Progress: September 2013

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Publications Citing Koch Institute Faculty Members

1. Dominant Role of Oncogene Dosage and Absence of Tumor Suppressor Activity in Nras-Driven Hematopoietic Transformation. Xu J, Haigis KM, Firestone AJ, McNerney ME, Li Q, Davis E, Chen SC, Nakitandwe J, Downing J, Jacks T, Le Beau MM, Shannon K. Cancer Discov. pubmed:23733505;  doi:10.1158/2159-8290.CD-13-0096

2. Bidentate Ligands on Osmium(VI) Nitrido Complexes Control Intracellular Targeting and Cell Death Pathways. Suntharalingam K, Johnstone TC, Bruno PM, Lin W, Hemann MT, Lippard SJ. J Am Chem Soc. pubmed:24041161;  doi:10.1021/ja4075375

3. Profoundly different prion diseases in knock-in mice carrying single PrP codon substitutions associated with human diseases. Jackson WS, Borkowski AW, Watson NE, King OD, Faas H, Jasanoff A, Lindquist S. Proc Natl Acad Sci U S A. pubmed:23959875;  doi:10.1073/pnas.1312006110

4. A Meiosis-Specific Form of the APC/C Promotes the Oocyte-to-Embryo Transition by Decreasing Levels of the Polo Kinase Inhibitor Matrimony. Whitfield ZJ, Chisholm J, Hawley RS, Orr-Weaver TL. PLoS Biol. pubmed:24019759;  doi:10.1371/journal.pbio.1001648

5. An Integrin-Linked Machinery of Cytoskeletal Regulation that Enables Experimental Tumor Initiation and Metastatic Colonization. Shibue T, Brooks MW, Weinberg RA. Cancer Cell. pubmed:24035453;  doi:10.1016/j.ccr.2013.08.012

6. Protein Kinase C alpha Is a Central Signaling Node and Therapeutic Target for Breast Cancer Stem Cells. Tam WL, Lu H, Buikhuisen J, Soh BS, Lim E, Reinhardt F, Wu ZJ, Krall JA, Bierie B, Guo W, Chen X, Liu XS, Brown M, Lim B, Weinberg RA. Cancer Cell. pubmed:24029232;  doi:10.1016/j.ccr.2013.08.005

7. Poised with purpose: Cell plasticity enhances tumorigenicity. Marjanovic ND, Weinberg RA, Chaffer CL. Cell Cycle. pubmed:23966153;  doi:10.4161/cc.26075

8. Phospho-Ser/Thr-binding domains: navigating the cell cycle and DNA damage response. Reinhardt HC, Yaffe MB. Nat Rev Mol Cell Biol. pubmed:23969844;  doi:10.1038/nrm3640

9. Cardiac Overexpression of Mammalian enabled (Mena) Exacerbates Heart Failure in Mice. Belmonte SL, Ram R, Mickelsen DM, Gertler FB, Blaxall BC. Am J Physiol Heart Circ Physiol. pubmed:23832697;  doi:10.1152/ajpheart.00342.2013

10. Cloning Expeditions: Risky but Rewarding. Lodish H. Mol Cell Biol. pubmed:24061478;  doi:10.1128/MCB.01111-13

11. MicroRNA networks regulate development of brown adipocytes. Trajkovski M, Lodish H. Trends Endocrinol Metab. pubmed:23809233;  doi:10.1016/j.tem.2013.05.002

12. Exploiting tumor metabolism: challenges for clinical translation. Vander Heiden MG. J Clin Invest. pubmed:23999437;  doi:10.1172/JCI72391

13. Vascular Endothelial Growth Factor and Platelet Factor 4 Inputs Modulate Human Microvascular Endothelial Signaling in a Three-Dimensional Matrix Migration Context. Hang TC, Tedford NC, Reddy RJ, Rimchala T, Wells A, White FM, Kamm RD, Lauffenburger DA. Mol Cell Proteomics. pubmed:24023389;  doi:10.1074/mcp.M113.030528

14. Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Rudenko A, Dawlaty MM, Seo J, Cheng AW, Meng J, Le T, Faull KF, Jaenisch R, Tsai LH. Neuron. pubmed:24050401;  doi:10.1016/j.neuron.2013.08.003

15. One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering. Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R. Cell. pubmed:23992847;  doi:10.1016/j.cell.2013.08.022

16. Visualization of Peroxynitrite-Induced Changes of Labile Zn2+ in the Endoplasmic Reticulum with Benzoresorufin-based Fluorescent Probes. Buccella D, Lippard SJ, Lin W. J Am Chem Soc. pubmed:23902285;  doi:10.1021/ja4059487

17. Effect of a Monofunctional Phenanthriplatin-DNA Adduct on RNA Polymerase II Transcriptional Fidelity and Translesion Synthesis. Kellinger MW, Park GY, Chong J, Lippard SJ, Wang D. J Am Chem Soc. pubmed:23927577;  doi:10.1021/ja405475y

18. Synthesis and Characterization of Pt(IV) Fluorescein Conjugates to Investigate Pt(IV) Intracellular Transformations. Song Y, Suntharalingam K, Yeung J, Royzen M, Lippard SJ. Bioconjug Chem. pubmed:23957697;  doi:10.1021/bc400281a

19. The Effect of Ligand Lipophilicity on the Nanoparticle Encapsulation of Pt(IV) Prodrugs. Johnstone TC, Lippard SJ. Inorg Chem. pubmed:23859129;  doi:10.1021/ic4010642

20. Hepatic signaling by the mechanistic target of rapamycin complex 2 (mTORC2). Lamming DW, Demirkan G, Boylan JM, Mihaylova MM, Peng T, Ferreira J, Neretti N, Salomon A, Sabatini DM, Gruppuso PA. FASEB J. pubmed:24072782;  doi:10.1096/fj.13-237743

21. Lipid-Modified Aminoglycoside Derivatives for in vivo siRNA Delivery. Zhang Y, Pelet JM, Heller DA, Dong Y, Chen D, Gu Z, Joseph BJ, Wallas J, Anderson DG. Adv Mater. pubmed:23813808;  doi:10.1002/adma.201301917

22. 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. ACS Synth Biol. pubmed:23713956;  doi:10.1021/sb400019s

23. Dysfunctional endothelial cells directly stimulate cancer inflammation and metastasis. Franses JW, Drosu NC, Gibson WJ, Chitalia VC, Edelman ER. Int J Cancer. pubmed:23463345;  doi:10.1002/ijc.28146

24. Synthesis of Highly Stable Sub-8 nm TiO Nanoparticles and Their Multilayer Electrodes of TiO/MWNT for Electrochemical Applications. Hyder MN, Gallant BM, Shah NJ, Shao-Horn Y, Hammond PT. Nano Lett. pubmed:24003950;  doi:10.1021/nl401387s

25. Scalable Manufacture of Built-to-Order Nanomedicine: Spray-Assisted Layer-by-Layer Functionalization of PRINT Nanoparticles. Morton SW, Herlihy KP, Shopsowitz KE, Deng ZJ, Chu KS, Bowerman CJ, Desimone JM, Hammond PT. Adv Mater. pubmed:23813892;  doi:10.1002/adma.201302025

26. A photo-triggered layered surface coating producing reactive oxygen species. Gabriel D, Monteiro IP, Huang D, Langer R, Kohane DS. Biomaterials. pubmed:24074838;  doi:10.1016/j.biomaterials.2013.09.021

27. 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. J Biomed Mater Res A. pubmed:23723136;  doi:10.1002/jbm.a.34811

28. Single cells from human primary colorectal tumors exhibit polyfunctional heterogeneity in secretions of ELR+ CXC chemokines. Adalsteinsson VA, Tahirova N, Tallapragada N, Yao X, Campion L, Angelini A, Douce TB, Huang C, Bowman B, Williamson CA, Kwon DS, Wittrup KD, Love JC. Integr Biol (Camb). pubmed:23995780;  doi:10.1039/c3ib40059j

29. Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Kim DH, Grun D, van Oudenaarden A. Nat Genet. pubmed:24036951;  doi:10.1038/ng.2763

30. 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. Virus Res. pubmed:23707399;  doi:10.1016/j.virusres.2013.04.017

31. Single-molecule mRNA detection and counting in mammalian tissue. Lyubimova A, Itzkovitz S, Junker JP, Fan ZP, Wu X, van Oudenaarden A. Nat Protoc. pubmed:23949380;  doi:10.1038/nprot.2013.109

32. Rational Design of a Biomimetic Cell Penetrating Peptide Library. Karagiannis ED, Urbanska AM, Sahay G, Pelet JM, Jhunjhunwala S, Langer R, Anderson DG. ACS Nano. pubmed:24047542;  doi:10.1021/nn4027382

33. Nanoparticles That Sense Thrombin Activity As Synthetic Urinary Biomarkers of Thrombosis. Lin KY, Kwong GA, Warren AD, Wood DK, Bhatia SN. ACS Nano. pubmed:24015809;  doi:10.1021/nn403550c

34. Human (alpha2-->6) and avian (alpha2-->3) sialylated receptors of influenza A virus show distinct conformations and dynamics in solution. Sassaki GL, Elli S, Rudd TR, Macchi E, Yates EA, Naggi A, Shriver Z, Raman R, Sasisekharan R, Torri G, Guerrini M. Biochemistry. pubmed:24015903;  doi:10.1021/bi400677n

35. Immunogenicity of membrane-bound HIV-1 gp41 MPER segments is dominated by residue accessibility and modulated by stereochemistry. Kim M, Song L, Moon J, Sun ZY, Bershteyn A, Hanson M, Cain D, Goka S, Kelsoe G, Wagner G, Irvine D, Reinherz EL. J Biol Chem. pubmed:24047898;  doi:10.1074/jbc.M113.494609

36. Generation of effector memory T cell-based mucosal and systemic immunity with pulmonary nanoparticle vaccination. Li AV, Moon JJ, Abraham W, Suh H, Elkhader J, Seidman MA, Yen M, Im EJ, Foley MH, Barouch DH, Irvine DJ. Sci Transl Med. pubmed:24068737;  doi:10.1126/scitranslmed.3006516

37. Effect of particle diameter and surface composition on the spontaneous fusion of monolayer-protected gold nanoparticles with lipid bilayers. Van Lehn RC, Atukorale PU, Carney RP, Yang YS, Stellacci F, Irvine DJ, Alexander-Katz A. Nano Lett. pubmed:23915118;  doi:10.1021/nl401365n

38. Targeted cytolysins synergistically potentiate cytoplasmic delivery of gelonin immunotoxin. Pirie CM, Liu DV, Wittrup KD. Mol Cancer Ther. pubmed:23832121;  doi:10.1158/1535-7163.MCT-12-1023

39. Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers. Hagerstrand D, Tong A, Schumacher SE, Ilic N, Shen RR, Cheung HW, Vazquez F, Shrestha Y, Kim SY, Giacomelli AO, Rosenbluh J, Schinzel AC, Spardy NA, Barbie DA, Mermel CH, Weir BA, Garraway LA, Tamayo P, Mesirov JP, Beroukhim R, Hahn WC. Cancer Discov. pubmed:23764425;  doi:10.1158/2159-8290.CD-12-0592

40. Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals. Mazzoni EO, Mahony S, Peljto M, Patel T, Thornton SR, McCuine S, Reeder C, Boyer LA, Young RA, Gifford DK, Wichterle H. Nat Neurosci. pubmed:23955559;  doi:10.1038/nn.3490

41. SIRT1 redresses tissue inhibitor of matrix metalloproteinase-1/matrix metalloproteinase-9 imbalance in the development of mouse emphysema and human COPD. Yao H, Hwang JW, Sundar IK, Friedman AE, McBurney MW, Guarente LP, Gu W, Kinnula VL, Rahman I. Am J Physiol Lung Cell Mol Physiol. pubmed:24039251;  doi:10.1152/ajplung.00249.2012

42. A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis. Lesch BJ, Dokshin GA, Young RA, McCarrey JR, Page DC. Proc Natl Acad Sci U S A. pubmed:24043772;  doi:10.1073/pnas.1315204110

43. Production of unnaturally linked chimeric proteins using a combination of sortase-catalyzed transpeptidation and click chemistry. Witte MD, Theile CS, Wu T, Guimaraes CP, Blom AE, Ploegh HL. Nat Protoc. pubmed:23989675;  doi:10.1038/nprot.2013.103

44. Site-specific N-terminal labeling of proteins using sortase-mediated reactions. Theile CS, Witte MD, Blom AE, Kundrat L, Ploegh HL, Guimaraes CP. Nat Protoc. pubmed:23989674;  doi:10.1038/nprot.2013.102

45. Site-specific C-terminal and internal loop labeling of proteins using sortase-mediated reactions. Guimaraes CP, Witte MD, Theile CS, Bozkurt G, Kundrat L, Blom AE, Ploegh HL. Nat Protoc. pubmed:23989673;  doi:10.1038/nprot.2013.101

46. Standing up for GMOs. Alberts B, Beachy R, Baulcombe D, Blobel G, Datta S, Fedoroff N, Kennedy D, Khush GS, Peacock J, Rees M, Sharp P. Science. pubmed:24052276;  doi:10.1126/science.1245017

47. The Cancer Genome Atlas Pan-Cancer analysis project. Chang K, et. al. Nat Genet. pubmed:24071849;  doi:10.1038/ng.2764

48. 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Spies N, Burge CB, Bartel DP. Genome Res. pubmed:24072873;  doi:10.1101/gr.156919.113

49. Zanamivir Conjugated to Poly-L-Glutamine is Much More Active Against Influenza Viruses in Mice and Ferrets Than the Drug Itself. Weight AK, Belser JA, Tumpey TM, Chen J, Klibanov AM. Pharm Res. pubmed:24065587;  doi:10.1007/s11095-013-1175-4