Lung Cancer Metabolism Working Group: Publications

Lung Cancer Metabolism Publication Authors

All Lung Cancer Metabolism Working Group investigators are underlined.

2019
  • Gordian E, Welsh EA, Gimbrone N, Siegel EM, Shibata D, Creelan BC, Cress WD, Eschrich SA, Haura EB, Munoz-Antonia T. Transforming growth factor beta-induced epithelial-to-mesenchymal signature predicts metastasis-free survival in non-small cell lung cancer. Oncotarget. 2019;10(8):810-24. PubMed: 30783512
  • Li Q, Fisher K, Meng W, Fang B, Welsh EA, Haura EB, Koomen JM, Eschrich SA, Fridley BL, Chen YA. GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. Bioinformatics, 2019 Jun 14; https://doi.org/10.1093/bioinformatics/btz488
  • Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D. An immunoproteomic approach to characterize the CAR interactome and signalosome. Sci Signal. 2019 Feb 12;12(568).
  • Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB. Proteogenomic landscape of squamous cell lung cancer.Nat Commun. 2019 Aug 8;10(1):3578. 
  • Stewart P, Welsh E, Slebos R, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng C, Thapa R, Thompson Z, Fellows K, Francis J, Saller J, Mesa T, Zhang C, Yoder S, DeNicola G, Beg A, Boyle T, Teer J, Chen Y, Koomen J, Eschrich S, Haura E. Proteogenomic Landscape of Squamous Cell Lung Cancer. Nature Communications 2019. In press.
  • Trillo-Tinoco J, Sierra RA, Mohamed E, Cao Y, deMingo-Pulido A, Gilvary D, Anadon CA, Costich TL, Wei1 S, Ruffel B, Flores ER, Conejo-Garcia J, Rodriguez PC. AMPKa1 intrinsically regulates the function and differentiation of tumor-related MDSC. Cancer Res. 2019 Aug 13. pii: canres.0880.2019. doi: 10.1158/0008-5472.CAN-19-0880. [Epub ahead of print] PMID:31409640
  • Xie M, Zheng H, Madan-Lala R, Dai W, Gimbrone NT, Chen Z, Kinose F, Blackstone SA, Smalley KSM, Cress WD, Haura EB, Rix U, Beg AA. MEK inhibition modulates cytokine response to mediate therapeutic efficacy in lung cancer. Cancer Res. 2019. PubMed: 31362929
  • Zhao X, Ren Y, Lawlor M, Shah BD, Park PMC, Lwin T, Wang X, Liu K, Wang M, Gao J, Li T, Xu M, Silva AS, Lee K, Zhang T, Koomen JM, Jiang H, Sudalagunta PR, Meads MB, Cheng F, Bi C, Fu K, Fan H, Dalton WS, Moscinski LC, Shain KH, Sotomayor EM, Wang GG, Gray NS, Cleveland JL, Qi J, Tao J. BCL2 amplicon loss and transcriptional remodeling drives ABT-199 resistance in B cell lymphoma models. Cancer Cell 35, 752-766, 2019. PMID: 31085176.
2018
  • Ctortecka C, Palve V, Kuenzi BM, Fang B, Sumi NJ, Izumi V, Novakova S, Kinose F, Remsing Rix LL, Haura EB, Koomen JM, Rix U. Functional Proteomics and Deep Network Interrogation Reveal a Complex Mechanism of Action of Midostaurin in Lung Cancer Cells. Mol Cell Proteomics. 2018 Dec;17(12):2434-2447.
  • Farago AF, Taylor MS, Doebele RC, Zhu VW, Kummar S, Spira AI, Boyle TA, Haura EB, Arcila ME, Benayed R, Aisner DL, Horick NK, Lennerz JK, Le LP, Iafrate AJ, Ou SI, Shaw AT, Mino-Kenudson M, Drilon A. Clinicopathologic Features of Non-Small-Cell Lung Cancer Harboring an NTRK Gene Fusion. JCO Precis Oncol. 2018
  • Gray JE, Chiappori A, Williams CC, Tanvetyanon T, Haura EB, Creelan BC, Kim J, Boyle TA, Pinder-Schenck M, Khalil F, Altiok S, Devane R, Noyes D, Mediavilla-Varela M, Smilee R, Hopewell EL, Kelley L, Antonia SJ. A phase I/randomized phase II study of GM.CD40L vaccine in combination with CCL21 in patients with advanced lung adenocarcinoma. Cancer Immunol Immunother. 2018 Dec;67(12):1853-1862.
  • Hoffman MA, Fang B, Haura EB, Rix U, Koomen JM. Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer. J Proteome Res. 2018 Jan 5;17(1):63-75. doi:10.1021/acs.jproteome.7b00329. Epub 2017 Nov 22.
  • Perez-Morales J, Mejias-Morales D, Rivera-Rivera S, Gonzalez-Flores J, Gonzalez-Loperena M, Cordero-Baez FY, Pedreira-Garcia WM, Chardon-Colon C, Caban-Rivera J, Cress WD, Gordian ER, Munoz-Antonia T, Cabrera-Rios M, Isidro A, Coppola D, Rosa M, Boyle TA, Izumi V, Koomen JM, Santiago-Cardona PG. Hyper-phosphorylation of Rb S249 together with CDK5R2/p39 overexpression are associated with impaired cell adhesion and epithelial-to-mesenchymal transition: Implications as a potential lung cancer grading and staging biomarker. PLoS One. 2018;13(11):e0207483. PubMed: 30452490
  • Quinn GP, Pentz RD, Muñoz-Antonia T, Boyle TA, Schabath MB, Pratt CL, Shaffer A, Duarte LF, Bowman-Curci M, Antonia SJ, Chiappori AA, Creelan BC, Gray JE, Williams CC, Haura EB. Patient, caregiver and physician perspectives on participating in a thoracic rapid tissue donation program. Patient Educ Couns. 2018 Apr;101(4):703-710.
  • Ren Y, Chengfeng B, Zhao X, Lwin T, Wang C, Yuan J, Silva AS, Shah BD, Fang B, Koomen JM, Jiang H, Chavez JC, Pham L, Sudalagunta PR, Wan L, Dalton WS, Moscinski LC, Shain KH, Vose J, Cleveland JL, Sotomayor EM, Fu K, Tao J. PLK1 stabilizes a MYC-dependent kinase network in aggressive B cell lymphomas. Clin. Invest. 128:5517-5530, 2018. PMCID: PMC6264635.
2017
  • Kuenzi BM, Remsing Rix LL, Stewart PA, Fang B, Kinose F, Bryant AT, Boyle TA, Koomen JM, Haura EB, Rix U. Polypharmacology-based ceritinib repurposing using integrated functional proteomics. Nat Chem Biol. 2017 Dec;13(12):1222-1231.
  • Smith MA, Licata T, Lakhani A, Garcia MV, Schildhaus HU, Vuaroqueaux V, Halmos B, Borczuk AC, Chen YA, Creelan BC, Boyle TA, Haura EB. MET-GRB2 Signaling-Associated Complexes Correlate with Oncogenic MET Signaling and Sensitivity to MET Kinase Inhibitors. Clin Cancer Res. 2017 Nov 15;23(22):7084-7096.
  • Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics. 2017 Mar;17(6)
2016
  • Challa S, Guo JP, Ding X, Xu CX, Li Y, Kim D, Smith MA, Cress DW, Coppola D, Haura EB, Cheng JQ. IKBKE Is a Substrate of EGFR and a Therapeutic Target in Non-Small Cell Lung Cancer with Activating Mutations of EGFR. Cancer Res. 2016;76(15):4418-29. PubMed: 27287717
  • Chen DT, Huang PY, Lin HY, Haura EB, Antonia SJ, Cress WD, Gray JE. Strategies for power calculations in predictive biomarker studies in survival data. Oncotarget. 2016. PubMed: 27661007
  • Chen L, Engel BE, Welsh EA, Yoder SJ, Brantley SG, Chen DT, Beg AA, Cao C, Kaye FJ, Haura EB, Schabath MB, Cress WD. A sensitive NanoString-based assay to score STK11 (LKB1) pathway disruption in lung adenocarcinoma. J Thorac Oncol. 2016;11(16):838-49. PubMed: 26917230
  • Chen L, Kurtyka CA, Welsh EA, Rivera JI, Engel BE, Munoz-Antonia T, Yoder SJ, Eschrich SA, Creelan BC, Chiappori AA, Gray JE, Ramirez JL, Rosell R, Schabath MB, Haura EB, Chen DT, Cress WD. Early2 factor (E2F) deregulation is a prognostic and predictive biomarker in lung adenocarcinoma. Oncotarget. 2016;7(50):82254-65. PubMed: 27756884
  • Chen Z, Li JL, Lin S, Cao C, Gimbrone NT, Yang R, Fu DA, Carper MB, Haura EB, Schabath MB, Lu J, Amelio AL, Cress WD, Kaye FJ, Wu L. cAMP/CREB-regulated LINC00473 marks LKB1-inactivated lung cancer and mediates tumor growth. The Journal of clinical investigation. 2016;126(6):2267-79. PubMed: 27140397
  • Haake SM, Li J, Bai Y, Kinose F, Fang B, Welsh EA, Zent R, Dhillon J, Pow-Sang JM, Chen YA, Koomen JM, Rathmell WK, Fishman M, Haura EB. Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics. Clin Cancer Res. 2016 Nov 15;22(22):5605-5616
  • Jhuraney A, Woods NT, Wright G, Rix L, Kinose F, Kroeger JL, Remily-Wood E, Cress WD, Koomen JM, Brantley SG, Gray JE, Haura EB, Rix U, Monteiro AN. PAXIP1 Potentiates the Combination of WEE1 Inhibitor AZD1775 and Platinum Agents in Lung Cancer. Mol Cancer Ther. 2016 Jul;15(7):1669-81.
  • Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Apr 27;4(2):16
  • Kim JY, Welsh EA, Fang B, Bai Y, Kinose F, Eschrich SA, Koomen JM, Haura EB. Phosphoproteomics Reveals MAPK Inhibitors Enhance MET- and EGFR-Driven AKT Signaling in KRAS-Mutant Lung Cancer. Mol Cancer Res. 2016 Oct;14(10):1019-1029.
  • Knezevic CE, Wright G, Rix LLR, Kim W, Kuenzi BM, Luo Y, Watters JM, Koomen JM, Haura EB, Monteiro AN, Radu C, Lawrence HR, Rix U. Proteome-wide Profiling of Clinical PARP Inhibitors Reveals Compound-Specific Secondary Targets. Cell Chem Biol. 2016 Dec 22;23(12):1490-1503
  • Kuenzi BM, Borne AL, Li J, Haura EB, Eschrich SA, Koomen JM, Rix U, Stewart PA. APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res. 2016 Dec 2;15(12):4747-4754
  • Li J, Fang B, Kinose F, Bai Y, Kim JY, Chen YA, Rix U, Koomen JM, Haura EB. Target Identification in Small Cell Lung Cancer via Integrated Phenotypic Screening and Activity-Based Protein Profiling. Mol Cancer Ther. 2016 Feb;15(2):334-42
  • Schabath MB, Welsh EA, Fulp WJ, Chen L, Teer JK, Thompson ZJ, Engel BE, Xie M, Berglund AE, Creelan BC, Antonia SJ, Gray JE, Eschrich SA, Chen DT, Cress WD, Haura EB, Beg AA. Differential association of STK11 and TP53 with KRAS mutation-associated gene expression, proliferation and immune surveillance in lung adenocarcinoma. Oncogene. 2016;35(24):3209-16. PubMed: 26477306
2015
  • Baldelli E, Bellezza G, Haura EB, Crino L, Cress WD, Deng J, Ludovini V, Sidoni A, Schabath MB, Puma F, Vannucci J, Siggillino A, Liotta LA, Petricoin EF, 3rd, Pierobon M. Functional signaling pathway analysis of lung adenocarcinomas identifies novel therapeutic targets for KRAS mutant tumors. Oncotarget. 2015;6(32):32368-79. PubMed: 26468985
  • Baldelli E, Haura EB, Crino L, Cress WD, Ludovini V, Schabath MB, Liotta LA, Petricoin EF, Pierobon M. Impact of upfront cellular enrichment by laser capture microdissection on protein and phosphoprotein drug target signaling activation measurements in human lung cancer: Implications for personalized medicine. Proteomics Clinical applications. 2015. PubMed: 25676683
  • Cao C, Gao R, Zhang M, Amelio AL, Fallahi M, Chen Z, Gu Y, Hu C, Welsh EA, Engel BE, Haura EB, Cress WD, Wu L, Zajac-Kaye M, Kaye FJ. Role of LKB1-CRTC1 on glycosylated COX-2 and response to COX-2 inhibition in lung cancer. Journal of the National Cancer Institute. 2015;107(1):358. PubMed: 25465874
  • DeNicola GM, Karreth FA, Adams DA, Wong C. The utility of transposon mutagenesis for cancer studies in the era of genome editing. Review. Genome Biology. 2015. Oct 19;16(1):229.
  • Fang B, Hoffman MA, Mirza AS, Mishall KM, Li J, Peterman SM, Smalley KS, Shain KH, Weinberger PM, Wu J, Rix U, Haura EB, Koomen JM. Evaluating kinase ATP uptake and tyrosine phosphorylation using multiplexed quantification of chemically labeled and post-translationally modified peptides. Methods. 2015 Jun 15;81:41-9.
  • Schneeberger VE, Ren Y, Luetteke N, Huang Q, Chen L, Lawrence HR, Lawrence NJ, Haura EB, Koomen JM, Coppola D, Wu J. Inhibition of Shp2 suppresses mutant EGFR-induced lung tumors in transgenic mouse model of lung adenocarcinoma. Oncotarget. 2015 Mar 20;6(8):6191-202.
  • Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One. 2015 Nov 5;10(11):e0142162
2002-2014
  • Bai Y, Kim JY, Watters JM, Fang B, Kinose F, Song L, Koomen JM, Teer JK, Fisher K, Chen YA, Rix U, Haura EB. Adaptive responses to dasatinib-treated lung squamous cell cancer cells harboring DDR2 mutations. Cancer Res. 2014 Dec 15;74(24):7217-7228
  • Donatelli SS, Zhou JM, Gilvary DL, Eksioglu EA, Chen X, Cress WD, Haura EB, Schabath MB, Coppola D, Wei S, Djeu JY. TGF-beta-inducible microRNA-183 silences tumor-associated natural killer cells. Proc Natl Acad Sci U S A. 2014;111(11):4203-8. PubMed: 24586048
  • Remsing Rix LL, Kuenzi BM, Luo Y, Remily-Wood E, Kinose F, Wright G, Li J, Koomen JM, Haura EB, Lawrence HR, Rix U. GSK3 alpha and beta are new functionally relevant targets of tivantinib in lung cancer cells. ACS Chem Biol. 2014 Feb 21;9(2):353-8
  • Kim JY, Welsh EA, Oguz U, Fang B, Bai Y, Kinose F, Bronk C, Remsing Rix LL, Beg AA, Rix U, Eschrich SA, Koomen JM, Haura EB. Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12414-9.
  • Gopinathan A, DeNicola GM, Frese KK, Cook N, Karreth FA, Mayerle J, Lerch MM, Reinheckel T, Tuveson DA. Cathepsin B promotes the progression of pancreatic ductal adenocarcinoma in mice. Gut. 2012 Jun;61(6)877-84.
  • Chen DT, Hsu YL, Fulp WJ, Coppola D, Haura EB, Yeatman TJ, Cress WD. Prognostic and predictive value of a malignancy-risk gene signature in early-stage non-small cell lung cancer. Journal of the National Cancer Institute. 2011;103(24):1859-70. PubMed: 22157961
  • DeNicola GM, Karreth FA, Humpton TJ, Gopinathan A, Wei C, Frese K, Mangal D, Yu KH, Yeo CJ, Calhoun ES, Scrimieri F, Winter JM, Hruban RH, Iacobuzio-Donahue C, Kern SE, Blair IA, and Tuveson DA. Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis. Nature. 2011 Jul 6;475(7354):106-9.
  • Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, DeNicola G, Webster KA, Weiss D, Perez-Mancera PA, Krauthammer M, Halaban R, Provero P, Adams DJ, Tuveson DA, Pandolfi PP. In vivo identification of tumor suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell. 2011 Oct 14;147(2):382-95.
  • Karreth FA, Frese KK, DeNicola GM, Baccarini M, and Tuveson DA. C-Raf is required for the initiation of lung cancer by K-RasG12D. Cancer Discov. 2011 Jul;1(2):128-136.
  • Brazelle W, Kreahling JM, Gemmer J, Ma Y, Cress WD, Haura E, Altiok S. Histone deacetylase inhibitors downregulate checkpoint kinase 1 expression to induce cell death in non-small cell lung cancer cells. PLoS ONE. 2010;5(12):e14335. PubMed: 21179472
  • Fang B, Haura EB, Smalley KS, Eschrich SA, Koomen JM. Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling. Biochem Pharmacol. 2010 Sep 1;80(5):739-47.
  • Karreth FA, DeNicola GM, Winter SP, Tuveson DA. C-Raf inhibits MAPK activation and transformation by BRaf(V600E). Mol Cell. 2009 Nov 13;36(3):477-86.
  • Koomen JM, Haura EB, Bepler G, Sutphen R, Remily-Wood ER, Benson K, Hussein M, Hazlehurst LA, Yeatman TJ, Hildreth LT, Sellers TA, Jacobsen PB, Fenstermacher DA, Dalton WS. Proteomic contributions to personalized cancer care. Mol Cell Proteomics. 2008 Oct;7(10):1780-94.
  • Bepler G, Zheng Z, Gautam A, Sharma S, Cantor A, Sharma A, Cress WD, Kim YC, Rosell R, McBride C, Robinson L, Sommers E, Haura E. Ribonucleotide reductase M1 gene promoter activity, polymorphisms, population frequencies, and clinical relevance. Lung cancer (Amsterdam, Netherlands). 2005;47(2):183-92. PubMed: 15639717
  • Freeman SN, Bepler G, Haura E, Sutphen R, Cress WD. Prognostic significance of a short sequence insertion in the MCL-1 promoter in chronic lymphocytic leukemia. Journal of the National Cancer Institute. 2005;97(14):1088-9. PubMed: 16030308
  • Freeman SN, Bepler G, Haura E, Sutphen R, Cress WD. Re: Prognostic significance of a short sequence insertion in the MCL-1 promoter in chronic lymphocytic leukemia. Journal of the National Cancer Institute. 2005;97(14):1088-9; author reply 93-5. PubMed: 16030308
  • Song L, Coppola D, Livingston S, Cress D, Haura EB. Mcl-1 regulates survival and sensitivity to diverse apoptotic stimuli in human non-small cell lung cancer cells. Cancer biology & therapy. 2005;4(3):267-76. PubMed: 1575366
  • Haura EB, Cress WD, Chellappan S, Zheng Z, Belper G. Antiapoptotic signaling pathways in non-small-cell lung cancer: biology and therapeutic strategies. Clinical lung cancer. 2004;6(2):113-22. PubMed: 15476597
  • Hauser P, Ma L, Agrawal D, Haura E, Cress WD, Pledger WJ. Efficient down-regulation of cyclin A-associated activity and expression in suspended primary keratinocytes requires p21(Cip1). Molecular cancer research : MCR. 2004;2(2):96-104. PubMed: 14985466
  • Ma Y, Cress WD, Haura EB. Flavopiridol-induced apoptosis is mediated through up-regulation of E2F1 and repression of Mcl-1. Mol Cancer Ther. 2003;2(1):73-81. PubMed: 1253367
  • Croxton R, Ma Y, Song L, Haura EB, Cress WD. Direct repression of the Mcl-1 promoter by E2F1. Oncogene. 2002;21(9):1359-69. PubMed: 11857079
Under Revision
  • Davis A, Tsinkevich M, Rodencal J, Abbas HA, Su X, Rajapakshe K, Fang B, Coarfa C, Gunaratne P, Koomen JM, Tsai KY, Flores TAp63-regulated miRNAs inhibit UV induced cutaneous squamous cell carcinoma progression by targeting cell cycle regulation. Under Revision
  • Mohamed E, Sierra RA, Trillo-Tinoco J, Cao Y, deMingo-Pulido A, Innamarato P, Pilon-Thomas S, Costich TL, Ruffel B, Mehrotra S, Flores ER, Conejo-Garcia J, Munn D, Rodriguez ER stress mediator Perk orchestrates tumor-MDSC activity through Nrf2-controlled mitochondrial homeostasis and STING pathway activation. Under Revision
  • Hesterberg RS, Beatty MS, Han Y,  Fernandez MR, Akuffo AA, Yang C, Alontaga AY, Goodheart WE, McDaniel JM, Mailloux AW, Billington JMR, Yu L, Russell S, Gillies RJ, Ayaz M, Lawrence NJ, Lawrence HR, Darville LN, Koomen JM, Ren X, Messina J, Jiang K, Garrett TJ, Rajadhyaksha AM, Cleveland JL, Epling-Burnette P.Cereblon Harnesses c-Myc-Dependent Bioenergetics and Anti-Tumor Activity of CD8+ T lymphocytes. Under Revision.
  • Yurdagul A Jr, Subramanian M, Wang X, Crown SB, Darville L, Kolluru GK, Rymond CC, Zhang Z, Kuriakose G, Kevil CG, Koomen JM, Cleveland JL, Muoio D, Tabas I. Metabolism of Apoptotic Cell-Derived Arginine into Putrescine by Macrophages Promotes Continual Efferocytosis. Under Revision.
  • Ward NP, Kang YP, Falzone A, Boyle TA, DeNicola GM. NNT regulates mitochondrial metabolism in NSCLC through maintenance of Fe-S protein function. Under Revision.