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: September 2014

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Publications Citing Koch Institute Faculty Members

1. Myocardial drug distribution generated from local epicardial application: Potential impact of cardiac capillary perfusion in a swine model using epinephrine. Maslov MY, Edelman ER, Pezone MJ, Wei AE, Wakim MG, Murray MR, Tsukada H, Gerogiannis IS, Groothuis A, Lovich MA. J Control Releasepubmed:25234821;  doi:10.1016/j.jconrel.2014.09.012

2. Target-responsive DNA/RNA nanomaterials for microRNA sensing and inhibition: The jack-of-all-trades in cancer nanotheranostics?. Conde J, Edelman ER, Artzi N. Adv Drug Deliv Rev.pubmed:25220355;  doi:10.1016/j.addr.2014.09.003

3. Innervation patterns may limit response to endovascular renal denervation. Tzafriri AR, Mahfoud F, Keating JH, Markham PM, Spognardi A, Wong G, Fuimaono K, Bohm M, Edelman ER. J Am Coll Cardiol.pubmed:25212640;  doi:10.1016/j.jacc.2014.07.937

4. A microphysiological system model of therapy for liver micrometastases. Clark AM, Wheeler SE, Taylor DP, Pillai VC, Young CL, Prantil-Baun R, Nguyen T, Stolz DB, Borenstein JT, Lauffenburger DA, Venkataramanan R, Griffith LG, Wells A. Exp Biol Med (Maywood)pubmed:24821820;  doi:10.1177/1535370214532596

5. Equilibrium And Dynamic Design Principles For Binding Molecules Engineered For Reagentless Biosensors. de Picciotto S, Imperiali B, Griffith LG, Dane Wittrup K. Anal Biochem.pubmed:24814226;  doi:10.1016/j.ab.2014.04.036

6. Adaptive growth factor delivery from a polyelectrolyte coating promotes synergistic bone tissue repair and reconstruction. Shah NJ, Hyder MN, Quadir MA, Dorval Courchesne NM, Seeherman HJ, Nevins M, Spector M, Hammond PT. Proc Natl Acad Sci U S Apubmed:25136093;  doi:10.1073/pnas.1408035111

7. 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

8. Microneedles for Drug Delivery via the Gastrointestinal Tract. Traverso G, Schoellhammer CM, Schroeder A, Maa R, Lauwers GY, Polat BE, Anderson DG, Blankschtein D, Langer R. J Pharm Sci.pubmed:25250829;  doi:10.1002/jps.24182

9. A Perspective on the Clinical Translation of Scaffolds for Tissue Engineering. Webber MJ, Khan OF, Sydlik SA, Tang BC, Langer R. Ann Biomed Engpubmed:25201605;  doi:10.1007/s10439-014-1104-7

10. Overcoming the challenges in administering biopharmaceuticals: formulation and delivery strategies. Mitragotri S, Burke PA, Langer R. Nat Rev Drug Discovpubmed:25103255;  doi:10.1038/nrd4363

11. High throughput screening for biomaterials discovery. Algahtani MS, Scurr DJ, Hook AL, Anderson DG, Langer RS, Burley JC, Alexander MR, Davies MC. J Control Release.pubmed:24993427;  doi:10.1016/j.jconrel.2014.06.045

12. Single compartment drug delivery. Cima MJ, Lee H, Daniel K, Tanenbaum LM, Mantzavinou A, Spencer KC, Ong Q, Sy JC, Santini JJr, Schoellhammer CM, Blankschtein D, Langer RS. J Control Release.pubmed:24798478;  doi:10.1016/j.jconrel.2014.04.049

13. Lipid-Like Nanomaterials for Simultaneous Gene Expression and Silencing In Vivo. Dong Y, Eltoukhy AA, Alabi CA, Khan OF, Veiseh O, Dorkin JR, Sirirungruang S, Yin H, Tang BC, Pelet JM, Chen D, Gu Z, Xue Y, Langer R, Anderson DG. Adv Healthc Materpubmed:24623658;  doi:10.1002/adhm.201400054

14. Stochastic Particle Barcoding for Single-Cell Tracking and Multiparametric Analysis. Castellarnau M, Szeto GL, Su HW, Tokatlian T, Love JC, Irvine DJ, Voldman J. Small.pubmed:25180800;  doi:10.1002/smll.201401369

15. Enhancing Radiotherapy by Lipid Nanocapsule-Mediated Delivery of Amphiphilic Gold Nanoparticles to Intracellular Membranes. Yang YS, Carney RP, Stellacci F, Irvine DJ. ACS Nano.pubmed:25123510;  doi:10.1021/nn502146r

16. 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

17. Human Vascular Tissue Models Formed from Human Induced Pluripotent Stem Cell Derived Endothelial Cells. Belair DG, Whisler JA, Valdez J, Velazquez J, Molenda JA, Vickerman V, Lewis R, Daigh C, Hansen TD, Mann DA, Thomson JA, Griffith LG, Kamm RD, Schwartz MP, Murphy WL. Stem Cell Revpubmed:25190668;  doi:10.1007/s12015-014-9549-5

18. Reply to Azuaje: Predicting effective combined therapies for heterogeneous tumors. Zhao B, Hemann MT, Lauffenburger DA. Proc Natl Acad Sci U S Apubmed:25253893;  doi:10.1073/pnas.1415737111

19. Repair of endogenous DNA base lesions modulate lifespan in mice. Meira LB, Calvo JA, Shah D, Klapacz J, Moroski-Erkul CA, Bronson RT, Samson LD. DNA Repair (Amst).pubmed:24994062;  doi:10.1016/j.dnarep.2014.05.012

20. SirT1 is required in the male germ cell for differentiation and fecundity in mice. Bell EL, Nagamori I, Williams EO, Del Rosario AM, Bryson BD, Watson N, White FM, Sassone-Corsi P, Guarente L.Developmentpubmed:25142464;  doi:10.1242/dev.110627

21. Deep, noninvasive imaging and surgical guidance of submillimeter tumors using targeted M13-stabilized single-walled carbon nanotubes. Ghosh D, Bagley AF, Na YJ, Birrer MJ, Bhatia SN, Belcher AM. Proc Natl Acad Sci U S Apubmed:25214538;  doi:10.1073/pnas.1400821111

22. Self-Titrating Anticoagulant Nanocomplexes That Restore Homeostatic Regulation of the Coagulation Cascade. Lin KY, Lo JH, Consul N, Kwong GA, Bhatia SN. ACS Nano.pubmed:25119520;  doi:10.1021/nn501129q

23. Mechanisms of cooperation in cancer nanomedicine: towards systems nanotechnology. Hauert S, Bhatia SN. Trends Biotechnolpubmed:25086728;  doi:10.1016/j.tibtech.2014.06.010

24. Genetic and molecular identification of three human TPP1 functions in telomerase action: recruitment, activation, and homeostasis set point regulation. Sexton AN, Regalado SG, Lai CS, Cost GJ, O'Neil CM, Urnov FD, Gregory PD, Jaenisch R, Collins K, Hockemeyer D. Genes Devpubmed:25128433;  doi:10.1101/gad.246819.114

25. RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites. Engreitz JM, Sirokman K, McDonel P, Shishkin AA, Surka C, Russell P, Grossman SR, Chow AY, Guttman M, Lander ES. Cellpubmed:25259926;  doi:10.1016/j.cell.2014.08.018

26. Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA. Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, Leon-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A. Cellpubmed:25219674;  doi:10.1016/j.cell.2014.08.028

27. The genomic substrate for adaptive radiation in African cichlid fish. Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alfoldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SC, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F. Naturepubmed:25186727;  doi:10.1038/nature13726

28. The Developmental Potential of iPSCs Is Greatly Influenced by Reprogramming Factor Selection. Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R. Cell Stem Cell.pubmed:25192464;  doi:10.1016/j.stem.2014.07.003

29. Cpeb4-Mediated Translational Regulatory Circuitry Controls Terminal Erythroid Differentiation. Hu W, Yuan B, Lodish HF. Dev Cellpubmed:25220394;  doi:10.1016/j.devcel.2014.07.008

30. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC. Sciencepubmed:25214632;  doi:10.1126/science.1259657

31. From yeast to patient neurons and back again: A powerful new discovery platform. Tardiff DF, Khurana V, Chung CY, Lindquist S. Mov Disordpubmed:25131316;  doi:10.1002/mds.25989

32. Aging research-where do we stand and where are we going?. Guarente L. Cellpubmed:25259916;  doi:10.1016/j.cell.2014.08.041

33. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Knouse KA, Wu J, Whittaker CA, Amon A. Proc Natl Acad Sci U S Apubmed:25197050;  doi:10.1073/pnas.1415287111

34. Multiple Functions for Mcm2-7 ATPase Motifs during Replication Initiation. Kang S, Warner MD, Bell SP. Mol Cellpubmed:25087876;  doi:10.1016/j.molcel.2014.06.033

35. PLAAC: a web and command-line application to identify proteins with Prion-Like Amino Acid Composition. Lancaster AK, Nutter-Upham A, Lindquist S, King OD. Bioinformatics.pubmed:24825614;  doi:10.1093/bioinformatics/btu310

36. 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

37. Cell-state-specific metabolic dependency in hematopoiesis and leukemogenesis. Wang YH, Israelsen WJ, Lee D, Yu VW, Jeanson NT, Clish CB, Cantley LC, Vander Heiden MG, Scadden DT. Cell.pubmed:25215489;  doi:10.1016/j.cell.2014.07.048

38. 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

39. Unraveling the Physiological Complexities of Antibiotic Lethality. Dwyer DJ, Collins JJ, Walker GC. Annu Rev Pharmacol Toxicolpubmed:25251995;  doi:10.1146/annurev-pharmtox-010814-124712

40. Selective Mitogen Activated Protein Kinase Activity Sensors through the Application of Directionally Programmable D Domain Motifs. Peterson LB, Yaffe MB, Imperiali B. Biochemistry.pubmed:25153342;  doi:10.1021/bi500862c

41. 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

42. Light-Induced NO Production from a Non-heme Iron-Nitrosyl Dimer. Jiang Y, Hayashi T, Matsumura H, Do LH, Majumdar A, Lippard SJ, Moenne-Loccoz P. J Am Chem Soc.pubmed:25158917;  doi:10.1021/ja504343t

43. De-Differentiation Confers Multidrug Resistance Via Noncanonical PERK-Nrf2 Signaling. Del Vecchio CA, Feng Y, Sokol ES, Tillman EJ, Sanduja S, Reinhardt F, Gupta PB. PLoS Biol.pubmed:25203443;  doi:10.1371/journal.pbio.1001945

44. Ena/VASP regulates mDia2-initiated filopodial length, dynamics, and function. Barzik M, McClain LM, Gupton SL, Gertler FB. Mol Biol Cellpubmed:24989797;  doi:10.1091/mbc.E14-02-0712

45. Alternative Splicing of Endothelial Fibronectin Is Induced by Disturbed Hemodynamics and Protects Against Hemorrhage of the Vessel Wall. Murphy PA, Hynes RO. Arterioscler Thromb Vasc Biol.pubmed:24903094;  doi:10.1161/ATVBAHA.114.303879

46. Biological cost of pyocin production during the SOS response in Pseudomonas aeruginosa. Penterman J, Singh PK, Walker GC. J Bacteriolpubmed:25022851;  doi:10.1128/JB.01889-14

47. A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages. Lu H, Clauser KR, Tam WL, Frose J, Ye X, Eaton EN, Reinhardt F, Donnenberg VS, Bhargava R, Carr SA, Weinberg RA. Nat Cell Biolpubmed:25266422;  doi:10.1038/ncb3041