Progress: July 2013

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Publications Citing Koch Institute Faculty Members

1. Predicting cancer drug mechanisms of action using molecular network signatures. Pritchard JR, Bruno PM, Hemann MT, Lauffenburger DA. Mol Biosyst. pubmed:23287973;  doi:10.1039/c2mb25459j

2. 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. Cancer Discov. pubmed:23719831;  doi:10.1158/2159-8290.CD-12-0507

3. Xk-Related Protein 8 and CED-8 Promote Phosphatidylserine Exposure in Apoptotic Cells. Suzuki J, Denning DP, Imanishi E, Horvitz HR, Nagata S. Science. pubmed:23845944;  doi:10.1126/science.1236758

4. Changes in Cell Morphology Are Coordinated with Cell Growth through the TORC1 Pathway. Goranov AI, Gulati A, Dephoure N, Takahara T, Maeda T, Gygi SP, Manalis S, Amon A. Curr Biol. pubmed:23810534;  doi:10.1016/j.cub.2013.05.035

5. An Sp1 transcription factor coordinates caspase-dependent and -independent apoptotic pathways. Hirose T, Horvitz HR. Nature. pubmed:23851392;  doi:10.1038/nature12329

6. Chaperones as thermodynamic sensors of drug-target interactions reveal kinase inhibitor specificities in living cells. Taipale M, Krykbaeva I, Whitesell L, Santagata S, Zhang J, Liu Q, Gray NS, Lindquist S. Nat Biotechnol. pubmed:23811600;  doi:10.1038/nbt.2620

7. Autophagy suppresses progression of K-ras-induced lung tumors to oncocytomas and maintains lipid homeostasis. Guo JY, Karsli-Uzunbas G, Mathew R, Aisner SC, Kamphorst JJ, Strohecker AM, Chen G, Price S, Lu W, Teng X, Snyder E, Santanam U, Dipaola RS, Jacks T, Rabinowitz JD, White E. Genes Dev. pubmed:23824538;  doi:10.1101/gad.219642.113

8. Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B, Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JAJr, Whitesell L, Lindquist S. Science. pubmed:23869022;  doi:10.1126/science.1238303

9. Targeting H3K4 trimethylation in Huntington disease. Vashishtha M, Ng CW, Yildirim F, Gipson TA, Kratter IH, Bodai L, Song W, Lau A, Labadorf A, Vogel-Ciernia A, Troncosco J, Ross CA, Bates GP, Krainc D, Sadri-Vakili G, Finkbeiner S, Marsh JL, Housman DE, Fraenkel E, Thompson LM. Proc Natl Acad Sci U S A. pubmed:23872847;  doi:10.1073/pnas.1311323110

10. Differential Tks5 isoform expression contributes to metastatic invasion of lung adenocarcinoma. Li CM, Chen G, Dayton TL, Kim-Kiselak C, Hoersch S, Whittaker CA, Bronson RT, Beer DG, Winslow MM, Jacks T. Genes Dev. pubmed:23873940;  doi:10.1101/gad.222745.113

11. Single-Cell Analysis Reveals that Expression of Nanog Is Biallelic and Equally Variable as that of Other Pluripotency Factors in Mouse ESCs. Faddah DA, Wang H, Cheng AW, Katz Y, Buganim Y, Jaenisch R. Cell Stem Cell. pubmed:23827708;  doi:10.1016/j.stem.2013.04.019

12. In Vivo RNAi Screening Identifies a Leukemia-Specific Dependence on Integrin Beta 3 Signaling. Miller PG, Al-Shahrour F, Hartwell KA, Chu LP, Jaras M, Puram RV, Puissant A, Callahan KP, Ashton J, McConkey ME, Poveromo LP, Cowley GS, Kharas MG, Labelle M, Shterental S, Fujisaki J, Silberstein L, Alexe G, Al-Hajj MA, Shelton CA, Armstrong SA, Root DE, Scadden DT, Hynes RO, Mukherjee S, Stegmaier K, Jordan CT, Ebert BL. Cancer Cell. pubmed:23770013;  doi:10.1016/j.ccr.2013.05.004

13. 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

14. MicroRNA-126-mediated control of cell fate in B-cell myeloid progenitors as a potential alternative to transcriptional factors. Okuyama K, Ikawa T, Gentner B, Hozumi K, Harnprasopwat R, Lu J, Yamashita R, Ha D, Toyoshima T, Chanda B, Kawamata T, Yokoyama K, Wang S, Ando K, Lodish HF, Tojo A, Kawamoto H, Kotani A. Proc Natl Acad Sci U S A. pubmed:23893300;  doi:10.1073/pnas.1220710110

15. ZFP36L2 is required for self-renewal of early burst-forming unit erythroid progenitors. Zhang L, Prak L, Rayon-Estrada V, Thiru P, Flygare J, Lim B, Lodish HF. Nature. pubmed:23748442;  doi:10.1038/nature12215

16. BCAT1 defines gliomas by IDH status. Mayers JR, Vander Heiden MG. Nat Med. pubmed:23836221;  doi:10.1038/nm.3263

17. 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. Cancer Res. pubmed:23687346;  doi:10.1158/0008-5472.CAN-13-0080

18. Poised Chromatin at the ZEB1 Promoter Enables Breast Cancer Cell Plasticity and Enhances Tumorigenicity. Chaffer CL, Marjanovic ND, Lee T, Bell G, Kleer CG, Reinhardt F, D'Alessio AC, Young RA, Weinberg RA. Cell. pubmed:23827675;  doi:10.1016/j.cell.2013.06.005

19. 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

20. mTORC1 phosphorylation sites encode their sensitivity to starvation and rapamycin. Kang SA, Pacold ME, Cervantes CL, Lim D, Lou HJ, Ottina K, Gray NS, Turk BE, Yaffe MB, Sabatini DM. Science. pubmed:23888043;  doi:10.1126/science.1236566

21. 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. Integr Biol (Camb). pubmed:23685806;  doi:10.1039/c3ib40013a

22. Visualizing Inhibition of Nucleosome Mobility and Transcription by Cisplatin-DNA Interstrand Crosslinks in Live Mammalian Cells. Zhu G, Song L, Lippard SJ. Cancer Res. pubmed:23695549;  doi:10.1158/0008-5472.CAN-13-0198

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

24. 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

25. Glucose-Responsive Microgels Integrated with Enzyme Nanocapsules for Closed-Loop Insulin Delivery. Gu Z, Dang TT, Ma M, Tang BC, Cheng H, Jiang S, Dong Y, Zhang Y, Anderson DG. ACS Nano. pubmed:23834678;  doi:10.1021/nn401617u

26. A Microscale Human Liver Platform that Supports the Hepatic Stages of Plasmodium falciparum and vivax. March S, Ng S, Velmurugan S, Galstian A, Shan J, Logan DJ, Carpenter AE, Thomas D, Sim BK, Mota MM, Hoffman SL, Bhatia SN. Cell Host Microbe. pubmed:23870318;  doi:10.1016/j.chom.2013.06.005

27. Modifications of Microvascular EC Surface Modulate Phototoxicity of a Porphycene anti-ICAM-1 Immunoconjugate; Therapeutic Implications. Rosas E, Santoma P, Duran-Frigola M, Hernandez B, Llinas MC, Ruiz-Gonzalez R, Nonell S, Sanchez-Garcia D, Edelman ER, Balcells M. Langmuir. pubmed:23844929;  doi:10.1021/la401067d

28. Inhibition of vein graft stenosis with a c-jun targeting DNAzyme in a cationic liposomal formulation containing 1,2-dioleoyl-3-trimethylammonium propane (DOTAP)/1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). Li Y, Bhindi R, Deng ZJ, Morton SW, Hammond PT, Khachigian LM. Int J Cardiol. pubmed:23886527;  doi:10.1016/j.ijcard.2013.05.092

29. Mechanical and Transport Properties of Layer-by-Layer Electrospun Composite Proton Exchange Membranes for Fuel Cell Applications. Mannarino MM, Liu DS, Hammond PT, Rutledge GC. ACS Appl Mater Interfaces. pubmed:23876250;  doi:10.1021/am402204v

30. An Engineered Bivalent Neuregulin Protects Against Doxorubicin-Induced Cardiotoxicity with Reduced Pro-Neoplastic Potential. Jay SM, Murthy AC, Hawkins JF, Wortzel JR, Steinhauser ML, Alvarez LM, Gannon J, Macrae CA, Griffith LG, Lee RT. Circulation. pubmed:23757312;  doi:10.1161/CIRCULATIONAHA.113.002203

31. Implantable Silk Composite Microneedles for Programmable Vaccine Release Kinetics and Enhanced Immunogenicity in Transcutaneous Immunization. Demuth PC, Min Y, Irvine DJ, Hammond PT. Adv Healthc Mater. pubmed:23847143;  doi:10.1002/adhm.201300139

32. 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

33. A Versatile Three-Dimensional Virus-Based Template for Dye-Sensitized Solar Cells with Improved Electron Transport and Light Harvesting. Chen PY, Dang X, Klug MT, Qi J, Courchesne NM, Burpo FJ, Fang N, Hammond PT, Belcher AM. ACS Nano. pubmed:23808626;  doi:10.1021/nn4014164

34. Multiparametric approach for the evaluation of lipid nanoparticles for siRNA delivery. Alabi CA, Love KT, Sahay G, Yin H, Luly KM, Langer R, Anderson DG. Proc Natl Acad Sci U S A. pubmed:23882076;  doi:10.1073/pnas.1306529110

35. Efficiency of siRNA delivery by lipid nanoparticles is limited by endocytic recycling. Sahay G, Querbes W, Alabi C, Eltoukhy A, Sarkar S, Zurenko C, Karagiannis E, Love K, Chen D, Zoncu R, Buganim Y, Schroeder A, Langer R, Anderson DG. Nat Biotechnol. pubmed:23792629;  doi:10.1038/nbt.2614

36. Enhanced function of immuno-isolated islets in diabetes therapy by co-encapsulation with an anti-inflammatory drug. Dang TT, Thai AV, Cohen J, Slosberg JE, Siniakowicz K, Doloff JC, Ma M, Hollister-Lock J, Tang KM, Gu Z, Cheng H, Weir GC, Langer R, Anderson DG. Biomaterials. pubmed:23660251;  doi:10.1016/j.biomaterials.2013.04.016

37. Thin-Capped Atheromata With Reduced Collagen Content in Pigs Develop in Coronary Arterial Regions Exposed to Persistently Low Endothelial Shear Stress. Koskinas KC, Sukhova GK, Baker AB, Papafaklis MI, Chatzizisis YS, Coskun AU, Quillard T, Jonas M, Maynard C, Antoniadis AP, Shi GP, Libby P, Edelman ER, Feldman CL, Stone PH. Arterioscler Thromb Vasc Biol. pubmed:23640495;  doi:10.1161/ATVBAHA.112.300827

38. The architecture and biological performance of drug-loaded LbL nanoparticles. Morton SW, Poon Z, Hammond PT. Biomaterials. pubmed:23618629;  doi:10.1016/j.biomaterials.2013.03.059

39. 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

40. Tumor suppressor gene Rb is required for self-renewal of spermatogonial stem cells in mice. Hu YC, de Rooij DG, Page DC. Proc Natl Acad Sci U S A. pubmed:23858447;  doi:10.1073/pnas.1311548110

41. Getting to the heart of the matter: long non-coding RNAs in cardiac development and disease. Scheuermann JC, Boyer LA. EMBO J. pubmed:23756463;  doi:10.1038/emboj.2013.134

42. Reductive glutamine metabolism is a function of the alpha-ketoglutarate to citrate ratio in cells. Fendt SM, Bell EL, Keibler MA, Olenchock BA, Mayers JR, Wasylenko TM, Vokes NI, Guarente L, Heiden MG, Stephanopoulos G. Nat Commun. pubmed:23900562;  doi:10.1038/ncomms3236

43. The NAD(+)/Sirtuin Pathway Modulates Longevity through Activation of Mitochondrial UPR and FOXO Signaling. Mouchiroud L, Houtkooper RH, Moullan N, Katsyuba E, Ryu D, Canto C, Mottis A, Jo YS, Viswanathan M, Schoonjans K, Guarente L, Auwerx J. Cell. pubmed:23870130;  doi:10.1016/j.cell.2013.06.016

44. The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome. Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M. Science. pubmed:23828888;  doi:10.1126/science.1237973

45. Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins. Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Cell. pubmed:23810193;  doi:10.1016/j.cell.2013.06.009

46. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortes ML, Auclair D, Saksena G, Voet D, Noble M, Dicara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CW, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Nature. pubmed:23770567;  doi:10.1038/nature12213

47. Comprehensive molecular characterization of clear cell renal cell carcinoma. Creighton CJ, Morgan M, Gunaratne PH, Wheeler DA, Gibbs RA, Gordon Robertson A, Chu A, Beroukhim R, Cibulskis K, Signoretti S, Vandin Hsin-Ta Wu F, Raphael BJ, Verhaak RG, Tamboli P, Torres-Garcia W, Akbani R, Weinstein JN, Reuter V, Hsieh JJ, Rose Brannon A, Ari Hakimi A, Jacobsen A, Ciriello G, Reva B, Ricketts CJ, Marston Linehan W, Stuart JM, Kimryn Rathmell W, Shen H, Laird PW, Muzny D, Davis C, Morgan M, Xi L, Chang K, Kakkar N, Trevino LR, Benton S, Reid JG, Morton D, Doddapaneni H, Han Y, Lewis L, Dinh H, Kovar C, Zhu Y, Santibanez J, Wang M, Hale W, Kalra D, Creighton CJ, Wheeler DA, Gibbs RA, Getz G, Cibulskis K, Lawrence MS, Sougnez C, Carter SL, Sivachenko A, Lichtenstein L, Stewart C, Voet D, Fisher S, Gabriel SB, Lander E, Beroukhim R, Schumacher SE, Tabak B, Saksena G, Onofrio RC, Carter SL, Cherniack AD, Gentry J, Ardlie K, Sougnez C, Getz G, Gabriel SB, Meyerson M, Gordon Robertson A, Chu A, Chun HJ, Mungall AJ, Sipahimalani P, Stoll D, Ally A, Balasundaram M, Butterfield YS, Carlsen R, Carter C, Chuah E, Coope RJ, Dhalla N, Gorski S, Guin R, Hirst C, Hirst M, Holt RA, Lebovitz C, Lee D, Li HI, Mayo M, Moore RA, Pleasance E, Plettner P, Schein JE, Shafiei A, Slobodan JR, Tam A, Thiessen N, Varhol RJ, Wye N, Zhao Y, Birol I, Jones SJ, Marra MA, Auman JT, Tan D, Jones CD, Hoadley KA, Mieczkowski PA, Mose LE, Jefferys SR, Topal MD, Liquori C, Turman YJ, Shi Y, Waring S, Buda E, Walsh J, Wu J, Bodenheimer T, Hoyle AP, Simons JV, Soloway MG, Balu S, Parker JS, Neil Hayes D, Perou CM, Kucherlapati R, Park P, Shen H, Triche Jr T, Weisenberger DJ, Lai PH, Bootwalla MS, Maglinte DT, Mahurkar S, Berman BP, Van Den Berg DJ, Cope L, Baylin SB, Laird PW, Creighton CJ, Wheeler DA, Getz G, Noble MS, Dicara D, Zhang H, Cho J, Heiman DI, Gehlenborg N, Voet D, Mallard W, Lin P, Frazer S, Stojanov P, Liu Y, Zhou L, Kim J, Lawrence MS, Chin L, Vandin F, Wu HT, Raphael BJ, Benz C, Yau C, Reynolds SM, Shmulevich I, Verhaak RG, Torres-Garcia W, Vegesna R, Kim H, Zhang W, Cogdell D, Jonasch E, Ding Z, Lu Y, Akbani R, Zhang N, Unruh AK, Casasent TD, Wakefield C, Tsavachidou D, Chin L, Mills GB, Weinstein JN, Jacobsen A, Rose Brannon A, Ciriello G, Schultz N, Ari Hakimi A, Reva B, Antipin Y, Gao J, Cerami E, Gross B, Arman Aksoy B, Sinha R, Weinhold N, Onur Sumer S, Taylor BS, Shen R, Ostrovnaya I, Hsieh JJ, Berger MF, Ladanyi M, Sander C, Fei SS, Stout A, Spellman PT, Rubin DL, Liu TT, Stuart JM, Ng S, Paull EO, Carlin D, Goldstein T, Waltman P, Ellrott K, Zhu J, Haussler D, Gunaratne PH, Xiao W, Shelton C, Gardner J, Penny R, Sherman M, Mallery D, Morris S, Paulauskis J, Burnett K, Shelton T, Signoretti S, Kaelin WG, Choueiri T, Atkins MB, Penny R, Burnett K, Mallery D, Curley E, Tickoo S, Reuter V, Kimryn Rathmell W, Thorne L, Boice L, Huang M, Fisher JC, Marston Linehan W, Vocke CD, Peterson J, Worrell R, Merino MJ, Schmidt LS, Tamboli P, Czerniak BA, Aldape KD, Wood CG, Boyd J, Weaver J, Iacocca MV, Petrelli N, Witkin G, Brown J, Czerwinski C, Huelsenbeck-Dill L, Rabeno B, Myers J, Morrison C, Bergsten J, Eckman J, Harr J, Smith C, Tucker K, Anne Zach L, Bshara W, Gaudioso C, Morrison C, Dhir R, Maranchie J, Nelson J, Parwani A, Potapova O, Fedosenko K, Cheville JC, Houston Thompson R, Signoretti S, Kaelin WG, Atkins MB, Tickoo S, Reuter V, Marston Linehan W, Vocke CD, Peterson J, Merino MJ, Schmidt LS, Tamboli P, Mosquera JM, Rubin MA, Blute ML, Kimryn Rathmell W, Pihl T, Jensen M, Sfeir R, Kahn A, Chu A, Kothiyal P, Snyder E, Pontius J, Ayala B, Backus M, Walton J, Baboud J, Berton D, Nicholls M, Srinivasan D, Raman R, Girshik S, Kigonya P, Alonso S, Sanbhadti R, Barletta S, Pot D, Sheth M, Demchok JA, Davidsen T, Wang Z, Yang L, Tarnuzzer RW, Zhang J, Eley G, Ferguson ML, Mills Shaw KR, Guyer MS, Ozenberger BA, Sofia HJ. Nature. pubmed:23792563;  doi:10.1038/nature12222

48. Gata4 is required for formation of the genital ridge in mice. Hu YC, Okumura LM, Page DC. PLoS Genet. pubmed:23874227;  doi:10.1371/journal.pgen.1003629

49. Independent specialization of the human and mouse X chromosomes for the male germ line. Mueller JL, Skaletsky H, Brown LG, Zaghlul S, Rock S, Graves T, Auger K, Warren WC, Wilson RK, Page DC. Nat Genet. pubmed:23872635;  doi:10.1038/ng.2705

50. PIKfyve, a Class III PI Kinase, Is the Target of the Small Molecular IL-12/IL-23 Inhibitor Apilimod and a Player in Toll-like Receptor Signaling. Cai X, Xu Y, Cheung AK, Tomlinson RC, Alcazar-Roman A, Murphy L, Billich A, Zhang B, Feng Y, Klumpp M, Rondeau JM, Fazal AN, Wilson CJ, Myer V, Joberty G, Bouwmeester T, Labow MA, Finan PM, Porter JA, Ploegh HL, Baird D, De Camilli P, Tallarico JA, Huang Q. Chem Biol. pubmed:23890009;  doi:10.1016/j.chembiol.2013.05.010

51. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA. Nature. pubmed:23792564;  doi:10.1038/nature12349

52. Amino Acid Copolymers That Alleviate Experimental Autoimmune Encephalomyelitis In Vivo Interact with Heparan Sulfates and Glycoprotein 96 in APCs. Koenig PA, Spooner E, Kawamoto N, Strominger JL, Ploegh HL. J Immunol. pubmed:23740953;  doi:10.4049/jimmunol.1300345