Progress: May 2014

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Publications Citing Koch Institute Faculty Members

1. Extent of flow recirculation governs expression of atherosclerotic and thrombotic biomarkers in arterial bifurcations. Martorell J, Santoma P, Kolandaivelu K, Kolachalama VB, Melgar-Lesmes P, Molins JJ, Garcia L, Edelman ER, Balcells M. Cardiovasc Respubmed:24841070;  doi:10.1093/cvr/cvu124

2. Three dimensional human small intestine models for ADME-Tox studies. Yu J, Carrier RL, March JC, Griffith LG. Drug Discov Today.pubmed:24853950;  doi:10.1016/j.drudis.2014.05.003

3. Profiling human antibody responses by integrated single-cell analysis. Ogunniyi AO, Thomas BA, Politano TJ, Varadarajan N, Landais E, Poignard P, Walker BD, Kwon DS, Love JC. Vaccinepubmed:24602776;  doi:10.1016/j.vaccine.2014.02.020

4. Equilibrium And Dynamic Design Principles For Binding Molecules Engineered For Reagentless Biosensors. de Picciotto S, Imperiali B, Griffith LG, Dane Wittrup K. Anal Biochempubmed:24814226;  doi:10.1016/j.ab.2014.04.036

5. 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 Proteomicspubmed:24719451;  doi:10.1074/mcp.M113.036392

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. 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

8. 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 Biotechnolpubmed:24752078;  doi:10.1038/nbt.2892

9. Co-regulation of primary mouse hepatocyte viability and function by oxygen and matrix. Buck LD, Inman SW, Rusyn I, Griffith LG. Biotechnol Bioeng.pubmed:24222008;  doi:10.1002/bit.25152

10. Adjuvant-carrying synthetic vaccine particles augment the immune response to encapsulated antigen and exhibit strong local immune activation without inducing systemic cytokine release. Ilyinskii PO, Roy CJ, O'Neil CP, Browning EA, Pittet LA, Altreuter DH, Alexis F, Tonti E, Shi J, Basto PA, Iannacone M, Radovic-Moreno AF, Langer RS, Farokhzad OC, von Andrian UH, Johnston LP, Kishimoto TK. Vaccinepubmed:24593999;  doi:10.1016/j.vaccine.2014.02.027

11. Small Molecule Targeting Malaria Merozoite Surface Protein-1 (MSP-1) Prevent Host Invasion of Divergent Plasmodial Species. Chandramohanadas R, Basappa, Russell B, Liew K, Yau YH, Chong A, Min L, Gunalan K, Raman R, Renia L, Nosten F, Shochat SG, Dao M, Sasisekharan R, Suresh S, Preiser P. J Infect Dispubmed:24864124;  doi:10.1093/infdis/jiu296

12. 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

13. Single compartment drug delivery. Cima MJ, Lee H, Daniel K, Tanenbaum LM, Mantzavinou A, Spencer KC, Ong Q, Sy JC, Santini JJr, Schoellhammer CM, Blankschtein D, Langer RS. J Control Releasepubmed:24798478;  doi:10.1016/j.jconrel.2014.04.049

14. Global microRNA depletion suppresses tumor angiogenesis. Chen S, Xue Y, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA. Genes Dev.pubmed:24788094;  doi:10.1101/gad.239681.114

15. CRISPR transcriptional repression devices and layered circuits in mammalian cells. Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. Nat Methodspubmed:24797424;  doi:10.1038/nmeth.2969

16. A microphysiological system model of therapy for liver micrometastases. Clark AM, Wheeler SE, Taylor DP, Pillai VC, Young CL, Prantil-Baun R, Nguyen T, Stolz DB, Borenstein JT, Lauffenburger DA, Venkataramanan R, Griffith LG, Wells A. Exp Biol Med (Maywood).pubmed:24821820;  doi:10.1177/1535370214532596

17. Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture. Tape CJ, Norrie IC, Worboys JD, Lim L, Lauffenburger DA, Jorgensen C. Mol Cell Proteomicspubmed:24820872;  doi:10.1074/mcp.O113.037119

18. Ultra-High Throughput Synthesis of Nanoparticles with Homogeneous Size Distribution Using a Coaxial Turbulent Jet Mixer. Lim JM, Swami A, Gilson LM, Chopra S, Choi S, Wu J, Langer R, Karnik R, Farokhzad OC. ACS Nanopubmed:24824296;  doi:10.1021/nn501371n

19. A nanoparticle-based combination chemotherapy delivery system for enhanced tumor killing by dynamic rewiring of signaling pathways. Morton SW, Lee MJ, Deng ZJ, Dreaden EC, Siouve E, Shopsowitz KE, Shah NJ, Yaffe MB, Hammond PT. Sci Signalpubmed:24825919;  doi:10.1126/scisignal.2005261

20. Broadly Neutralizing Influenza Hemagglutinin Stem-Specific Antibody CR8020 Targets Residues that Are Prone to Escape due to Host Selection Pressure. Tharakaraman K, Subramanian V, Cain D, Sasisekharan V, Sasisekharan R. Cell Host Microbepubmed:24832457;  doi:10.1016/j.chom.2014.04.009

21. CD26/DPPIV down-regulation in endometrial stromal cell migration in endometriosis. Tan CW, Lee YH, Tan HH, Lau MS, Choolani M, Griffith L, Chan JK. Fertil Sterilpubmed:24825423;  doi:10.1016/j.fertnstert.2014.04.001

22. Towards Engineered Processes for Sequencing-Based Analysis of Single Circulating Tumor Cells. Adalsteinsson VA, Love JC. Curr Opin Chem Eng.pubmed:24839591;  doi:10.1016/j.coche.2014.01.011

23. Insights into Human Glycan Receptor conformation of 1918 Pandemic Haemagglutinin-Glycan Complexes derived from NMR and MD studies. Elli S, Macchi E, Rudd TR, Raman R, Sassaki GL, Viswanathan K, Yates EA, Shriver Z, Naggi A, Torri G, Sasisekharan R, Guerrini M. Biochemistry.pubmed:24878075;  doi:10.1021/bi500338r

24. Enriched Protein Screening of Human Bone Marrow Mesenchymal Stromal Cell Secretions Reveals MFAP5 and PENK as Novel IL-10 Modulators. Milwid JM, Elman JS, Li M, Shen K, Manrai A, Gabow A, Yarmush J, Jiao Y, Fletcher A, Lee J, Cima MJ, Yarmush ML, Parekkadan B. Mol Ther.pubmed:24496384;  doi:10.1038/mt.2014.17

25. Capillary Flow Layer-by-Layer: A Microfluidic Platform for the High Throughput Assembly and Screening of Nanolayered Film Libraries. Castleberry SA, Li W, Deng D, Mayner S, Hammond PT. ACS Nanopubmed:24836460;  doi:10.1021/nn501963q

26. Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib. Wagle N, Grabiner BC, Van Allen EM, Hodis E, Jacobus S, Supko JG, Stewart M, Choueiri TK, Gandhi L, Cleary JM, Elfiky AA, Taplin ME, Stack EC, Signoretti S, Loda M, Shapiro GI, Sabatini D, Lander ES, Gabriel SB, Kantoff PW, Garraway LA, Rosenberg JE. Cancer Discovpubmed:24625776;  doi:10.1158/2159-8290.CD-13-0353

27. Transcriptional profiling of cells sorted by RNA abundance. Klemm S, Semrau S, Wiebrands K, Mooijman D, Faddah DA, Jaenisch R, van Oudenaarden A.Nat Methodspubmed:24681693;  doi:10.1038/nmeth.2910

28. Long noncoding RNAs during normal and malignant hematopoiesis. Alvarez-Dominguez JR, Hu W, Gromatzky AA, Lodish HF. Int J Hematol.pubmed:24609766;  doi:10.1007/s12185-014-1552-8

29. Distal enhancers: new insights into heart development and disease. Wamstad JA, Wang X, Demuren OO, Boyer LA. Trends Cell Biol.pubmed:24321408;  doi:10.1016/j.tcb.2013.10.008

30. Affinity enhancement of antibodies: how low-affinity antibodies produced early in immune responses are followed by high-affinity antibodies later and in memory B-cell responses. Eisen HN. Cancer Immunol Respubmed:24795350;  doi:10.1158/2326-6066.CIR-14-0029

31. A Chromatin-Dependent Role of the Fragile X Mental Retardation Protein FMRP in the DNA Damage Response. Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stutzer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W, Warren ST, Page DC, Shi Y. Cellpubmed:24813610;  doi:10.1016/j.cell.2014.03.040

32. Tumor suppressor functions of Dnmt3a and Dnmt3b in the prevention of malignant mouse lymphopoiesis. Peters SL, Hlady RA, Opavska J, Klinkebiel D, Pirruccello SJ, Talmon GA, Sharp JG, Wu L, Jaenisch R, Simpson MA, Karpf AR, Opavsky R. Leukemiapubmed:24292811;  doi:10.1038/leu.2013.364

33. Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Cheng AW, Shi J, Wong P, Luo KL, Trepman P, Wang ET, Choi H, Burge CB, Lodish HF. Bloodpubmed:24869935;  doi:10.1182/blood-2013-12-542209

34. 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

35. A fundamental trade off in covalent switching and its circumvention by enzyme bifunctionality in glucose homeostasis. Dasgupta T, Croll DH, Owen JA, Vander Heiden MG, Locasale JW, Alon U, Cantley LC, Gunawardena J. J Biol Chempubmed:24634222;  doi:10.1074/jbc.M113.546515

36. PLAAC: a web and command-line application to identify proteins with Prion-Like Amino Acid Composition. Lancaster AK, Nutter-Upham A, Lindquist S, King OD. Bioinformaticspubmed:24825614;  doi:10.1093/bioinformatics/btu310

37. 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 Cellpubmed:24768164;  doi:10.1016/j.devcel.2014.03.017

38. 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 Discovpubmed:24631838;  doi:10.1158/2159-8290.CD-13-0929

39. Tracing Compartmentalized NADPH Metabolism in the Cytosol and Mitochondria of Mammalian Cells. Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Vander Heiden MG, Metallo CM. Mol Cellpubmed:24882210;  doi:10.1016/j.molcel.2014.05.008

40. SIRT1 protects against cigarette smoke-induced lung oxidative stress via FOXO3-dependent mechanism. Yao H, Sundar IK, Ahmad T, Lerner C, Gerloff J, Friedman AE, Phipps RP, Sime PJ, McBurney MW, Guarente LP, Rahman I. Am J Physiol Lung Cell Mol Physiol.pubmed:24633890;  doi:10.1152/ajplung.00323.2013

41. The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells. Petschnigg J, Groisman B, Kotlyar M, Taipale M, Zheng Y, Kurat CF, Sayad A, Sierra JR, Usaj MM, Snider J, Nachman A, Krykbaeva I, Tsao MS, Moffat J, Pawson T, Lindquist S, Jurisica I, Stagljar I. Nat Methodspubmed:24658140;  doi:10.1038/nmeth.2895

42. 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 Apubmed:24757053;  doi:10.1073/pnas.1405154111

43. Cell-State Transitions Regulated by SLUG Are Critical for Tissue Regeneration and Tumor Initiation. Phillips S, Prat A, Sedic M, Proia T, Wronski A, Mazumdar S, Skibinski A, Shirley SH, Perou CM, Gill G, Gupta PB, Kuperwasser C. Stem Cell Reportspubmed:24936451;  doi:10.1016/j.stemcr.2014.03.008

44. From breaking bad to worse: exploiting homologous DNA repair deficiency in cancer. Hemann MT. Cancer Discovpubmed:24795010;  doi:10.1158/2159-8290.CD-14-0316

45. 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 Biol.pubmed:24858485;  doi:10.1016/j.ydbio.2014.05.006

46. 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

47. Polymerase exchange on single DNA molecules reveals processivity clamp control of translesion synthesis. Kath JE, Jergic S, Heltzel JM, Jacob DT, Dixon NE, Sutton MD, Walker GC, Loparo JJ. Proc Natl Acad Sci U S Apubmed:24825884;  doi:10.1073/pnas.1321076111

48. Antibiotics induce redox-related physiological alterations as part of their lethality. Dwyer DJ, Belenky PA, Yang JH, Macdonald IC, Martell JD, Takahashi N, Chan CT, Lobritz MA, Braff D, Schwarz EG, Ye JD, Pati M, Vercruysse M, Ralifo PS, Allison KR, Khalil AS, Ting AY, Walker GC, Collins JJ. Proc Natl Acad Sci U S Apubmed:24803433;  doi:10.1073/pnas.1401876111

49. 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 Reppubmed:24767987;  doi:10.1016/j.celrep.2014.03.057