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: February 2015

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Publications Citing Koch Institute Faculty Members

1. HDL-Mimetic PLGA Nanoparticle To Target Atherosclerosis Plaque Macrophages. Sanchez-Gaytan BL, Fay F, Lobatto ME, Tang J, Ouimet M, Kim Y, van der Staay SE, van Rijs SM, Priem B, Zhang L, Fisher EA, Moore KJ, Langer R, Fayad ZA, Mulder WJ. Bioconjug Chempubmed:25650634;  doi:10.1021/bc500517k

2. Synthetic biology devices and circuits for RNA-based 'smart vaccines': a propositional review. Andries O, Kitada T, Bodner K, Sanders NN, Weiss R. Expert Rev Vaccines.pubmed:25566800;  doi:10.1586/14760584.2015.997714

3. Low-volume multiplexed proteolytic activity assay and inhibitor analysis through a pico-injector array. Ng EX, Miller MA, Jing T, Lauffenburger DA, Chen C. Lab Chip.pubmed:25553996;  doi:10.1039/c4lc01162g

4. Phosphotyrosine signaling analysis in human tumors is confounded by systemic Ischemia-driven artifacts and intra-specimen heterogeneity. Gajadhar AS, Johnson H, Slebos RJ, Shaddox K, Wiles K, Washington MK, Herline AJ, Levine DA, Liebler DC, White FM. Cancer Respubmed:25670172;  doi:10.1158/0008-5472.CAN-14-2309

5. Liposomal vaccines incorporating molecular adjuvants and intrastructural T-cell help promote the immunogenicity of HIV membrane-proximal external region peptides. Hanson MC, Abraham W, Crespo MP, Chen SH, Liu H, Szeto GL, Kim M, Reinherz EL, Irvine DJ. Vaccinepubmed:25559188;  doi:10.1016/j.vaccine.2014.12.045

6. Manipulating the Selection Forces during Affinity Maturation to Generate Cross-Reactive HIV Antibodies. Wang S, Mata-Fink J, Kriegsman B, Hanson M, Irvine DJ, Eisen HN, Burton DR, Wittrup KD, Kardar M, Chakraborty AK. Cellpubmed:25662010;  doi:10.1016/j.cell.2015.01.027

7. Aberrant glycosylation promotes lung cancer metastasis through adhesion to galectins in the metastatic niche. Reticker-Flynn NE, Bhatia SN. Cancer Discovpubmed:25421439;  doi:10.1158/2159-8290.CD-13-0760

8. Adsorption of hyaluronic acid on solid supports: Role of pH and surface chemistry in thin film self-assembly. Choi JH, Kim SO, Linardy E, Dreaden EC, Zhdanov VP, Hammond PT, Cho NJ. J Colloid Interface Scipubmed:25734222;  doi:10.1016/j.jcis.2015.01.060

9. Glucose-responsive insulin activity by covalent modification with aliphatic phenylboronic acid conjugates. Chou DH, Webber MJ, Tang BC, Lin AB, Thapa LS, Deng D, Truong JV, Cortinas AB, Langer R, Anderson DG. Proc Natl Acad Sci U S Apubmed:25675515;  doi:10.1073/pnas.1424684112

10. 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

11. Efficacy of a device to narrow the coronary sinus in refractory angina. Verheye S, Jolicoeur EM, Behan MW, Pettersson T, Sainsbury P, Hill J, Vrolix M, Agostoni P, Engstrom T, Labinaz M, de Silva R, Schwartz M, Meyten N, Uren NG, Doucet S, Tanguay JF, Lindsay S, Henry TD, White CJ, Edelman ER, Banai S. N Engl J Medpubmed:25651246;  doi:10.1056/NEJMoa1402556

12. Tying up a transcription factor. Chen A, Koehler AN. Sciencepubmed:25678644;  doi:10.1126/science.aaa6119

13. HypE-specific Nanobodies as Tools to modulate HypE-mediated Target AMPylation. Truttmann MC, Wu Q, Stiegeler S, Duarte JN, Ingram J, Ploegh HL. J Biol Chem.pubmed:25678711;  doi:10.1074/jbc.M114.634287

14. Transcriptional Reversion of Cardiac Myocyte Fate During Mammalian Cardiac Regeneration. O'Meara C, Wamstad JA, Gladstone R, Fomovsky G, Butty V, Shrikumar A, Gannon J, Boyer L, Lee RT. Circ Respubmed:25477501;  doi:10.1161/CIRCRESAHA.116.304269

15. Cutting the Gordian Helix - Regulating Genomic Testing in the Era of Precision Medicine. Lander ES. N Engl J Medpubmed:25689017;  doi:10.1056/NEJMp1501964

16. Genome-wide Association Study Identifies Shared Risk Loci Common to Two Malignancies in Golden Retrievers. Tonomura N, Elvers I, Thomas R, Megquier K, Turner-Maier J, Howald C, Sarver AL, Swofford R, Frantz AM, Ito D, Mauceli E, Arendt M, Noh HJ, Koltookian M, Biagi T, Fryc S, Williams C, Avery AC, Kim JH, Barber L, Burgess K, Lander ES, Karlsson EK, Azuma C, Modiano JF, Breen M, Lindblad-Toh K. PLoS Genetpubmed:25642983;  doi:10.1371/journal.pgen.1004922

17. Systematic Cell-Based Phenotyping of Missense Alleles Empowers Rare Variant Association Studies: A Case for LDLR and Myocardial Infarction. Thormaehlen AS, Schuberth C, Won HH, Blattmann P, Joggerst-Thomalla B, Theiss S, Asselta R, Duga S, Merlini PA, Ardissino D, Lander ES, Gabriel S, Rader DJ, Peloso GM, Pepperkok R, Kathiresan S, Runz H. PLoS Genet.pubmed:25647241;  doi:10.1371/journal.pgen.1004855

18. Evasion of Innate Cytosolic DNA Sensing by a Gammaherpesvirus Facilitates Establishment of Latent Infection. Sun C, Schattgen SA, Pisitkun P, Jorgensen JP, Hilterbrand AT, Wang LJ, West JA, Hansen K, Horan KA, Jakobsen MR, O'Hare P, Adler H, Sun R, Ploegh HL, Damania B, Upton JW, Fitzgerald KA, Paludan SR. J Immunolpubmed:25595793;  doi:10.4049/jimmunol.1402495

19. A one-step enzymatic modification of the cell surface redirects cellular cytotoxicity and parasite tropism. Swee LK, Lourido S, Bell GW, Ingram JR, Ploegh HL. ACS Chem Biol.pubmed:25360987;  doi:10.1021/cb500462t

20. Integrative analysis of 111 reference human epigenomes. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Naturepubmed:25693563;  doi:10.1038/nature14248

21. Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Do R, Stitziel NO, Won HH, Jorgensen AB, Duga S, Angelica Merlini P, Kiezun A, Farrall M, Goel A, Zuk O, Guella I, Asselta R, Lange LA, Peloso GM, Auer PL, Girelli D, Martinelli N, Farlow DN, DePristo MA, Roberts R, Stewart AF, Saleheen D, Danesh J, Epstein SE, Sivapalaratnam S, Kees Hovingh G, Kastelein JJ, Samani NJ, Schunkert H, Erdmann J, Shah SH, Kraus WE, Davies R, Nikpay M, Johansen CT, Wang J, Hegele RA, Hechter E, Marz W, Kleber ME, Huang J, Johnson AD, Li M, Burke GL, Gross M, Liu Y, Assimes TL, Heiss G, Lange EM, Folsom AR, Taylor HA, Olivieri O, Hamsten A, Clarke R, Reilly DF, Yin W, Rivas MA, Donnelly P, Rossouw JE, Psaty BM, Herrington DM, Wilson JG, Rich SS, Bamshad MJ, Tracy RP, Adrienne Cupples L, Rader DJ, Reilly MP, Spertus JA, Cresci S, Hartiala J, Wilson Tang WH, Hazen SL, Allayee H, Reiner AP, Carlson CS, Kooperberg C, Jackson RD, Boerwinkle E, Lander ES, Schwartz SM, Siscovick DS, McPherson R, Tybjaerg-Hansen A, Abecasis GR, Watkins H, Nickerson DA, Ardissino D, Sunyaev SR, O'Donnell CJ, Altshuler D, Gabriel S, Kathiresan S. Naturepubmed:25487149;  doi:10.1038/nature13917

22. Human Phosphoglycerate Dehydrogenase Produces the Oncometabolite d-2-Hydroxyglutarate. Fan J, Teng X, Liu L, Mattaini KR, Looper RE, Vander Heiden MG, Rabinowitz JD. ACS Chem Biol.pubmed:25406093;  doi:10.1021/cb500683c

23. Mitotic entry in the presence of DNA damage is a widespread property of aneuploidy in yeast. Blank HM, Sheltzer JM, Meehl CM, Amon A. Mol Biol Cellpubmed:25694455;  doi:10.1091/mbc.E14-10-1442

24. Light and Hydrogen Peroxide Inhibit C elegans Feeding through Gustatory Receptor Orthologs and Pharyngeal Neurons. Bhatla N, Horvitz HR. Neuron.pubmed:25640076;  doi:10.1016/j.neuron.2014.12.061

25. The comparative pathology of genetically engineered mouse models for neuroendocrine carcinomas of the lung. Gazdar AF, Savage TK, Johnson JE, Berns A, Sage J, Linnoila RI, MacPherson D, McFadden DG, Farago A, Jacks T, Travis WD, Brambilla E. J Thorac Oncolpubmed:25675280;  doi:10.1097/JTO.0000000000000459

26. A roadmap for interpreting C metabolite labeling patterns from cells. Buescher JM, Antoniewicz MR, Boros LG, Burgess SC, Brunengraber H, Clish CB, DeBerardinis RJ, Feron O, Frezza C, Ghesquiere B, Gottlieb E, Hiller K, Jones RG, Kamphorst JJ, Kibbey RG, Kimmelman AC, Locasale JW, Lunt SY, Maddocks OD, Malloy C, Metallo CM, Meuillet EJ, Munger J, Noh K, Rabinowitz JD, Ralser M, Sauer U, Stephanopoulos G, St-Pierre J, Tennant DA, Wittmann C, Vander Heiden MG, Vazquez A, Vousden K, Young JD, Zamboni N, Fendt SM. Curr Opin Biotechnol.pubmed:25731751;  doi:10.1016/j.copbio.2015.02.003

27. Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein. Kamphorst JJ, Nofal M, Commisso C, Hackett SR, Lu W, Grabocka E, Vander Heiden MG, Miller G, Drebin JA, Bar-Sagi D, Thompson CB, Rabinowitz JD. Cancer Respubmed:25644265;  doi:10.1158/0008-5472.CAN-14-2211

28. Stress response: PARP1 911. Bock FJ, Chang P. Nat Chem Biolpubmed:25689334;  doi:10.1038/nchembio.1756

29. alpha5 and alphav integrins cooperate to regulate vascular smooth muscle and neural crest functions in vivo. Turner CJ, Badu-Nkansah K, Crowley D, van der Flier A, Hynes RO. Development.pubmed:25670798;  doi:10.1242/dev.117572

30. Peptide-Based, Two-Fluorophore, Ratiometric Probe for Quantifying Mobile Zinc in Biological Solutions. Zhang DY, Azrad M, Demark-Wahnefried W, Frederickson CJ, Lippard SJ, Radford RJ.ACS Chem Biolpubmed:25382858;  doi:10.1021/cb500617c

31. Encapsulation of Pt(IV) Prodrugs within a Pt(II) Cage for Drug Delivery. Zheng YR, Suntharalingam K, Johnstone TC, Lippard SJ. Chem Scipubmed:25621144;  doi:10.1039/C4SC01892C

32. Material properties of biofilms-a review of methods for understanding permeability and mechanics. Billings N, Birjiniuk A, Samad TS, Doyle PS, Ribbeck K. Rep Prog Phys.pubmed:25719969;  doi:10.1088/0034-4885/78/3/036601

33. Stretching self-entangled DNA molecules in elongational fields. Renner CB, Doyle PS. Soft Matterpubmed:25693945;  doi:10.1039/c4sm02738h

34. Sensitive and Multiplexed On-chip microRNA Profiling in Oil-Isolated Hydrogel Chambers. Lee H, Srinivas RL, Gupta A, Doyle PS. Angew Chem Int Ed Engl.pubmed:25565630;  doi:10.1002/anie.201409489