The David H. Koch Institute for Integrative Cancer Research at MITThe David H. Koch Institute for Integrative Cancer Research at MIT

Massachusetts Institute of Technology

National Cancer Institute Cancer Center

Science + Engineering... Conquering Cancer Together

Progress: November 2014

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Publications Citing Koch Institute Faculty Members

1. Aberrant glycosylation promotes lung cancer metastasis through adhesion to galectins in the metastatic niche. Reticker-Flynn NE, Bhatia SN. Cancer Discovpubmed:25421439;  doi:10.1158/2159-8290.CD-13-0760

2. Patterning vascular networks in vivo for tissue engineering applications. Chaturvedi RR, Stevens KR, Solorzano RD, Schwartz RE, Eyckmans JE PhD Student, Baranski JD, Stapleton SC, Bhatia SN, Chen CS.Tissue Eng Part C Methodspubmed:25390971;  doi:10.1089/ten.TEC.2014.0258

3. Multilayer Transfer Printing of Electroactive Thin Film Composites. Cebeci FC, Schmidt DJ, Hammond PT. ACS Appl Mater Interfacespubmed:25372508;  doi:10.1021/am506120e

4. Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition. Davidsohn N, Beal J, Kiani S, Adler A, Yaman F, Li Y, Xie Z, Weiss R. ACS Synth Biol.pubmed:25369267;  doi:10.1021/sb500263b

5. A load driver device for engineering modularity in biological networks. Mishra D, Rivera PM, Lin A, Del Vecchio D, Weiss R. Nat Biotechnolpubmed:25419739;  doi:10.1038/nbt.3044

6. DNA glycosylase activity and cell proliferation are key factors in modulating homologous recombination in vivo. Kiraly O, Gong G, Roytman MD, Yamada Y, Samson LD, Engelward BP. Carcinogenesis.pubmed:25155011;  doi:10.1093/carcin/bgu177

7. Aag-initiated base excision repair promotes ischemia reperfusion injury in liver, brain, and kidney. Ebrahimkhani MR, Daneshmand A, Mazumder A, Allocca M, Calvo JA, Abolhassani N, Jhun I, Muthupalani S, Ayata C, Samson LD. Proc Natl Acad Sci U S Apubmed:25349415;  doi:10.1073/pnas.1413582111

8. ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets. Sarma K, Cifuentes-Rojas C, Ergun A, Del Rosario A, Jeon Y, White F, Sadreyev R, Lee JT. Cell.pubmed:25417162;  doi:10.1016/j.cell.2014.10.019

9. Quantitative Analysis of Signaling Networks Across Differentially Embedded Tumors Highlights Inter-Patient Heterogeneity in Human Glioblastoma. Johnson H, White FM. J Proteome Res.pubmed:24927040;  doi:10.1021/pr500418w

10. Versatile de novo enzyme activity in capsid proteins from an engineered M13 bacteriophage library. Casey JP, Barbero RJ, Heldman NC, Belcher AM. J Am Chem Soc.pubmed:25343220;  doi:10.1021/ja506346f

11. In vitro alterations do not reflect a requirement for host cell cycle progression during Plasmodium liver stage infection. Hanson KK, March S, Ng S, Bhatia S, Mota MM. Eukaryot Cell.pubmed:25416236;  doi:10.1128/EC.00166-14

12. Intravascular Ultrasound Guidance to Minimize the Use of Iodine Contrast in Percutaneous Coronary Intervention: The MOZART Randomized Controlled Trial. Mariani JJr, Guedes C, Soares P, Zalc S, Campos CM, Lopes AC, Spadaro AG, Perin MA, Filho AE, Takimura CK, Ribeiro E, Kalil-Filho R, Edelman ER, Serruys PW, Lemos PA. JACC Cardiovasc Interv.pubmed:25326742;  doi:10.1016/j.jcin.2014.05.024

13. Myocardial drug distribution generated from local epicardial application: Potential impact of cardiac capillary perfusion in a swine model using epinephrine. Maslov MY, Edelman ER, Pezone MJ, Wei AE, Wakim MG, Murray MR, Tsukada H, Gerogiannis IS, Groothuis A, Lovich MA. J Control Releasepubmed:25234821;  doi:10.1016/j.jconrel.2014.09.012

14. Use of Pressure-volume Conductance Catheters in Real-time Cardiovascular Experimentation. Wei AE, Maslov MY, Pezone MJ, Edelman ER, Lovich MA. Heart Lung Circ.pubmed:24954709;  doi:10.1016/j.hlc.2014.04.130

15. Photopatterning of Hydrogel Scaffolds Coupled to Filter Materials Using Stereolithography for Perfused 3D Culture of Hepatocytes. Neiman JA, Raman R, Chan V, Rhoads MG, Raredon MS, Velazquez JJ, Dyer RL, Bashir R, Hammond PT, Griffith LG. Biotechnol Bioengpubmed:25384798;  doi:10.1002/bit.25494

16. Non-Cell-Adhesive Substrates for Printing of Arrayed Biomaterials. Appel EA, Larson BL, Luly KM, Kim JD, Langer R. Adv Healthc Materpubmed:25430948;  doi:10.1002/adhm.201400594

17. Managing diabetes with nanomedicine: challenges and opportunities. Veiseh O, Tang BC, Whitehead KA, Anderson DG, Langer R. Nat Rev Drug Discovpubmed:25430866;  doi:10.1038/nrd4477

18. Synthesis and Characterization of a Library of In-Situ Curing, Nonswelling Ethoxylated Polyol Thiol-ene Hydrogels for Tailorable Macromolecule Delivery. O'Shea TM, Aimetti AA, Kim E, Yesilyurt V, Langer R. Adv Materpubmed:25381960;  doi:10.1002/adma.201403724

19. Simple battery armor to protect against gastrointestinal injury from accidental ingestion. Laulicht B, Traverso G, Deshpande V, Langer R, Karp JM. Proc Natl Acad Sci U S A.pubmed:25368176;  doi:10.1073/pnas.1418423111

20. Intracranial microcapsule chemotherapy delivery for the localized treatment of rodent metastatic breast adenocarcinoma in the brain. Upadhyay UM, Tyler B, Patta Y, Wicks R, Spencer K, Scott A, Masi B, Hwang L, Grossman R, Cima M, Brem H, Langer R. Proc Natl Acad Sci U S Apubmed:25349381;  doi:10.1073/pnas.1313420110

21. Glycan receptor specificity as a useful tool for characterization and surveillance of influenza A virus. Raman R, Tharakaraman K, Shriver Z, Jayaraman A, Sasisekharan V, Sasisekharan R. Trends Microbiol.pubmed:25108746;  doi:10.1016/j.tim.2014.07.002

22. 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

23. Systematic Transfer of Prokaryotic Sensors and Circuits to Mammalian Cells. Stanton BC, Siciliano V, Ghodasara A, Wroblewska L, Clancy K, Trefzer AC, Chesnut JD, Weiss R, Voigt CA. ACS Synth Biol.pubmed:25360681;  doi:10.1021/sb5002856

24. Inactivating mutations in NPC1L1 and protection from coronary heart disease. Stitziel NO, Won HH, Morrison AC, Peloso GM, Do R, Lange LA, Fontanillas P, Gupta N, Duga S, Goel A, Farrall M, Saleheen D, Ferrario P, Konig I, Asselta R, Merlini PA, Marziliano N, Notarangelo MF, Schick U, Auer P, Assimes TL, Reilly M, Wilensky R, Rader DJ, Hovingh GK, Meitinger T, Kessler T, Kastrati A, Laugwitz KL, Siscovick D, Rotter JI, Hazen SL, Tracy R, Cresci S, Spertus J, Jackson R, Schwartz SM, Natarajan P, Crosby J, Muzny D, Ballantyne C, Rich SS, O'Donnell CJ, Abecasis G, Sunyaev S, Nickerson DA, Buring JE, Ridker PM, Chasman DI, Austin E, Ye Z, Kullo IJ, Weeke PE, Shaffer CM, Bastarache LA, Denny JC, Roden DM, Palmer C, Deloukas P, Lin DY, Tang ZZ, Erdmann J, Schunkert H, Danesh J, Marrugat J, Elosua R, Ardissino D, McPherson R, Watkins H, Reiner AP, Wilson JG, Altshuler D, Gibbs RA, Lander ES, Boerwinkle E, Gabriel S, Kathiresan S. N Engl J Medpubmed:25390462;  doi:10.1056/NEJMoa1405386

25. Measuring missing heritability: Inferring the contribution of common variants. Golan D, Lander ES, Rosset S. Proc Natl Acad Sci U S Apubmed:25422463;  doi:10.1073/pnas.1419064111

26. SCNT-Derived ESCs with Mismatched Mitochondria Trigger an Immune Response in Allogeneic Hosts. Deuse T, Wang D, Stubbendorff M, Itagaki R, Grabosch A, Greaves LC, Alawi M, Grunewald A, Hu X, Hua X, Velden J, Reichenspurner H, Robbins RC, Jaenisch R, Weissman IL, Schrepfer S. Cell Stem Cellpubmed:25465116;  doi:10.1016/j.stem.2014.11.003

27. Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state. Katz Y, Li F, Lambert NJ, Sokol ES, Tam WL, Cheng AW, Airoldi EM, Lengner CJ, Gupta PB, Yu Z, Jaenisch R, Burge CB. Elifepubmed:25380226;  doi:10.7554/eLife.03915

28. Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence. Genovese G, Kahler AK, Handsaker RE, Lindberg J, Rose SA, Bakhoum SF, Chambert K, Mick E, Neale BM, Fromer M, Purcell SM, Svantesson O, Landen M, Hoglund M, Lehmann S, Gabriel SB, Moran JL, Lander ES, Sullivan PF, Sklar P, Gronberg H, Hultman CM, McCarroll SA. N Engl J Med.pubmed:25426838;  doi:10.1056/NEJMoa1409405

29. Sequencing the mouse y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Soh YQ, Alfoldi J, Pyntikova T, Brown LG, Graves T, Minx PJ, Fulton RS, Kremitzki C, Koutseva N, Mueller JL, Rozen S, Hughes JF, Owens E, Womack JE, Murphy WJ, Cao Q, de Jong P, Warren WC, Wilson RK, Skaletsky H, Page DC. Cellpubmed:25417157;  doi:10.1016/j.cell.2014.09.052

30. Excess cholesterol induces mouse egg activation and may cause female infertility. Yesilaltay A, Dokshin GA, Busso D, Wang L, Galiani D, Chavarria T, Vasile E, Quilaqueo L, Orellana JA, Walzer D, Shalgi R, Dekel N, Albertini DF, Rigotti A, Page DC, Krieger M. Proc Natl Acad Sci U S Apubmed:25368174;  doi:10.1073/pnas.1418954111

31. tRNA Thiolation Links Translation to Stress Responses in Saccharomyces cerevisiae. Damon JR, Pincus D, Ploegh HL. Mol Biol Cellpubmed:25392298;  doi:10.1091/mbc.E14-06-1145

32. Bispecific antibody generated with sortase and click chemistry has broad antiinfluenza virus activity. Wagner K, Kwakkenbos MJ, Claassen YB, Maijoor K, Bohne M, van der Sluijs KF, Witte MD, van Zoelen DJ, Cornelissen LA, Beaumont T, Bakker AQ, Ploegh HL, Spits H. Proc Natl Acad Sci U S Apubmed:25385586;  doi:10.1073/pnas.1408605111

33. A one-step enzymatic modification of the cell surface redirects cellular cytotoxicity and parasite tropism. Swee LK, Lourido S, Bell GW, Ingram JR, Ploegh HL. ACS Chem Biol.pubmed:25360987;  doi:10.1021/cb500462t

34. Direct Lineage Conversion of Adult Mouse Liver Cells and B Lymphocytes to Neural Stem Cells. Cassady JP, D'Alessio AC, Sarkar S, Dani VS, Fan ZP, Ganz K, Roessler R, Sur M, Young RA, Jaenisch R.Stem Cell Reportspubmed:25454632;  doi:10.1016/j.stemcr.2014.10.001

35. CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer. Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, Abraham BJ, Sharma B, Yeung C, Altabef A, Perez-Atayde A, Wong KK, Yuan GC, Gray NS, Young RA, George RE. Cellpubmed:25416950;  doi:10.1016/j.cell.2014.10.024

36. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Mansour MR, Abraham BJ, Anders L, Berezovskaya A, Gutierrez A, Durbin AD, Etchin J, Lawton L, Sallan SE, Silverman LB, Loh ML, Hunger SP, Sanda T, Young RA, Look AT. Sciencepubmed:25394790;  doi:10.1126/science.1259037

37. Potential function for the Huntingtin protein as a scaffold for selective autophagy. Ochaba J, Lukacsovich T, Csikos G, Zheng S, Margulis J, Salazar L, Mao K, Lau AL, Yeung SY, Humbert S, Saudou F, Klionsky DJ, Finkbeiner S, Zeitlin SO, Marsh JL, Housman DE, Thompson LM, Steffan JS. Proc Natl Acad Sci U S Apubmed:25385587;  doi:10.1073/pnas.1420103111

38. Directed evolution of APEX2 for electron microscopy and proximity labeling. Lam SS, Martell JD, Kamer KJ, Deerinck TJ, Ellisman MH, Mootha VK, Ting AY. Nat Methods.pubmed:25419960;  doi:10.1038/nmeth.3179

39. Mono-anionic phosphopeptides produced by unexpected histidine alkylation exhibit high plk1 polo-box domain-binding affinities and enhanced antiproliferative effects in hela cells. Qian WJ, Park JE, Lim D, Lai CC, Kelley JA, Park SY, Lee KW, Yaffe MB, Lee KS, Burke TRJr. Biopolymerspubmed:25283071;  doi:10.1002/bip.22569

40. Peptide-Based, Two-Fluorophore, Ratiometric Probe for Quantifying Mobile Zinc in Biological Solutions. Zhang DY, Azrad M, Demark-Wahnefried W, Frederickson CJ, Lippard SJ, Radford RJ. ACS Chem Biolpubmed:25382858;  doi:10.1021/cb500617c

41. Human Phosphoglycerate Dehydrogenase Produces the Oncometabolite d-2-Hydroxyglutarate. Fan J, Teng X, Liu L, Mattaini KR, Looper RE, Vander Heiden MG, Rabinowitz JD. ACS Chem Biol.pubmed:25406093;  doi:10.1021/cb500683c

42. Linking DNA Damage, NAD(+)/SIRT1, and Aging. Guarente L. Cell Metabpubmed:25440052;  doi:10.1016/j.cmet.2014.10.015

43. Combating neurodegenerative disease with chemical probes and model systems. Narayan P, Ehsani S, Lindquist S. Nat Chem Biolpubmed:25325702;  doi:10.1038/nchembio.1663

44. DNA Copy-Number Control through Inhibition of Replication Fork Progression. Nordman JT, Kozhevnikova EN, Verrijzer CP, Pindyurin AV, Andreyeva EN, Shloma VV, Zhimulev IF, Orr-Weaver TL. Cell Reppubmed:25437540;  doi:10.1016/j.celrep.2014.10.005

45. Quantitative proteomics reveals the dynamics of protein changes during Drosophila oocyte maturation and the oocyte-to-embryo transition. Kronja I, Whitfield ZJ, Yuan B, Dzeyk K, Kirkpatrick J, Krijgsveld J, Orr-Weaver TL. Proc Natl Acad Sci U S Apubmed:25349405;  doi:10.1073/pnas.1418657111

46. Synthesis of Bis(imidazole) Metal Complexes and Their Use in Rapid NO Detection and Quantification Devices. Victor E, Kim S, Lippard SJ. Inorg Chempubmed:25419858;  doi:10.1021/ic501765g

47. The Epithelial-Mesenchymal Transition Factor SNAIL Paradoxically Enhances Reprogramming. Unternaehrer JJ, Zhao R, Kim K, Cesana M, Powers JT, Ratanasirintrawoot S, Onder T, Shibue T, Weinberg RA, Daley GQ. Stem Cell Reportspubmed:25316190;  doi:10.1016/j.stemcr.2014.09.008

48. A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages. Lu H, Clauser KR, Tam WL, Frose J, Ye X, Eaton EN, Reinhardt F, Donnenberg VS, Bhargava R, Carr SA, Weinberg RA. Nat Cell Biolpubmed:25266422;  doi:10.1038/ncb3041