring mass spectrometry: Insights from quantitation of activated kinases. Mol Cell Proteomics. 2016 Dec 11. PMID: 27940637.
  • Miller RE, Brough R, Bajrami I, Williamson CT, McDade S, Campbell J, Kigozi A, Rafiq R, Pemberton H, Natrajan R, Joel J, Astley H, Mahoney C, Moore JD, Torrance C, Gordan JD, Webber JT, Levin RS, Shokat KM, Bandyopadhyay S, Lord CJ, Ashworth A. Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib. Mol Cancer Ther. 2016 Jul; 15(7):1472-84. PMID: 27364904.
  • Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT, Damon LJ, Egan RK, Greninger P, McDermott U, Garnett MJ, Jenkins RL, Rieger-Christ KM, Sullivan TB, Hezel AF, Liss AS, Mizukami Y, Goyal L, Ferrone CR, Zhu AX, Joung JK, Shokat KM, Benes CH, Bardeesy N. Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma. Cancer Discov. 2016 Jul; 6(7):727-39. PMID: 27231123. 

2014-2015

  • Evason KJ, Francisco MT, Juric V, Balakrishnan S, Lopez Pazmino Mdel P, Gordan JD, Kakar S, Spitsbergen J, Goga A, Stainier DY. Identification of Chemical Inhibitors of ß-Catenin-Driven Liver Tumorigenesis in Zebrafish. PLoS Genet. 2015 Jul; 11(7):e1005305. PMID: 26134322. PMCID: PMC4489858.
  • Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Linking Tumor Mutations to Drug Responses via a Quantitative Chemical-Genetic Interaction Map. Cancer Discov. 2015 Feb; 5(2):154-67. PMID: 25501949. PMCID: PMC4407699.
  • Sos ML, Levin RS, Gordan JD, Oses-Prieto JA, Webber JT, Salt M, Hann B, Burlingame AL, McCormick F, Bandyopadhyay S, Shokat KM. Oncogene mimicry as a mechanism of primary resistance to BRAF inhibitors. Cell Rep. 2014 Aug 21; 8(4):1037-48. PMID: 25127139. PMCID: PMC4294625.