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: December 2012

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Publications Citing Intramural Faculty

1. Activation of the Yeast Hippo Pathway by Phosphorylation-Dependent Assembly of Signaling Complexes.
Rock JM, Lim D, Stach L, Ogrodowicz RW, Keck JM, Jones MH, Wong CC, Yates JR3rd, Winey M, Smerdon SJ, Yaffe MB, Amon A. 
Publication: Science.
pubmed:23579499;  doi:10.1126/science.1235822

2. Aneuploid yeast strains exhibit defects in cell growth and passage through START.
Thorburn RR, Gonzalez C, Brar GA, Christen S, Carlile TM, Ingolia NT, Sauer U, Weissman JS, Amon A.
Publication: Mol Biol Cell.
pubmed:23468524;  doi:10.1091/mbc.E12-07-0520

3. Characterizing deformability and surface friction of cancer cells.
Byun S, Son S, Amodei D, Cermak N, Shaw J, Kang JH, Hecht VC, Winslow MM, Jacks T, Mallick P, Manalis SR. 
Publication: Proc Natl Acad Sci U S A.
pubmed:23610435;  doi:10.1073/pnas.1218806110

4. The retinoblastoma protein induces apoptosis directly at the mitochondria.
Hilgendorf KI, Leshchiner ES, Nedelcu S, Maynard MA, Calo E, Ianari A, Walensky LD, Lees JA.
Publication: Genes Dev
;  doi:10.1101/gad.211326.112

5. Development of cyclic peptomer inhibitors targeting the polo-box domain of polo-like kinase 1.
Murugan RN, Park JE, Lim D, Ahn M, Cheong C, Kwon T, Nam KY, Choi SH, Kim BY, Yoon DY, Yaffe MB, Yu DY, Lee KS, Bang JK. 
Publication: Bioorg Med Chem.
pubmed:23498919;  doi:10.1016/j.bmc.2013.02.020

6. Metformin decreases glucose oxidation and increases the dependency of prostate cancer cells on reductive glutamine metabolism.
Fendt SM, Bell EL, Keibler MA, Davidson SM, Wirth GJ, Fiske B, Mayers JR, Schwab M, Bellinger G, Csibi A, Patnaik A, Blouin MJ, Cantley LC, Guarente LP, Blenis J, Pollak MN, Olumi AF, Vander Heiden M, Stephanopoulos G.
Publication: Cancer Res.
pubmed:23687346;  doi:10.1158/0008-5472.CAN-13-0080

7. Macropinocytosis of protein is an amino acid supply route in Ras-transformed cells.
Commisso C, Davidson SM, Soydaner-Azeloglu RG, Parker SJ, Kamphorst JJ, Hackett S, Grabocka E, Nofal M, Drebin JA, Thompson CB, Rabinowitz JD, Metallo CM, Vander Heiden MG, Bar-Sagi D.
Publication: Nature.
pubmed:23665962;  doi:10.1038/nature12138

8. Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice.
Miraldi ER, Sharfi H, Friedline RH, Johnson H, Zhang T, Lau KS, Ko HJ, Curran TG, Haigis KM, Yaffe MB, Bonneau R, Lauffenburger DA, Kahn BB, Kim JK, Neel BG, Saghatelian A, White FM. 
Publication: Integr Biol (Camb).
pubmed:23685806;  doi:10.1039/c3ib40013a

9. Nanoparticle Encapsulation of Mitaplatin and the Effect Thereof on In Vivo Properties.
Johnstone TC, Kulak N, Pridgen EM, Farokhzad OC, Langer R, Lippard SJ. 
Publication: ACS Nano
pubmed:23697579;  doi:10.1021/nn401905g

10. Synergistic cytotoxicity of irinotecan and cisplatin in dual-drug targeted polymeric nanoparticles.
Valencia PM, Pridgen EM, Perea B, Gadde S, Sweeney C, Kantoff PW, Bander NH, Lippard SJ, Langer R, Karnik R, Farokhzad OC. 
Publication: Nanomedicine (Lond)

;  doi:10.2217/nnm.12.134

11. Discovery of Novel Materials with Broad Resistance to Bacterial Attachment Using Combinatorial Polymer Microarrays.
Hook AL, Chang CY, Yang J, Atkinson S, Langer R, Anderson DG, Davies MC, Williams P, Alexander MR. 
Publication: Adv Mater
;  doi:10.1002/adma.201204936

12. Safety and tolerability of an intratumorally injected DNAzyme, Dz13, in patients with nodular basal-cell carcinoma: a phase 1 first-in-human trial (DISCOVER).
Cho EA, Moloney FJ, Cai H, Au-Yeung A, China C, Scolyer RA, Yosufi B, Raftery MJ, Deng JZ, Morton SW, Hammond PT, Arkenau HT, Damian DL, Francis DJ, Chesterman CN, Barnetson RS, Halliday GM, Khachigian LM. 
Publication: Lancet
;  doi:10.1016/S0140-6736(12)62166-7

13. Nano approaches to using nucleic acids.
Hammond P. 
Publication: ACS Nano
;  doi:10.1021/nn402448e

14. Recognition of heparan sulfate by clinical strains of dengue virus serotype 1 using recombinant subviral particles.
Artpradit C, Robinson LN, Gavrilov BK, Rurak TT, Ruchirawat M, Sasisekharan R. 
Publication: Virus Res
;  doi:10.1016/j.virusres.2013.04.017

15. Flow-based pipeline for systematic modulation and analysis of 3D tumor microenvironments.
Li CY, Wood DK, Huang JH, Bhatia SN. 
Publication: Lab Chip
pubmed:23563587;  doi:10.1039/c3lc41300d

16. Monocyte-Directed RNAi Targeting CCR2 Improves Infarct Healing in Atherosclerosis-Prone Mice.
Majmudar MD, Keliher EJ, Heidt T, Leuschner F, Truelove J, Sena BF, Gorbatov R, Iwamoto Y, Dutta P, Wojtkiewicz G, Courties G, Sebas M, Borodovsky A, Fitzgerald K, Nolte MW, Dickneite G, Chen JW, Anderson DG, Swirski FK, Weissleder R, Nahrendorf M. 
Publication: Circulation.
pubmed:23616627;  doi:10.1161/CIRCULATIONAHA.112.000116

17. Core-Shell Hydrogel Microcapsules for Improved Islets Encapsulation.
Ma M, Chiu A, Sahay G, Doloff JC, Dholakia N, Thakrar R, Cohen J, Vegas A, Chen D, Bratlie KM, Dang T, York RL, Hollister-Lock J, Weir GC, Anderson DG. 
Publication: Adv Healthc Mater.
pubmed:23208618;  doi:10.1002/adhm.201200341

18. Orthogonal Labeling of M13 Minor Capsid Proteins with DNA to Self-Assemble End-to-End Multiphage Structures.
Hess GT, Guimaraes CP, Spooner E, Ploegh HL, Belcher AM. 
Publication: ACS Synth Biol

;  doi:10.1021/sb400019s

19. Mitochondrial Localization and the Persistent Migration of Epithelial Cancer cells.
Desai SP, Bhatia SN, Toner M, Irimia D. 
Publication: Biophys J
;  doi:10.1016/j.bpj.2013.03.025

20. Nano-Layered siRNA Dressing for Sustained Localized Knockdown.
Castleberry S, Wang M, Hammond PT. 
Publication: ACS Nano.
;  doi:10.1021/nn401011n

21. Biomaterials and biotechnology: From the discovery of the first angiogenesis inhibitors to the development of controlled drug delivery systems and the foundation of tissue engineering.
Langer R. 
Publication: J Biomed Mater Res A.
pubmed:23723136;  doi:10.1002/jbm.a.34811

22. Injectable Nano-Network for Glucose-Mediated Insulin Delivery.
Gu Z, Aimetti AA, Wang Q, Dang TT, Zhang Y, Veiseh O, Cheng H, Langer RS, Anderson DG. 
Publication: ACS Nano.
pubmed:23638642;  doi:10.1021/nn400630x

23. Microtools for single-cell analysis in biopharmaceutical development and manufacturing.
Love KR, Bagh S, Choi J, Love JC.
Publication: Trends Biotechnol.
pubmed:23582471;  doi:10.1016/j.tibtech.2013.03.001

24. Antigenically intact hemagglutinin in circulating avian and swine influenza viruses and potential for H3N2 pandemic.
Tharakaraman K, Raman R, Stebbins NW, Viswanathan K, Sasisekharan V, Sasisekharan R. 
Publication: Sci Rep
;  doi:10.1038/srep01822

25. Enhanced phagocytic activity of HIV-specific antibodies correlates with natural production of immunoglobulins with skewed affinity for FcgammaR2a and FcgammaR2b.
Ackerman ME, Dugast AS, McAndrew EG, Tsoukas S, Licht AF, Irvine DJ, Alter G. 
Publication: J Virol.
pubmed:23468489;  doi:10.1128/JVI.03403-12

Publications Citing Extramural Faculty

26. PTEN-null Tumors Cohabiting the Same Lung Display Differential Akt Activation and Sensitivity to Dietary Restriction.
Curry NL, Mino-Kenudson M, Oliver TG, Yilmaz OH, Yilmaz VO, Moon JY, Jacks T, Sabatini DM, Kalaany NY. 
Publication: Cancer Discov.
pubmed:23719831;  doi:10.1158/2159-8290.CD-12-0507

27. Models of signalling networks - what cell biologists can gain from them and give to them.
Janes KA, Lauffenburger DA. 
Publication: J Cell Sci.
;  doi:10.1242/jcs.112045

28. Visualizing Inhibition of Nucleosome Mobility and Transcription by Cisplatin-DNA Interstrand Crosslinks in Live Mammalian Cells.
Zhu G, Song L, Lippard SJ. 
Publication: Cancer Res
;  doi:10.1158/0008-5472.CAN-13-0198

29. One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering.
Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R. 
Publication: Cell
;  doi:10.1016/j.cell.2013.04.025

30. Tris(2-pyridylmethyl)amine (TPA) as a membrane-permeable chelator for interception of biological mobile zinc.
Huang Z, Zhang XA, Bosch M, Smith SJ, Lippard SJ. 
Publication: Metallomics
;  doi:10.1039/c3mt00103b

31. Fetal hepatic progenitors support long-term expansion of hematopoietic stem cells. Chou S, Flygare J, Lodish HF. 
Publication: Exp Hematol.
;  doi:10.1016/j.exphem.2013.02.003

32. A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1.
Bar-Peled L, Chantranupong L, Cherniack AD, Chen WW, Ottina KA, Grabiner BC, Spear ED, Carter SL, Meyerson M, Sabatini DM. 
Publication: Science.
pubmed:23723238;  doi:10.1126/science.1232044

33. Human ALKBH7 is required for alkylation and oxidation-induced programmed necrosis.
Fu D, Jordan JJ, Samson LD. 
Publication: Genes Dev.
;  doi:10.1101/gad.215533.113

34. Targeting tumor cell motility as a strategy against invasion and metastasis.
Wells A, Grahovac J, Wheeler S, Ma B, Lauffenburger D. 
Publication: Trends Pharmacol Sci.
pubmed:23571046;  doi:10.1016/

35. ADAM-10 and -17 regulate endometriotic cell migration via concerted ligand and receptor shedding feedback on kinase signaling.
Miller MA, Meyer AS, Beste MT, Lasisi Z, Reddy S, Jeng KW, Chen CH, Han J, Isaacson K, Griffith LG, Lauffenburger DA. 
Publication: Proc Natl Acad Sci U S A.
;  doi:10.1073/pnas.1222387110

36. Young and old genetically heterogeneous HET3 mice on a rapamycin diet are glucose intolerant but insulin sensitive.
Lamming DW, Ye L, Astle MC, Baur JA, Sabatini DM, Harrison DE. 
Publication: Aging Cell
;  doi:10.1111/acel.12097

37. Mechanisms of Tissue Uptake and Retention in Zotarolimus-Coated Balloon Therapy.
Kolachalama VB, Pacetti SD, Franses JW, Stankus JJ, Zhao HQ, Shazly T, Nikanorov A, Schwartz LB, Tzafriri AR, Edelman ER. 
Publication: Circulation.
pubmed:23584359;  doi:10.1161/CIRCULATIONAHA.113.002051

38. Enhanced phagocytic activity of HIV-specific antibodies correlates with natural production of immunoglobulins with skewed affinity for FcgammaR2a and FcgammaR2b.
Ackerman ME, Dugast AS, McAndrew EG, Tsoukas S, Licht AF, Irvine DJ, Alter G. 
Publication: J Virol.
pubmed:23468489;  doi:10.1128/JVI.03403-12

39. SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase.
Ji X, Zhou Y, Pandit S, Huang J, Li H, Lin CY, Xiao R, Burge CB, Fu XD. 
Publication: Cell
;  doi:10.1016/j.cell.2013.04.028

40. Integrated genomic characterization of endometrial carcinoma.
Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. 
Publication: Nature.
pubmed:23636398;  doi:10.1038/nature12113

41. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity.
Dulak AM, Stojanov P, Peng S, Lawrence MS, Fox C, Stewart C, Bandla S, Imamura Y, Schumacher SE, Shefler E, McKenna A, Carter SL, Cibulskis K, Sivachenko A, Saksena G, Voet D, Ramos AH, Auclair D, Thompson K, Sougnez C, Onofrio RC, Guiducci C, Beroukhim R, Zhou Z, Lin L, Lin J, Reddy R, Chang A, Landrenau R, Pennathur A, Ogino S, Luketich JD, Golub TR, Gabriel SB, Lander ES, Beer DG, Godfrey TE, Getz G, Bass AJ.
Publication: Nat Genet.
pubmed:23525077;  doi:10.1038/ng.2591

42. Acidic Amino Acid Residues in the Juxtamembrane Region of the Nucleotide-Sensing TLRs Are Important for UNC93B1 Binding and Signaling.
Kim J, Huh J, Hwang M, Kwon EH, Jung DJ, Brinkmann MM, Jang MH, Ploegh HL, Kim YM.
Publication: J Immunol.
pubmed:23585677;  doi:10.4049/jimmunol.1202767

43. Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells.
Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A.
Publication: Cell.
pubmed:23664763;  doi:10.1016/j.cell.2013.04.037

44. Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms.
Lange J, Noordam MJ, van Daalen SK, Skaletsky H, Clark BA, Macville MV, Page DC, Repping S.
Publication: Genomics.
pubmed:23643616;  doi:10.1016/j.ygeno.2013.04.018