Progress: April 2014

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Publications Citing Koch Institute Faculty Members

1. Matrilin-1 is an inhibitor of neovascularization. Foradori MJ, Chen Q, Fernandez CA, Harper J, Li X, Tsang PC, Langer R, Moses MA. J Biol Chem. pubmed:24692560;  doi:10.1074/jbc.M113.529982

2. 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

3. Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SA, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA. Mol Cell Proteomics. pubmed:24719451;  doi:10.1074/mcp.M113.036392

4. FRET-enabled biological characterization of polymeric micelles. Morton SW, Zhao X, Quadir MA, Hammond PT. Biomaterials. pubmed:24477190;  doi:10.1016/j.biomaterials.2014.01.027

5. Inter-individual variation in DNA repair capacity: A need for multi-pathway functional assays to promote translational DNA repair research. Nagel ZD, Chaim IA, Samson LD. DNA Repair (Amst). pubmed:24780560;  doi:10.1016/j.dnarep.2014.03.009

6. Multiplexed DNA repair assays for multiple lesions and multiple doses via transcription inhibition and transcriptional mutagenesis. Nagel ZD, Margulies CM, Chaim IA, McRee SK, Mazzucato P, Ahmad A, Abo RP, Butty VL, Forget AL, Samson LD. Proc Natl Acad Sci U S A. pubmed:24757057;  doi:10.1073/pnas.1401182111

7. In vivo silencing of the transcription factor IRF5 reprograms the macrophage phenotype and improves infarct healing. Courties G, Heidt T, Sebas M, Iwamoto Y, Jeon D, Truelove J, Tricot B, Wojtkiewicz G, Dutta P, Sager HB, Borodovsky A, Novobrantseva T, Klebanov B, Fitzgerald K, Anderson DG, Libby P, Swirski FK, Weissleder R, Nahrendorf M. J Am Coll Cardiol. pubmed:24361318;  doi:10.1016/j.jacc.2013.11.023

8. Solid MRI contrast agents for long-term, quantitative in vivo oxygen sensing. Liu VH, Vassiliou CC, Imaad SM, Cima MJ. Proc Natl Acad Sci U S A. pubmed:24753603;  doi:10.1073/pnas.1400015111

9. 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

10. A Convergent Synthetic Platform for Single-Nanoparticle Combination Cancer Therapy: Ratiometric Loading and Controlled Release of Cisplatin, Doxorubicin, and Camptothecin. Liao L, Liu J, Dreaden EC, Morton SW, Shopsowitz KE, Hammond PT, Johnson JA. J Am Chem Soc. pubmed:24724706;  doi:10.1021/ja502011g

11. Enhanced ex vivo expansion of adult mesenchymal stem cells by fetal mesenchymal stem cell ECM. Ng CP, Mohamed Sharif AR, Heath DE, Chow JW, Zhang CB, Chan-Park MB, Hammond PT, Chan JK, Griffith LG. Biomaterials. pubmed:24560460;  doi:10.1016/j.biomaterials.2014.01.081

12. Plasma membrane recovery kinetics of a microfluidic intracellular delivery platform. Sharei A, Poceviciute R, Jackson EL, Cho N, Mao S, Hartoularos GC, Jang DY, Jhunjhunwala S, Eyerman A, Schoettle T, Langer R, Jensen KF. Integr Biol (Camb). pubmed:24496115;  doi:10.1039/c3ib40215k

13. Combined Surface Micropatterning and Reactive Chemistry Maximizes Tissue Adhesion with Minimal Inflammation. Pereira MJ, Sundback CA, Lang N, Cho WK, Pomerantseva I, Ouyang B, Tao SL, McHugh K, Mwizerwa O, Vemula PK, Mochel MC, Carter DJ, Borenstein JT, Langer R, Ferreira LS, Karp JM, Masiakos PT. Adv Healthc Mater. pubmed:24106240;  doi:10.1002/adhm.201300264

14. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GS, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Nat Biotechnol. pubmed:24752078;  doi:10.1038/nbt.2892

15. Functional analysis of single cells identifies a rare subset of circulating tumor cells with malignant traits. Yao X, Choudhury AD, Yamanaka YJ, Adalsteinsson VA, Gierahn TM, Williamson CA, Lamb CR, Taplin ME, Nakabayashi M, Chabot MS, Li T, Lee GS, Boehm JS, Kantoff PW, Hahn WC, Wittrup KD, Love JC. Integr Biol (Camb). pubmed:24522233;  doi:10.1039/c3ib40264a

16. Realizing the potential of synthetic biology. Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R. Nat Rev Mol Cell Biol. pubmed:24622617;  doi:10.1038/nrm3767

17. 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. Blood. pubmed:24778153;  doi:10.1182/blood-2014-01-552067

18. A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. Konieczkowski DJ, Johannessen CM, Abudayyeh O, Kim JW, Cooper ZA, Piris A, Frederick DT, Barzily-Rokni M, Straussman R, Haq R, Fisher DE, Mesirov JP, Hahn WC, Flaherty KT, Wargo JA, Tamayo P, Garraway LA. Cancer Discov. pubmed:24771846;  doi:10.1158/2159-8290.CD-13-0424

19. The Protein Synthesis Inhibitor Blasticidin S Enters Mammalian Cells via Leucine-Rich Repeat-Containing Protein 8D. Lee CC, Freinkman E, Sabatini DM, Ploegh HL. J Biol Chem. pubmed:24782309;  doi:10.1074/jbc.M114.571257

20. Epithelial-to-mesenchymal transition activates PERK-eIF2a and sensitizes cells to endoplasmic reticulum stress. Feng Y, Sokol ES, Del Vecchio CA, Sanduja S, Claessen JH, Proia T, Jin DX, Reinhardt F, Ploegh HL, Wang Q, Gupta P. Cancer Discov. pubmed:24705811;  doi:10.1158/2159-8290.CD-13-0945

21. Loss of tet enzymes compromises proper differentiation of embryonic stem cells. Dawlaty MM, Breiling A, Le T, Barrasa MI, Raddatz G, Gao Q, Powell BE, Cheng AW, Faull KF, Lyko F, Jaenisch R. Dev Cell. pubmed:24735881;  doi:10.1016/j.devcel.2014.03.003

22. Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit. Zhu Z, Aref AR, Cohoon TJ, Barbie TU, Imamura Y, Yang S, Moody SE, Shen RR, Schinzel AC, Thai TC, Reibel JB, Tamayo P, Godfrey JT, Qian ZR, Page AN, Maciag K, Chan EM, Silkworth W, Labowsky MT, Rozhansky L, Mesirov JP, Gillanders WE, Ogino S, Hacohen N, Gaudet S, Eck MJ, Engelman JA, Corcoran RB, Wong KK, Hahn WC, Barbie DA. Cancer Discov. pubmed:24444711;  doi:10.1158/2159-8290.CD-13-0646

23. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Nature. pubmed:24759411;  doi:10.1038/nature13206

24. A mouse monoclonal antibody against alexa fluor 647. Wuethrich I, Guillen E, Ploegh HL. Monoclon Antib Immunodiagn Immunother. pubmed:24746152;  doi:10.1089/mab.2013.0088

25. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA. Nat Biotechnol. pubmed:24752079;  doi:10.1038/nbt.2889

26. Small-Molecule RORgammat Antagonists Inhibit T Helper 17 Cell Transcriptional Network by Divergent Mechanisms. Xiao S, Yosef N, Yang J, Wang Y, Zhou L, Zhu C, Wu C, Baloglu E, Schmidt D, Ramesh R, Lobera M, Sundrud MS, Tsai PY, Xiang Z, Wang J, Xu Y, Lin X, Kretschmer K, Rahl PB, Young RA, Zhong Z, Hafler DA, Regev A, Ghosh S, Marson A, Kuchroo VK. Immunity. pubmed:24745332;  doi:10.1016/j.immuni.2014.04.004

27. Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides. Birsoy K, Possemato R, Lorbeer FK, Bayraktar EC, Thiru P, Yucel B, Wang T, Chen WW, Clish CB, Sabatini DM. Nature. pubmed:24670634;  doi:10.1038/nature13110

28. IDH1 mutations alter citric acid cycle metabolism and increase dependence on oxidative mitochondrial metabolism. Grassian AR, Parker SJ, Davidson SM, Divakaruni AS, Green CR, Zhang X, Slocum KL, Pu M, Lin F, Vickers C, Joud-Caldwell C, Chung F, Yin H, Handly ED, Straub C, Growney JD, Vander Heiden MG, Murphy AN, Pagliarini R, Metallo CM. Cancer Res. pubmed:24755473;  doi:10.1158/0008-5472.CAN-14-0772-T

29. Targetable signaling pathway mutations are associated with malignant phenotype in IDH-mutant gliomas. Wakimoto H, Tanaka S, Curry WT, Loebel F, Zhao D, Tateishi K, Chen J, Klofas LK, Lelic N, Kim JC, Dias-Santagata D, Ellisen LW, Borger DR, Fendt SM, Vander Heiden M, Batchelor TT, Iafrate AJ, Cahill DP, Chi AS. Clin Cancer Res. pubmed:24714777;  doi:10.1158/1078-0432.CCR-13-3052

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

31. p53 constrains progression to anaplastic thyroid carcinoma in a Braf-mutant mouse model of papillary thyroid cancer. McFadden DG, Vernon A, Santiago PM, Martinez-McFaline R, Bhutkar A, Crowley DM, McMahon M, Sadow PM, Jacks T. Proc Natl Acad Sci U S A. pubmed:24711431;  doi:10.1073/pnas.1404357111

32. RagA, but Not RagB, Is Essential for Embryonic Development and Adult Mice. Efeyan A, Schweitzer LD, Bilate AM, Chang S, Kirak O, Lamming DW, Sabatini DM. Dev Cell. pubmed:24768164;  doi:10.1016/j.devcel.2014.03.017

33. Inhibition of ATPIF1 Ameliorates Severe Mitochondrial Respiratory Chain Dysfunction in Mammalian Cells. Chen WW, Birsoy K, Mihaylova MM, Snitkin H, Stasinski I, Yucel B, Bayraktar EC, Carette JE, Clish CB, Brummelkamp TR, Sabatini DD, Sabatini DM. Cell Rep. pubmed:24685140;  doi:10.1016/j.celrep.2014.02.046

34. A Diverse Array of Cancer-Associated MTOR Mutations Are Hyperactivating and Can Predict Rapamycin Sensitivity. Grabiner BC, Nardi V, Birsoy K, Possemato R, Shen K, Sinha S, Jordan A, Beck AH, Sabatini DM. Cancer Discov. pubmed:24631838;  doi:10.1158/2159-8290.CD-13-0929

35. Two-photon imaging of Zn2+ dynamics in mossy fiber boutons of adult hippocampal slices. Khan M, Goldsmith CR, Huang Z, Georgiou J, Luyben TT, Roder JC, Lippard SJ, Okamoto K. Proc Natl Acad Sci U S A. pubmed:24757053;  doi:10.1073/pnas.1405154111

36. A Tetranitrosyl [4Fe-4S] Cluster Forms En Route to Roussin's Black Anion: Nitric Oxide Reactivity of [FeS(LS)L']. Victor E, Lippard SJ. Inorg Chem. pubmed:24773390;  doi:10.1021/ic500586g

37. Synthetic Methods for the Preparation of Platinum Anticancer Complexes. Wilson JJ, Lippard SJ. Chem Rev. pubmed:24283498;  doi:10.1021/cr4004314

38. Constant Growth Rate Can Be Supported by Decreasing Energy Flux and Increasing Aerobic Glycolysis. Slavov N, Budnik BA, Schwab D, Airoldi EM, van Oudenaarden A. Cell Rep. pubmed:24767987;  doi:10.1016/j.celrep.2014.03.057