The David H. Koch Institute for Integrative Cancer Research at MITThe David H. Koch Institute for Integrative Cancer Research at MIT

Massachusetts Institute of Technology

National Cancer Institute Cancer Center

Science + Engineering... Conquering Cancer Together

Progress: October 2014

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Publications Citing Koch Institute Faculty Members

1. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Xue W, Chen S, Yin H, Tammela T, Papagiannakopoulos T, Joshi NS, Cai W, Yang G, Bronson R, Crowley DG, Zhang F, Anderson DG, Sharp PA, Jacks T. Naturepubmed:25119044;  doi:10.1038/nature13589

2. Reproducible Automated Phosphopeptide Enrichment using Magnetic TiO and Ti-IMAC. Tape CJ, Worboys JD, Sinclair J, Gourlay R, Vogt J, Broster KM, Trost M, Lauffenburger DA, Lamont DJ, Jorgensen C. Anal Chempubmed:25233145;  doi:10.1021/ac5025842

3. Spontaneous dormancy of metastatic breast cancer cells in an all human liver microphysiologic system. Wheeler SE, Clark AM, Taylor DP, Young CL, Pillai VC, Stolz DB, Venkataramanan R, Lauffenburger D, Griffith L, Wells A. Br J Cancerpubmed:25314052;  doi:10.1038/bjc.2014.533

4. Stem Cell Factor Gene Transfer Improves Cardiac Function After Myocardial Infarction in Swine. Ishikawa K, Fish K, Aguero J, Yaniz-Galende E, Jeong D, Kho C, Tilemann L, Fish L, Liang L, Eltoukhy AA, Anderson DG, Zsebo K, Costa K, Hajjar RJ. Circ Heart Failpubmed:25342737;  doi:10.1161/CIRCHEARTFAILURE.114.001711

5. Organ-targeted high-throughput in vivo biologics screen identifies materials for RNA delivery. Chang TY, Shi P, Steinmeyer JD, Chatnuntawech I, Tillberg P, Love KT, Eimon PM, Anderson DG, Yanik MF.Integr Biol (Camb)pubmed:25184623;  doi:10.1039/c4ib00150h

6. Disease Detection by Ultrasensitive Quantification of Microdosed Synthetic Urinary Biomarkers. Warren AD, Gaylord ST, Ngan KC, Dumont Milutinovic M, Kwong GA, Bhatia SN, Walt DR. J Am Chem Socpubmed:25198059;  doi:10.1021/ja505676h

7. Three dimensional human small intestine models for ADME-Tox studies. Yu J, Carrier RL, March JC, Griffith LG. Drug Discov Todaypubmed:24853950;  doi:10.1016/j.drudis.2014.05.003

8. Engineering Liver. Griffith LG, Wells A, Stolz DB. Hepatologypubmed:24668880;  doi:10.1002/hep.27150

9. Layer-by-Layer Assembled Anti-Sense DNA Microsponge Particles for Efficient Delivery of Cancer Therapeutics. Roh YH, Lee JB, Shopsowitz KE, Dreaden EC, Morton SW, Poon Z, Hong J, Yamin I, Bonner DK, Hammond PT. ACS Nanopubmed:25198246;  doi:10.1021/nn502596b

10. Ionizable Amphiphilic Dendrimer-Based Nanomaterials with Alkyl-Chain-Substituted Amines for Tunable siRNA Delivery to the Liver Endothelium In Vivo. Khan OF, Zaia EW, Yin H, Bogorad RL, Pelet JM, Webber MJ, Zhuang I, Dahlman JE, Langer R, Anderson DG. Angew Chem Int Ed Englpubmed:25354018;  doi:10.1002/anie.201408221

11. CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling. Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F. Cellpubmed:25263330;  doi:10.1016/j.cell.2014.09.014

12. In vivo volume and hemoglobin dynamics of human red blood cells. Malka R, Delgado FF, Manalis SR, Higgins JM. PLoS Comput Biolpubmed:25299941;  doi:10.1371/journal.pcbi.1003839

13. Identification of Orai1 Channel Inhibitors by Using Minimal Functional Domains to Screen Small Molecule Microarrays. Sadaghiani AM, Lee SM, Odegaard JI, Leveson-Gower DB, McPherson OM, Novick P, Kim MR, Koehler AN, Negrin R, Dolmetsch RE, Park CY. Chem Biolpubmed:25308275;  doi:10.1016/j.chembiol.2014.08.016

14. The E2 Ubiquitin Conjugating Enzyme UBE2J1 is Required for Spermiogenesis in Mice. Koenig PA, Nicholls PK, Schmidt FI, Hagiwara M, Maruyama T, Frydman GH, Watson N, Page DC, Ploegh HL. J Biol Chempubmed:25320092;  doi:10.1074/jbc.M114.604132

15. Negative Self-Regulation of TLR9 Signaling by Its N-Terminal Proteolytic Cleavage Product. Lee S, Kang D, Ra EA, Lee TA, Ploegh HL, Park B. J Immunol.pubmed:25187653;  doi:10.4049/jimmunol.1400210

16. TMEM14C is required for erythroid mitochondrial heme metabolism. Yien YY, Robledo RF, Schultz IJ, Takahashi-Makise N, Gwynn B, Bauer DE, Dass A, Yi G, Li L, Hildick-Smith GJ, Cooney JD, Pierce EL, Mohler K, Dailey TA, Miyata N, Kingsley PD, Garone C, Hattangadi SM, Huang H, Chen W, Keenan EM, Shah DI, Schlaeger TM, DiMauro S, Orkin SH, Cantor AB, Palis J, Koehler CM, Lodish HF, Kaplan J, Ward DM, Dailey HA, Phillips JD, Peters LL, Paw BH. J Clin Investpubmed:25157825;  doi:10.1172/JCI76979

17. Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia. Ntziachristos P, Tsirigos A, Welstead GG, Trimarchi T, Bakogianni S, Xu L, Loizou E, Holmfeldt L, Strikoudis A, King B, Mullanders J, Becksfort J, Nedjic J, Paietta E, Tallman MS, Rowe JM, Tonon G, Satoh T, Kruidenier L, Prinjha R, Akira S, Van Vlierberghe P, Ferrando AA, Jaenisch R, Mullighan CG, Aifantis I. Nature.pubmed:25132549;  doi:10.1038/nature13605

18. Poised chromatin in the mammalian germ line. Lesch BJ, Page DC. Developmentpubmed:25249456;  doi:10.1242/dev.113027

19. Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS. Cellpubmed:25307932;  doi:10.1016/j.cell.2014.09.029

20. Endogenous miRNA and Target Concentrations Determine Susceptibility to Potential ceRNA Competition. Bosson AD, Zamudio JR, Sharp PA. Mol Cell.pubmed:25449132;  doi:10.1016/j.molcel.2014.09.018

21. Building Robust Transcriptomes with Master Splicing Factors. Jangi M, Sharp PA. Cellpubmed:25417102;  doi:10.1016/j.cell.2014.09.054

22. Control of cell identity genes occurs in insulated neighborhoods in Mammalian chromosomes. Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schuijers J, Lee TI, Zhao K, Young RA. Cellpubmed:25303531;  doi:10.1016/j.cell.2014.09.030

23. CEACAM1 regulates TIM-3-mediated tolerance and exhaustion. Huang YH, Zhu C, Kondo Y, Anderson AC, Gandhi A, Russell A, Dougan SK, Petersen BS, Melum E, Pertel T, Clayton KL, Raab M, Chen Q, Beauchemin N, Yazaki PJ, Pyzik M, Ostrowski MA, Glickman JN, Rudd CE, Ploegh HL, Franke A, Petsko GA, Kuchroo VK, Blumberg RS. Naturepubmed:25363763;  doi:10.1038/nature13848

24. Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency. Theunissen TW, Powell BE, Wang H, Mitalipova M, Faddah DA, Reddy J, Fan ZP, Maetzel D, Ganz K, Shi L, Lungjangwa T, Imsoonthornruksa S, Stelzer Y, Rangarajan S, D'Alessio A, Zhang J, Gao Q, Dawlaty MM, Young RA, Gray NS, Jaenisch R. Cell Stem Cell.pubmed:25090446;  doi:10.1016/j.stem.2014.07.002

25. Response and acquired resistance to everolimus in anaplastic thyroid cancer. Wagle N, Grabiner BC, Van Allen EM, Amin-Mansour A, Taylor-Weiner A, Rosenberg M, Gray N, Barletta JA, Guo Y, Swanson SJ, Ruan DT, Hanna GJ, Haddad RI, Getz G, Kwiatkowski DJ, Carter SL, Sabatini DM, Janne PA, Garraway LA, Lorch JH. N Engl J Medpubmed:25295501;  doi:10.1056/NEJMoa1403352

26. DNA Replication Terminating the replisome. Bell SP. Sciencepubmed:25342784;  doi:10.1126/science.1261245

27. The Role of Transcription in the Activation of a Drosophila Amplification Origin. Hua BL, Li S, Orr-Weaver TL. G3 (Bethesda)pubmed:25320071;  doi:10.1534/g3.114.014050

28. Rapid modelling of cooperating genetic events in cancer through somatic genome editing. Sanchez-Rivera FJ, Papagiannakopoulos T, Romero R, Tammela T, Bauer MR, Bhutkar A, Joshi NS, Subbaraj L, Bronson RT, Xue W, Jacks T. Naturepubmed:25337879;  doi:10.1038/nature13906

29. The Sestrins Interact with GATOR2 to Negatively Regulate the Amino-Acid-Sensing Pathway Upstream of mTORC1. Chantranupong L, Wolfson RL, Orozco JM, Saxton RA, Scaria SM, Bar-Peled L, Spooner E, Isasa M, Gygi SP, Sabatini DM. Cell Reppubmed:25263562;  doi:10.1016/j.celrep.2014.09.014

30. Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development. Mayers JR, Wu C, Clish CB, Kraft P, Torrence ME, Fiske BP, Yuan C, Bao Y, Townsend MK, Tworoger SS, Davidson SM, Papagiannakopoulos T, Yang A, Dayton TL, Ogino S, Stampfer MJ, Giovannucci EL, Qian ZR, Rubinson DA, Ma J, Sesso HD, Gaziano JM, Cochrane BB, Liu S, Wactawski-Wende J, Manson JE, Pollak MN, Kimmelman AC, Souza A, Pierce K, Wang TJ, Gerszten RE, Fuchs CS, Vander Heiden MG, Wolpin BM. Nat Medpubmed:25261994;  doi:10.1038/nm.3686

31. Depletion of Rictor, an essential protein component of mTORC2, decreases male lifespan. Lamming DW, Mihaylova MM, Katajisto P, Baar EL, Yilmaz OH, Hutchins A, Gultekin Y, Gaither R, Sabatini DM.Aging Cellpubmed:25059582;  doi:10.1111/acel.12256

32. A Breast Cancer Stem Cell-Selective, Mammospheres-Potent Osmium(VI) Nitrido Complex. Suntharalingam K, Lin W, Johnstone TC, Bruno PM, Zheng YR, Hemann MT, Lippard SJ. J Am Chem Soc.pubmed:25247635;  doi:10.1021/ja508808v

33. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Liu DS, Nivon LG, Richter F, Goldman PJ, Deerinck TJ, Yao JZ, Richardson D, Phipps WS, Ye AZ, Ellisman MH, Drennan CL, Baker D, Ting AY. Proc Natl Acad Sci U S Apubmed:25313043;  doi:10.1073/pnas.1404736111