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: July 2016

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1. Application of Targeted Molecular and Material Property Optimization to Bacterial Attachment-Resistant (Meth)acrylate Polymers. Adlington K, Nguyen NT, Eaves E, Yang J, Chang CY, Li J, Gower AL, Stimpson A, Anderson DG, Langer R, Davies MC, Hook AL, Williams P, Alexander MR, Irvine DJ. Biomacromolecules. pubmed:27461341;  doi:10.1021/acs.biomac.6b00615

2. Injectable and glucose-responsive hydrogels based on boronic acid-glucose complexation. Dong Y, Wang W, Veiseh O, Appel EA, Xue K, Webber MJ, Tang B, Yang XW, Weir G, Langer R, Anderson DG. Langmuir. pubmed:27455412;  doi:10.1021/acs.langmuir.5b04755

3. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. Van Voorhis WC, Adams JH, Adelfio R, Ahyong V, Akabas MH, Alano P, Alday A, Aleman Resto Y, Alsibaee A, Alzualde A, Andrews KT, Avery SV, Avery VM, Ayong L, Baker M, Baker S, Ben Mamoun C, Bhatia S, Bickle Q, Bounaadja L, Bowling T, Bosch J, Boucher LE, Boyom FF, Brea J, Brennan M, Burton A, Caffrey CR, Camarda G, Carrasquilla M, Carter D, Belen Cassera M, Chih-Chien Cheng K, Chindaudomsate W, Chubb A, Colon BL, Colon-Lopez DD, Corbett Y, Crowther GJ, Cowan N, D'Alessandro S, Le Dang N, Delves M, DeRisi JL, Du AY, Duffy S, Abd El-Salam El-Sayed S, Ferdig MT, Fernandez Robledo JA, Fidock DA, Florent I, Fokou PV, Galstian A, Gamo FJ, Gokool S, Gold B, Golub T, Goldgof GM, Guha R, Guiguemde WA, Gural N, Guy RK, Hansen MA, Hanson KK, Hemphill A, Hooft van Huijsduijnen R, Horii T, Horrocks P, Hughes TB, Huston C, Igarashi I, Ingram-Sieber K, Itoe MA, Jadhav A, Naranuntarat Jensen A, Jensen LT, Jiang RH, Kaiser A, Keiser J, Ketas T, Kicka S, Kim S, Kirk K, Kumar VP, Kyle DE, Lafuente MJ, Landfear S, Lee N, Lee S, Lehane AM, Li F, Little D, Liu L, Llinas M, Loza MI, Lubar A, Lucantoni L, Lucet I, Maes L, Mancama D, Mansour NR, March S, McGowan S, Medina Vera I, Meister S, Mercer L, Mestres J, Mfopa AN, Misra RN, Moon S, Moore JP, Morais Rodrigues da Costa F, Muller J, Muriana A, Nakazawa Hewitt S, Nare B, Nathan C, Narraidoo N, Nawaratna S, Ojo KK, Ortiz D, Panic G, Papadatos G, Parapini S, Patra K, Pham N, Prats S, Plouffe DM, Poulsen SA, Pradhan A, Quevedo C, Quinn RJ, Rice CA, Abdo Rizk M, Ruecker A, St Onge R, Salgado Ferreira R, Samra J, Robinett NG, Schlecht U, Schmitt M, Silva Villela F, Silvestrini F, Sinden R, Smith DA, Soldati T, Spitzmuller A, Stamm SM, Sullivan DJ, Sullivan W, Suresh S, Suzuki BM, Suzuki Y, Swamidass SJ, Taramelli D, Tchokouaha LR, Theron A, Thomas D, Tonissen KF, Townson S, Tripathi AK, Trofimov V, Udenze KO, Ullah I, Vallieres C, Vigil E, Vinetz JM, Voong Vinh P, Vu H, Watanabe NA, Weatherby K, White PM, Wilks AF, Winzeler EA, Wojcik E, Wree M, Wu W, Yokoyama N, Zollo PH, Abla N, Blasco B, Burrows J, Laleu B, Leroy D, Spangenberg T, Wells T, Willis PA. PLoS Pathog. pubmed:27467575;  doi:10.1371/journal.ppat.1005763

4. Evolution of Antibody-Drug Conjugate Tumor Disposition Model to Predict Preclinical Tumor Pharmacokinetics of Trastuzumab-Emtansine (T-DM1). Singh AP, Maass KF, Betts AM, Wittrup KD, Kulkarni C, King LE, Khot A, Shah DK. AAPS J. pubmed:27029797;  doi:10.1208/s12248-016-9904-3

5. Pathway-based network modeling finds hidden genes in shRNA screen for regulators of acute lymphoblastic leukemia. Wilson JL, Dalin S, Gosline S, Hemann M, Fraenkel E, Lauffenburger DA. Integr Biol (Camb). pubmed:27315426;  doi:10.1039/c6ib00040a

6. Parp1 protects against Aag-dependent alkylation-induced nephrotoxicity in a sex-dependent manner. Calvo JA, Allocca M, Fake KR, Muthupalani S, Corrigan JJ, Bronson RT, Samson LD. Oncotarget. pubmed:27391435;  doi:10.18632/oncotarget.10440

7. A Thermodynamic Based Interpretation of Protein Expression Heterogeneity in Different GBM Tumors Identifies Tumor Specific Unbalanced Processes. Kravchenko-Balasha N, Johnson H, White FM, Heath JR, Levine RD. J Phys Chem B. pubmed:27035264;  doi:10.1021/acs.jpcb.6b01692

8. Spatial Control of Gene Expression by Nanocarriers Using Heparin Masking and Ultrasound-Targeted Microbubble Destruction. Chertok B, Langer R, Anderson DG. ACS Nano. pubmed:27472268;  doi:10.1021/acsnano.6b01199

9. Identification of polymer surface adsorbed proteins implicated in pluripotent human embryonic stem cell expansion. Hammad M, Rao W, Smith JG, Anderson DG, Langer R, Young LE, Barrett DA, Davies MC, Denning C, Alexander MR. Biomater Sci. pubmed:27466628;  doi:10.1039/c6bm00214e

10. Dendrimer-RNA nanoparticles generate protective immunity against lethal Ebola, H1N1 influenza, and Toxoplasma gondii challenges with a single dose. Chahal JS, Khan OF, Cooper CL, McPartlan JS, Tsosie JK, Tilley LD, Sidik SM, Lourido S, Langer R, Bavari S, Ploegh HL, Anderson DG. Proc Natl Acad Sci U S A. pubmed:27382155;  doi:10.1073/pnas.1600299113

11. Infection of laboratory colonies of Anopheles mosquitoes with Plasmodium vivax from cryopreserved clinical isolates. Shaw-Saliba K, Clarke D, Santos JM, Menezes MJ, Lim C, Mascarenhas A, Chery L, Gomes E, March S, Bhatia SN, Rathod PK, Ferreira MU, Catteruccia F, Duraisingh MT. Int J Parasitol. pubmed:27456552;  doi:10.1016/j.ijpara.2016.06.003

12. Self-Sealing Porous Silicon-Calcium Silicate Core-Shell Nanoparticles for Targeted siRNA Delivery to the Injured Brain. Kang J, Joo J, Kwon EJ, Skalak M, Hussain S, She ZG, Ruoslahti E, Bhatia SN, Sailor MJ. Adv Mater. pubmed:27383373;  doi:10.1002/adma.201600634

13. Engineering a perfusable 3D human liver platform from iPS cells. Schepers A, Li C, Chhabra A, Seney BT, Bhatia S. Lab Chip. pubmed:27296616;  doi:10.1039/c6lc00598e

14. Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies. Ramanan V, Trehan K, Ong ML, Luna JM, Hoffmann HH, Espiritu C, Sheahan TP, Chandrasekar H, Schwartz RE, Christine KS, Rice CM, van Oudenaarden A, Bhatia SN. Virology. pubmed:27128351;  doi:10.1016/j.virol.2016.04.020

15. Atherosclerotic plaque behind the stent changes after bare-metal and drug-eluting stent implantation in humans: Implications for late stent failure?. Andreou I, Takahashi S, Tsuda M, Shishido K, Antoniadis AP, Papafaklis MI, Mizuno S, Coskun AU, Saito S, Feldman CL, Edelman ER, Stone PH. Atherosclerosis. pubmed:27494445;  doi:10.1016/j.atherosclerosis.2016.07.914

16. Drug deposition in coronary arteries with overlapping drug-eluting stents. Rikhtegar F, Edelman ER, Olgac U, Poulikakos D, Kurtcuoglu V. J Control Release. pubmed:27432751;  doi:10.1016/j.jconrel.2016.07.023

17. A tunable delivery platform to provide local chemotherapy for pancreatic ductal adenocarcinoma. Indolfi L, Ligorio M, Ting DT, Xega K, Tzafriri AR, Bersani F, Aceto N, Thapar V, Fuchs BC, Deshpande V, Baker AB, Ferrone CR, Haber DA, Langer R, Clark JW, Edelman ER. Biomaterials. pubmed:27082874;  doi:10.1016/j.biomaterials.2016.03.044

18. Arterial Stiffening in Perspective: Advances in Physical and Physiological Science Over Centuries. O'Rourke MF, O'Brien C, Edelman ER. Am J Hypertens. pubmed:27001969;  doi:10.1093/ajh/hpw019

19. Vascular Response to Experimental Stent Malapposition and Under-Expansion. O'Brien CC, Lopes AC, Kolandaivelu K, Kunio M, Brown J, Kolachalama VB, Conway C, Bailey L, Markham P, Costa M, Ware J, Edelman ER. Ann Biomed Eng. pubmed:26732391;  doi:10.1007/s10439-015-1518-x

20. Nanolayered siRNA delivery platforms for local silencing of CTGF reduce cutaneous scar contraction in third-degree burns. Castleberry SA, Golberg A, Sharkh MA, Khan S, Almquist BD, Austen WGJr, Yarmush ML, Hammond PT. Biomaterials. pubmed:27108403;  doi:10.1016/j.biomaterials.2016.04.007

21. Generation of long-lived bone marrow plasma cells secreting antibodies specific for HIV-1 gp41 MPER in the absence of polyreactivity. Donius LR, Cheng Y, Choi J, Sun ZJ, Hanson M, Zhang M, Gierahn TM, Marquez S, Uduman M, Kleinstein SH, Irvine D, Love JC, Reinherz EL, Kim M. J Virol. pubmed:27466419;  doi:10.1128/JVI.01089-16

22. Inhibition of Zinc-Dependent Histone Deacetylases with a Chemically Triggered Electrophile. Boskovic ZV, Kemp MM, Freedy AM, Viswanathan VS, Pop MS, Fuller JH, Martinez NM, Figueroa Lazu SO, Hong JA, Lewis TA, Calarese D, Love JD, Vetere A, Almo SC, Schreiber SL, Koehler AN. ACS Chem Biol. pubmed:27064299;  doi:10.1021/acschembio.6b00012

23. Neuron-Targeted Nanoparticle for siRNA Delivery to Traumatic Brain Injuries. Kwon EJ, Skalak M, Lo Bu R, Bhatia SN. ACS Nano. pubmed:27429164;  doi:10.1021/acsnano.6b03858

24. Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology. Jusiak B, Cleto S, Perez-Pinera P, Lu TK. Trends Biotechnol. pubmed:26809780;  doi:10.1016/j.tibtech.2015.12.014

25. Synthetic recombinase-based state machines in living cells. Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK. Science. pubmed:27463678;  doi:10.1126/science.aad8559

26. Identification of new branch points and unconventional introns in Saccharomyces cerevisiae. Gould GM, Paggi JM, Guo Y, Phizicky DV, Zinshteyn B, Wang ET, Gilbert WV, Gifford DK, Burge CB. RNA. pubmed:27473169;  doi:10.1261/rna.057216.116

27. Molecular Criteria for Defining the Naive Human Pluripotent State. Theunissen TW, Friedli M, He Y, Planet E, O'Neil RC, Markoulaki S, Pontis J, Wang H, Iouranova A, Imbeault M, Duc J, Cohen MA, Wert KJ, Castanon R, Zhang Z, Huang Y, Nery JR, Drotar J, Lungjangwa T, Trono D, Ecker JR, Jaenisch R. Cell Stem Cell. pubmed:27424783;  doi:10.1016/j.stem.2016.06.011

28. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL. Cell Syst. pubmed:27467249;  doi:10.1016/j.cels.2016.07.002

29. Development and Validation of a Mass Spectrometry-Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease. Blumenstiel B, DeFelice M, Birsoy O, Bleyer AJ, Kmoch S, Carter TA, Gnirke A, Kidd K, Rehm HL, Ronco L, Lander ES, Gabriel S, Lennon NJ. J Mol Diagn. pubmed:27157321;  doi:10.1016/j.jmoldx.2016.03.003

30. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL. Cell Syst. pubmed:27467250;  doi:10.1016/j.cels.2015.07.012

31. Transnuclear CD8 T cells specific for the immunodominant epitope Gra6 lower acute phase Toxoplasma gondii burden. Sanecka A, Yoshida N, Dougan SK, Jackson J, Shastri N, Ploegh H, Blanchard N, Frickel EM. Immunology. pubmed:27377596;  doi:10.1111/imm.12643

32. JAK2 V617F stimulates proliferation of erythropoietin- dependent erythroid progenitors and delays their differentiation by activating Stat1 and other non-erythroid signaling pathways. Shi J, Yuan B, Hu W, Lodish H. Exp Hematol. pubmed:27473563;  doi:10.1016/j.exphem.2016.07.010

33. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Habib N, Li Y, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta JJ, Hession C, Zhang F, Regev A. Science. pubmed:27471252;  doi:10.1126/science.aad7038

34. RBPJ Controls Development of Pathogenic Th17 Cells by Regulating IL-23 Receptor Expression. Meyer Zu Horste G, Wu C, Wang C, Cong L, Pawlak M, Lee Y, Elyaman W, Xiao S, Regev A, Kuchroo VK. Cell Rep. pubmed:27346359;  doi:10.1016/j.celrep.2016.05.088

35. mRNA Poly(A)-tail Changes Specified by Deadenylation Broadly Reshape Translation in Drosophila Oocytes and Early Embryos. Eichhorn SW, Subtelny AO, Kronja I, Kwasnieski JC, Orr-Weaver TL, Bartel DP. Elife. pubmed:27474798;  doi:10.7554/eLife.16955

36. mTORC1 and SIRT1 Cooperate to Foster Expansion of Gut Adult Stem Cells during Calorie Restriction. Igarashi M, Guarente L. Cell. pubmed:27345368;  doi:10.1016/j.cell.2016.05.044

37. Chromosome Duplication in Saccharomyces cerevisiae. Bell SP, Labib K. Genetics. pubmed:27384026;  doi:10.1534/genetics.115.186452

38. Cell biology: The TORC1 pathway to protein destruction. Chantranupong L, Sabatini DM. Nature. pubmed:27462809;  doi:10.1038/nature18919

39. High fat diet and stem cells: Linking diet to intestinal tumor formation. Cangelosi AL, Yilmaz OH. Cell Cycle. pubmed:27097128;  doi:10.1080/15384101.2016.1175275

40. Defining the Essential Function of Yeast Hsf1 Reveals a Compact Transcriptional Program for Maintaining Eukaryotic Proteostasis. Solis EJ, Pandey JP, Zheng X, Jin DX, Gupta PB, Airoldi EM, Pincus D, Denic V. Mol Cell. pubmed:27320198;  doi:10.1016/j.molcel.2016.05.014

41. The Potent Inhibitory Effect of a Naproxen-Appended Cobalt(III)-Cyclam Complex on Cancer Stem Cells. Cressey P, Eskandari A, Bruno P, Lu C, Hemann M, Suntharalingam K. Chembiochem. pubmed:27377813;  doi:10.1002/cbic.201600368

42. Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation. Braun CJ, Bruno PM, Horlbeck MA, Gilbert LA, Weissman JS, Hemann MT. Proc Natl Acad Sci U S A. pubmed:27325776;  doi:10.1073/pnas.1600582113

43. A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY. Nat Biotechnol. pubmed:27240195;  doi:10.1038/nbt.3563