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 2015

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1. CNS Anticancer Drug Discovery and Development Conference White Paper. Levin VA, Tonge PJ, Gallo JM, Birtwistle MR, Dar AC, Iavarone A, Paddison PJ, Heffron TP, Elmquist WF, Lachowicz JE, Johnson TW, White FM, Sul J, Smith QR, Shen W, Sarkaria JN, Samala R, Wen PY, Berry DA, Petter RC. Neuro Oncol. pubmed:26403167;  doi:10.1093/neuonc/nov169

2. PTP1B-dependent regulation of receptor tyrosine kinase signaling by the actin-binding protein Mena. Hughes SK, Oudin MJ, Tadros J, Neil J, Del Rosario A, Joughin BA, Ritsma L, Wyckoff J, Vasile E, Eddy R, Philippar U, Lussiez A, Condeelis JS, van Rheenen J, White F, Lauffenburger DA, Gertler FB. Mol Biol Cell. pubmed:26337385;  doi:10.1091/mbc.E15-06-0442

3. Graphene Oxide Nanosheets Modified with Single-Domain Antibodies for Rapid and Efficient Capture of Cells. Chen GY, Li Z, Theile CS, Bardhan NM, Kumar PV, Duarte JN, Maruyama T, Rashidfarrokh A, Belcher AM, Ploegh HL. Chemistry. pubmed:26472062;  doi:10.1002/chem.201503057

4. Smart nanosystems: Bio-inspired technologies that interact with the host environment. Kwon EJ, Lo JH, Bhatia SN. Proc Natl Acad Sci U S A. pubmed:26598694;  doi:10.1073/pnas.1508522112

5. Depot delivery of dexamethasone and cediranib for the treatment of brain tumor associated edema in an intracranial rat glioma model. Ong Q, Hochberg FH, Cima MJ. J Control Release. pubmed:26285064;  doi:10.1016/j.jconrel.2015.08.028

6. Medical Adhesives: Bioinspired Nanoparticulate Medical Glues for Minimally Invasive Tissue Repair. Lee Y, Xu C, Sebastin M, Lee A, Holwell N, Xu C, Miranda Nieves D, Mu L, Langer RS, Lin C, Karp JM. Adv Healthc Mater. pubmed:26767735;  doi:10.1002/adhm.201570092

7. Control of liver size by RNAi-mediated multiplex knockdown and its application for discovery of regulatory mechanisms. Yin H, Bogorad RL, Barnes C, Walsh S, Zhuang I, Nonaka H, Ruda V, Kuchimanchi S, Nechev L, Akinc A, Xue W, Zerial M, Langer R, Anderson DG, Koteliansky V. J Hepatol. pubmed:26658687;  doi:10.1016/j.jhep.2015.11.028

8. Sustained Local Release of Methylprednisolone from a Thiol-Acrylate Poly(Ethylene Glycol) Hydrogel for Treating Chronic Compressive Radicular Pain. Slotkin JR, Ness JK, Snyder KM, Skiles AA, Woodard EJ, O'Shea T, Layer RT, Aimetti AA, Toms SA, Langer R, Tapinos N. Spine (Phila Pa 1976). pubmed:26630427;  doi:10.1097/BRS.0000000000001309

9. The Engineering of Biology and Medicine. Davis ME, Langer R. Proc Natl Acad Sci U S A. pubmed:26598670;  doi:10.1073/pnas.1517450112

10. Bioinspired Nanoparticulate Medical Glues for Minimally Invasive Tissue Repair. Lee Y, Xu C, Sebastin M, Lee A, Holwell N, Xu C, Miranda Nieves D, Mu L, Langer RS, Lin C, Karp JM. Adv Healthc Mater. pubmed:26227833;  doi:10.1002/adhm.201500419

11. Resonant microchannel volume and mass measurements show that suspended cells swell during mitosis. Son S, Kang JH, Oh S, Kirschner MW, Mitchison TJ, Manalis S. J Cell Biol. pubmed:26598613;  doi:10.1083/jcb.201505058

12. Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants. Zhu X, Viswanathan K, Raman R, Yu W, Sasisekharan R, Wilson IA. Cell Rep. pubmed:26586437;  doi:10.1016/j.celrep.2015.10.027

13. N-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice. Andries O, Cafferty SM, De Smedt SC, Weiss R, Sanders NN, Kitada T. J Control Release. pubmed:26342664;  doi:10.1016/j.jconrel.2015.08.051

14. Hydrogel microparticles for biosensing. Le Goff GC, Srinivas RL, Hill WA, Doyle PS. Eur Polym J. pubmed:26594056;  doi:10.1016/j.eurpolymj.2015.02.022

15. Cas9 gRNA engineering for genome editing, activation and repression. Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJ, Ebrahimkhani MR, Collins JJ, Weiss R, Church G. Nat Methods. pubmed:26344044;  doi:10.1038/nmeth.3580

16. Macrophage Notch Ligand Delta-Like 4 Promotes Vein Graft Lesion Development: Implications for the Treatment of Vein Graft Failure. Koga JI, Nakano T, Dahlman JE, Figueiredo JL, Zhang H, Decano J, Khan OF, Niida T, Iwata H, Aster JC, Yagita H, Anderson DG, Ozaki CK, Aikawa M. Arterioscler Thromb Vasc Biol. pubmed:26404485;  doi:10.1161/ATVBAHA.115.305516

17. Chemical materials and their regulation of the movement of molecules. Langer R. Q Rev Biophys. pubmed:26537401;  doi:10.1017/S0033583515000165

18. Optimization of Lipid Nanoparticle Formulations for mRNA Delivery in vivo with Fractional Factorial and Definitive Screening Designs. Kauffman KJ, Dorkin JR, Yang JH, Heartlein MW, DeRosa F, Mir FF, Fenton OS, Anderson DG. Nano Lett. pubmed:26469188;  doi:10.1021/acs.nanolett.5b02497

19. Big thinking for adjuvants. Dane EL, Irvine DJ. Nat Biotechnol. pubmed:26544144;  doi:10.1038/nbt.3398

20. Theranostic pretargeted radioimmunotherapy of colorectal cancer xenografts in mice using picomolar affinity Y- or Lu-DOTA-Bn binding scFv C825/GPA33 IgG bispecific immunoconjugates. Cheal SM, Xu H, Guo HF, Lee SG, Punzalan B, Chalasani S, Fung EK, Jungbluth A, Zanzonico PB, Carrasquillo JA, O'Donoghue J, Smith-Jones PM, Wittrup KD, Cheung NV, Larson SM. Eur J Nucl Med Mol Imaging. pubmed:26596724;  doi:10.1007/s00259-015-3254-8

21. Oct1 and OCA-B are selectively required for CD4 memory T cell function. Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D. J Exp Med. pubmed:26481684;  doi:10.1084/jem.20150363

22. Identification and characterization of essential genes in the human genome. Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, Lander ES, Sabatini DM. Science. pubmed:26472758;  doi:10.1126/science.aac7041

23. Transcription factor trapping by RNA in gene regulatory elements. Sigova AA, Abraham BJ, Ji X, Molinie B, Hannett NM, Guo YE, Jangi M, Giallourakis CC, Sharp PA, Young RA. Science. pubmed:26516199;  doi:10.1126/science.aad3346

24. Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Brastianos PK, Carter SL, Santagata S, Cahill DP, Taylor-Weiner A, Jones RT, Van Allen EM, Lawrence MS, Horowitz PM, Cibulskis K, Ligon KL, Tabernero J, Seoane J, Martinez-Saez E, Curry WT, Dunn IF, Paek SH, Park SH, McKenna A, Chevalier A, Rosenberg M, Barker FG2nd, Gill CM, Van Hummelen P, Thorner AR, Johnson BE, Hoang MP, Choueiri TK, Signoretti S, Sougnez C, Rabin MS, Lin NU, Winer EP, Stemmer-Rachamimov A, Meyerson M, Garraway L, Gabriel S, Lander ES, Beroukhim R, Batchelor TT, Baselga J, Louis DN, Getz G, Hahn WC. Cancer Discov. pubmed:26410082;  doi:10.1158/2159-8290.CD-15-0369

25. The Biology and Evolution of Mammalian Y Chromosomes. Hughes JF, Page DC. Annu Rev Genet. pubmed:26442847;  doi:10.1146/annurev-genet-112414-055311

26. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Rege M, Subramanian V, Zhu C, Hsieh TS, Weiner A, Friedman N, Clauder-Munster S, Steinmetz LM, Rando OJ, Boyer LA, Peterson CL. Cell Rep. pubmed:26586442;  doi:10.1016/j.celrep.2015.10.030

27. Combined Loss of Tet1 and Tet2 Promotes B Cell, but Not Myeloid Malignancies, in Mice. Zhao Z, Chen L, Dawlaty MM, Pan F, Weeks O, Zhou Y, Cao Z, Shi H, Wang J, Lin L, Chen S, Yuan W, Qin Z, Ni H, Nimer SD, Yang FC, Jaenisch R, Jin P, Xu M. Cell Rep. pubmed:26586431;  doi:10.1016/j.celrep.2015.10.037

28. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL. Proc Natl Acad Sci U S A. pubmed:26499245;  doi:10.1073/pnas.1518552112

29. A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity. D'Alessio AC, Fan ZP, Wert KJ, Baranov P, Cohen MA, Saini JS, Cohick E, Charniga C, Dadon D, Hannett NM, Young MJ, Temple S, Jaenisch R, Lee TI, Young RA. Stem Cell Reports. pubmed:26603904;  doi:10.1016/j.stemcr.2015.09.016

30. Stopping the Clock with MYC. Lau AN, Vander Heiden MG. Mol Cell. pubmed:26590710;  doi:10.1016/j.molcel.2015.11.008

31. Treatment response assessment in IDH-mutant glioma patients by non-invasive 3D functional Spectroscopic Mapping of 2-Hydroxyglutarate. Andronesi OC, Loebel F, Bogner W, Marjanska M, Vander Heiden MG, Iafrate AJ, Dietrich J, Batchelor T, Gerstner ER, Kaelin WJr, Chi AS, Rosen B, Cahill DP. Clin Cancer Res. pubmed:26534967;  doi:10.1158/1078-0432.CCR-15-0656

32. The Role of Pyruvate Kinase M2 in Cancer Metabolism. Liu VM, Vander Heiden MG. Brain Pathol. pubmed:26526946;  doi:10.1111/bpa.12311

33. Aneuploidy triggers a TFEB-mediated lysosomal stress response. Santaguida S, Amon A. Autophagy. pubmed:26571033;  doi:10.1080/15548627.2015.1110670

34. F NMR study of ligand dynamics in carboxylate-bridged diiron(ii) complexes supported by a macrocyclic ligand. Minier MA, Lippard SJ. Dalton Trans. pubmed:26418547;  doi:10.1039/c5dt02138c

35. Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage. Belenky P, Ye JD, Porter CB, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC, Collins JJ. Cell Rep. pubmed:26565910;  doi:10.1016/j.celrep.2015.09.059

36. Epithelial-Mesenchymal Plasticity: A Central Regulator of Cancer Progression. Ye X, Weinberg RA. Trends Cell Biol. pubmed:26437589;  doi:10.1016/j.tcb.2015.07.012

37. Neighbor-directed Histidine N(tau)-Alkylation: A Route to Imidazolium-containing Phosphopeptide Macrocycles. Qian WJ, Park JE, Grant R, Lai CC, Kelley JA, Yaffe MB, Lee KS, Burke TR. Biopolymers. pubmed:26152807;  doi:10.1002/bip.22698

38. Metal-Based Optical Probes for Live Cell Imaging of Nitroxyl (HNO). Rivera-Fuentes P, Lippard SJ. Acc Chem Res. pubmed:26550842;  doi:10.1021/acs.accounts.5b00388

39. A Pleiotropic RNA-Binding Protein Controls Distinct Cell Cycle Checkpoints to Drive Resistance of p53-Defective Tumors to Chemotherapy. Cannell IG, Merrick KA, Morandell S, Zhu CQ, Braun CJ, Grant RA, Cameron ER, Tsao MS, Hemann MT, Yaffe MB. Cancer Cell. pubmed:26602816;  doi:10.1016/j.ccell.2015.09.009