Progress: May 2014
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 Res. pubmed: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. Vaccine. pubmed: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 Biochem. pubmed: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 Proteomics. pubmed: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 Biotechnol. pubmed: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. Vaccine. pubmed: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 Dis. pubmed: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 Release. pubmed: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 Methods. pubmed: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 Proteomics. pubmed: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 Nano. pubmed: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 Signal. pubmed: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 Microbe. pubmed: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 Steril. pubmed: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 Nano. pubmed: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 Discov. pubmed: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 Methods. pubmed: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 Res. pubmed: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. Cell. pubmed: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. Leukemia. pubmed: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. Blood. pubmed: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 Discov. pubmed: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 Chem. pubmed: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. Bioinformatics. pubmed: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 Cell. pubmed: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 Discov. pubmed: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 Cell. pubmed: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 Methods. pubmed: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 A. pubmed: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 Reports. pubmed: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 Discov. pubmed: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 A. pubmed: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 A. pubmed: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 Rep. pubmed:24767987; doi:10.1016/j.celrep.2014.03.057