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: August 2014

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Publications Citing Koch Institute Faculty Members

1. Coronary artery disease and diabetes mellitus. Aronson D, Edelman ER. Cardiol Clinpubmed:25091969;  doi:10.1016/j.ccl.2014.04.001

2. Catheter-based renal denervation is no simple matter: lessons to be learned from our anatomy?. Mahfoud F, Edelman ER, Bohm M. J Am Coll Cardiolpubmed:25125293;  doi:10.1016/j.jacc.2014.05.037

3. Bimodal Tumor-Targeting From Microenvironment Responsive Hyaluronan Layer-by-Layer (LbL) Nanoparticles. Dreaden EC, Morton SW, Shopsowitz KE, Choi JH, Deng ZJ, Cho NJ, Hammond PT. ACS Nanopubmed:25100313;  doi:10.1021/nn502861t

4. Multimonth controlled small molecule release from biodegradable thin films. Hsu BB, Park MH, Hagerman SR, Hammond PT. Proc Natl Acad Sci U S Apubmed:25092310;  doi:10.1073/pnas.1323829111

5. Assembly of Viral Hydrogels for Three-Dimensional Conducting Nanocomposites. Chen PY, Hyder MN, Mackanic D, Courchesne NM, Qi J, Klug MT, Belcher AM, Hammond PT. Adv Mater.pubmed:24782428;  doi:10.1002/adma.201400828

6. Nanomedicine in the Management of Microbial Infection - Overview and Perspectives. Zhu X, Radovic-Moreno AF, Wu J, Langer R, Shi J. Nano Todaypubmed:25267927;  doi:10.1016/j.nantod.2014.06.003

7. Small RNA combination therapy for lung cancer. Xue W, Dahlman JE, Tammela T, Khan OF, Sood S, Dave A, Cai W, Chirino LM, Yang GR, Bronson R, Crowley DG, Sahay G, Schroeder A, Langer R, Anderson DG, Jacks T. Proc Natl Acad Sci U S Apubmed:25114235;  doi:10.1073/pnas.1412686111

8. In vivo endothelial siRNA delivery using polymeric nanoparticles with low molecular weight. Dahlman JE, Barnes C, Khan O, Thiriot A, Jhunjunwala S, Shaw TE, Xing Y, Sager HB, Sahay G, Speciner L, Bader A, Bogorad RL, Yin H, Racie T, Dong Y, Jiang S, Seedorf D, Dave A, Sandu KS, Webber MJ, Novobrantseva T, Ruda VM, Lytton-Jean AK, Levins CG, Kalish B, Mudge DK, Perez M, Abezgauz L, Dutta P, Smith L, Charisse K, Kieran MW, Fitzgerald K, Nahrendorf M, Danino D, Tuder RM, von Andrian UH, Akinc A, Panigrahy D, Schroeder A, Kotelianski V, Langer R, Anderson DG. Nat Nanotechnol.pubmed:24813696;  doi:10.1038/nnano.2014.84

9. EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. Francis JM, Zhang CZ, Maire CL, Jung J, Manzo VE, Adalsteinsson VA, Homer H, Haidar S, Blumenstiel B, Pedamallu CS, Ligon AH, Love JC, Meyerson M, Ligon KL. Cancer Discovpubmed:24893890;  doi:10.1158/2159-8290.CD-13-0879

10. Glycan receptor specificity as a useful tool for characterization and surveillance of influenza A virus. Raman R, Tharakaraman K, Shriver Z, Jayaraman A, Sasisekharan V, Sasisekharan R. Trends Microbiol.pubmed:25108746;  doi:10.1016/j.tim.2014.07.002

11. A growing place for nano in medicine. Hammond PT. ACS Nanopubmed:25154926;  doi:10.1021/nn504577x

12. Micropatterned cell-cell interactions enable functional encapsulation of primary hepatocytes in hydrogel microtissues. Li CY, Stevens KR, Schwartz RE, Alejandro BS, Huang JH, Bhatia SN. Tissue Eng Part A.pubmed:24498910;  doi:10.1089/ten.TEA.2013.0667

13. Histone Deacetylase Inhibitors Impair the Elimination of HIV-Infected Cells by Cytotoxic T-Lymphocytes. Jones RB, O'Connor R, Mueller S, Foley M, Szeto GL, Karel D, Lichterfeld M, Kovacs C, Ostrowski MA, Trocha A, Irvine DJ, Walker BD. PLoS Pathogpubmed:25122219;  doi:10.1371/journal.ppat.1004287

14. System level dynamics of post-translational modifications. Gajadhar AS, White FM. Curr Opin Biotechnolpubmed:24441143;  doi:10.1016/j.copbio.2013.12.009

15. Detecting kinase activities from single cell lysate using concentration-enhanced mobility shift assay. Cheow LF, Sarkar A, Kolitz SE, Lauffenburger DA, Han J. Anal Chem.pubmed:25025773;  doi:10.1021/ac502185v

16. DNA glycosylase activity and cell proliferation are key factors in modulating homologous recombination in vivo. Kiraly O, Gong G, Roytman MD, Yamada Y, Samson LD, Engelward BP. Carcinogenesis.pubmed:25155011;  doi:10.1093/carcin/bgu177

17. Adaptive protein and phosphoprotein networks which promote therapeutic sensitivity or acquired resistance. Haley J, White FM. Biochem Soc Transpubmed:25109954;  doi:10.1042/BST20140038

18. 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

19. Niemann-Pick C1 Affects the Gene Delivery Efficacy of Degradable Polymeric Nanoparticles. Eltoukhy AA, Sahay G, Cunningham JM, Anderson DG. ACS Nanopubmed:25010491;  doi:10.1021/nn501630h

20. Nucleic acid-mediated intracellular protein delivery by lipid-like nanoparticles. Eltoukhy AA, Chen D, Veiseh O, Pelet JM, Yin H, Dong Y, Anderson DG. Biomaterials.pubmed:24831975;  doi:10.1016/j.biomaterials.2014.04.014

21. Non-viral vectors for gene-based therapy. Yin H, Kanasty RL, Eltoukhy AA, Vegas AJ, Dorkin JR, Anderson DG. Nat Rev Genetpubmed:25022906;  doi:10.1038/nrg3763

22. M13 virus directed synthesis of nanostructured metal oxides for Li-oxygen batteries. Oh D, Qi J, Han B, Zhang G, Carney TJ, Ohmura J, Zhang Y, Shao-Horn Y, Belcher AM. Nano Lett.pubmed:25058851;  doi:10.1021/nl502078m

23. Microfluidic organs-on-chips. Bhatia SN, Ingber DE. Nat Biotechnolpubmed:25093883;  doi:10.1038/nbt.2989

24. Modeling host interactions with hepatitis B virus using primary and induced pluripotent stem cell-derived hepatocellular systems. Shlomai A, Schwartz RE, Ramanan V, Bhatta A, de Jong YP, Bhatia SN, Rice CM. Proc Natl Acad Sci U S Apubmed:25092305;  doi:10.1073/pnas.1412631111

25. 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

26. Genomic analysis of RNA localization. Taliaferro JM, Wang ET, Burge CB. RNA Biolpubmed:25136858;  

27. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alfoldi J, Barrio AM, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L. Sciencepubmed:25170157;  doi:10.1126/science.1253714

28. Somatic mutation as a mechanism of Wnt/beta-catenin pathway activation in CLL. Wang L, Shalek AK, Lawrence M, Ding R, Gaublomme JT, Pochet N, Stojanov P, Sougnez C, Shukla SA, Stevenson KE, Zhang W, Wong J, Sievers QL, Macdonald BT, Vartanov AR, Goldstein NR, Neuberg D, He X, Lander E, Hacohen N, Regev A, Getz G, Brown JR, Park H, Wu CJ. Bloodpubmed:24778153;  doi:10.1182/blood-2014-01-552067

29. Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Arking DE, Pulit SL, Crotti L, van der Harst P, Munroe PB, Koopmann TT, Sotoodehnia N, Rossin EJ, Morley M, Wang X, Johnson AD, Lundby A, Gudbjartsson DF, Noseworthy PA, Eijgelsheim M, Bradford Y, Tarasov KV, Dorr M, Muller-Nurasyid M, Lahtinen AM, Nolte IM, Smith AV, Bis JC, Isaacs A, Newhouse SJ, Evans DS, Post WS, Waggott D, Lyytikainen LP, Hicks AA, Eisele L, Ellinghaus D, Hayward C, Navarro P, Ulivi S, Tanaka T, Tester DJ, Chatel S, Gustafsson S, Kumari M, Morris RW, Naluai AT, Padmanabhan S, Kluttig A, Strohmer B, Panayiotou AG, Torres M, Knoflach M, Hubacek JA, Slowikowski K, Raychaudhuri S, Kumar RD, Harris TB, Launer LJ, Shuldiner AR, Alonso A, Bader JS, Ehret G, Huang H, Kao WH, Strait JB, Macfarlane PW, Brown M, Caulfield MJ, Samani NJ, Kronenberg F, Willeit J, Smith JG, Greiser KH, Meyer Zu Schwabedissen H, Werdan K, Carella M, Zelante L, Heckbert SR, Psaty BM, Rotter JI, Kolcic I, Polasek O, Wright AF, Griffin M, Daly MJ, Arnar DO, Holm H, Thorsteinsdottir U, Denny JC, Roden DM, Zuvich RL, Emilsson V, Plump AS, Larson MG, O'Donnell CJ, Yin X, Bobbo M, D'Adamo AP, Iorio A, Sinagra G, Carracedo A, Cummings SR, Nalls MA, Jula A, Kontula KK, Marjamaa A, Oikarinen L, Perola M, Porthan K, Erbel R, Hoffmann P, Jockel KH, Kalsch H, Nothen MM, den Hoed M, Loos RJ, Thelle DS, Gieger C, Meitinger T, Perz S, Peters A, Prucha H, Sinner MF, Waldenberger M, de Boer RA, Franke L, van der Vleuten PA, Beckmann BM, Martens E, Bardai A, Hofman N, Wilde AA, Behr ER, Dalageorgou C, Giudicessi JR, Medeiros-Domingo A, Barc J, Kyndt F, Probst V, Ghidoni A, Insolia R, Hamilton RM, Scherer SW, Brandimarto J, Margulies K, Moravec CE, Fabiola, Fuchsberger C, O'Connell JR, Lee WK, Watt GC, Campbell H, Wild SH, El Mokhtari NE, Frey N, Asselbergs FW, Leach IM, Navis G, van den Berg MP, van Veldhuisen DJ, Kellis M, Krijthe BP, Franco OH, Hofman A, Kors JA, Uitterlinden AG, Witteman JC, Kedenko L, Lamina C, Oostra BA, Abecasis GR, Lakatta EG, Mulas A, Orru M, Schlessinger D, Uda M, Markus MR, Volker U, Snieder H, Spector TD, Arnlov J, Lind L, Sundstrom J, Syvanen AC, Kivimaki M, Kahonen M, Mononen N, Raitakari OT, Viikari JS, Adamkova V, Kiechl S, Brion M, Nicolaides AN, Paulweber B, Haerting J, Dominiczak AF, Nyberg F, Whincup PH, Hingorani AD, Schott JJ, Bezzina CR, Ingelsson E, Ferrucci L, Gasparini P, Wilson JF, Rudan I, Franke A, Muhleisen TW, Pramstaller PP, Lehtimaki TJ, Paterson AD, Parsa A, Liu Y, van Duijn CM, Siscovick DS, Gudnason V, Jamshidi Y, Salomaa V, Felix SB, Sanna S, Ritchie MD, Stricker BH, Stefansson K, Boyer LA, Cappola TP, Olsen JV, Lage K, Schwartz PJ, Kaab S, Chakravarti A, Ackerman MJ, Pfeufer A, de Bakker PI, Newton-Cheh C. Nat Genetpubmed:24952745;  doi:10.1038/ng.3014

30. GPR107, a GPCR Essential for Intoxication by P aeruginosa Exotoxin A, Localizes to the Golgi and is Cleaved by Furin. Tafesse FG, Guimaraes CP, Maruyama T, Carette JE, Lory S, Brummelkamp TR, Ploegh HL. J Biol Chempubmed:25031321;  doi:10.1074/jbc.M114.589275

31. Generating genetically modified mice using CRISPR/Cas-mediated genome engineering. Yang H, Wang H, Jaenisch R. Nat Protocpubmed:25058643;  doi:10.1038/nprot.2014.134

32. D-Cyclins Repress Apoptosis in Hematopoietic Cells by Controlling Death Receptor Fas and Its Ligand FasL. Choi YJ, Saez B, Anders L, Hydbring P, Stefano J, Bacon NA, Cook C, Kalaszczynska I, Signoretti S, Young RA, Scadden DT, Sicinski P. Dev Cellpubmed:25087893;  doi:10.1016/j.devcel.2014.06.015

33. Histones to the cytosol: Exportin 7 is essential for normal terminal erythroid nuclear maturation. Hattangadi SM, Martinez-Morilla S, Patterson HC, Shi J, Burke K, Avila-Figueroa A, Venkatesan S, Wang J, Paulsen K, Gorlich D, Murata-Hori M, Lodish HF. Bloodpubmed:25092175;  doi:10.1182/blood-2013-11-537761

34. Retinoic Acid Activates Two Pathways Required for Meiosis in Mice. Koubova J, Hu YC, Bhattacharyya T, Soh YQ, Gill ME, Goodheart ML, Hogarth CA, Griswold MD, Page DC. PLoS Genet.pubmed:25102060;  doi:10.1371/journal.pgen.1004541

35. NAD and sirtuins in aging and disease. Imai SI, Guarente L. Trends Cell Biolpubmed:24786309;  doi:10.1016/j.tcb.2014.04.002

36. The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C elegans. Hirose T, Horvitz HR. PLoS Genetpubmed:25101958;  doi:10.1371/journal.pgen.1004512

37. Autophagy is Required for Glucose Homeostasis and Lung Tumor Maintenance. Karsli-Uzunbas G, Guo JY, Price SM, Teng X, Laddha SV, Khor S, Kalaany NY, Jacks T, Chan CS, Rabinowitz JD, White E.Cancer Discovpubmed:24875857;  doi:10.1158/2159-8290.CD-14-0363

38. Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformation of metabolism. Jarosz DF, Brown JC, Walker GA, Datta MS, Ung WL, Lancaster AK, Rotem A, Chang A, Newby GA, Weitz DA, Bisson LF, Lindquist S. Cellpubmed:25171409;  doi:10.1016/j.cell.2014.07.025

39. An Evolutionarily Conserved Prion-like Element Converts Wild Fungi from Metabolic Specialists to Generalists. Jarosz DF, Lancaster AK, Brown JC, Lindquist S. Cell.pubmed:25171408;  doi:10.1016/j.cell.2014.07.024

40. Calcineurin determines toxic versus beneficial responses to alpha-synuclein. Caraveo G, Auluck PK, Whitesell L, Chung CY, Baru V, Mosharov EV, Yan X, Ben-Johny M, Soste M, Picotti P, Kim H, Caldwell KA, Caldwell GA, Sulzer D, Yue DT, Lindquist S. Proc Natl Acad Sci U S Apubmed:25122673;  doi:10.1073/pnas.1413201111

41. Prion-like proteins sequester and suppress the toxicity of huntingtin exon 1. Kayatekin C, Matlack KE, Hesse WR, Guan Y, Chakrabortee S, Russ J, Wanker EE, Shah JV, Lindquist S. Proc Natl Acad Sci U S A.pubmed:25092318;  doi:10.1073/pnas.1412504111

42. Dihydropyrimidine accumulation is required for the epithelial-mesenchymal transition. Shaul YD, Freinkman E, Comb WC, Cantor JR, Tam WL, Thiru P, Kim D, Kanarek N, Pacold ME, Chen WW, Bierie B, Possemato R, Reinhardt F, Weinberg RA, Yaffe MB, Sabatini DM. Cellpubmed:25171410;  doi:10.1016/j.cell.2014.07.032

43. Integrin-alpha5beta1 is not required for mural cell functions during development of blood vessels but is required for lymphatic-blood vessel separation and lymphovenous valve formation. Turner CJ, Badu-Nkansah K, Crowley D, van der Flier A, Hynes RO. Dev Biolpubmed:24858485;  doi:10.1016/j.ydbio.2014.05.006

44. The tumour-induced systemic environment as a critical regulator of cancer progression and metastasis. McAllister SS, Weinberg RA. Nat Cell Biolpubmed:25082194;  doi:10.1038/ncb3015

45. Phosphorylation of ETS1 by Src Family Kinases Prevents Its Recognition by the COP1 Tumor Suppressor. Lu G, Zhang Q, Huang Y, Song J, Tomaino R, Ehrenberger T, Lim E, Liu W, Bronson RT, Bowden M, Brock J, Krop IE, Dillon DA, Gygi SP, Mills GB, Richardson AL, Signoretti S, Yaffe MB, Kaelin WGJr. Cancer Cellpubmed:25117710;  doi:10.1016/j.ccr.2014.06.026

46. Tumor microenvironment of metastasis and risk of distant metastasis of breast cancer. Rohan TE, Xue X, Lin HM, D'Alfonso TM, Ginter PS, Oktay MH, Robinson BD, Ginsberg M, Gertler FB, Glass AG, Sparano JA, Condeelis JS, Jones JG. J Natl Cancer Instpubmed:24895374;  doi:10.1093/jnci/dju136