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: February 2017

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1. Enhanced isolation and release of circulating tumor cells using nanoparticle binding and ligand exchange in a microfluidic chip. Park MH, Reategui E, Li W, Tessier SN, Wong KH, Jensen AE, Thapar V, Ting D, Toner M, Stott SL, Hammond PT. J Am Chem Socpubmed:28133963;  doi:10.1021/jacs.6b12236

2. Epigenetic Modulation using Small Molecules - Targeting Histone Acetyltransferases in Disease. Richters A, Koehler AN. Curr Med Chem.pubmed:28240169;  doi:10.2174/0929867324666170223153115

3. Antigen recognition-triggered drug delivery mediated by nanocapsule-functionalized cytotoxic T-cells. Jones RB, Mueller S, Kumari S, Vrbanac V, Genel S, Tager AM, Allen TM, Walker BD, Irvine DJ. Biomaterialspubmed:27936416;  doi:10.1016/j.biomaterials.2016.11.048

4. Virus-driven inflammation is associated with the development of bNAbs in spontaneous controllers of HIV. Dugast AS, Arnold K, Lofano G, Moore S, Hoffner M, Simek M, Poignard P, Seaman M, Suscovich T, Pereyra F, Walker BD, Lauffenburger D, Kwon D, Keele BF, Alter G. Clin Infect Dispubmed:28158448;  doi:10.1093/cid/cix057

5. Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. Tan L, Gurbani D, Weisberg EL, Jones DS, Rao S, Singer WD, Bernard FM, Mowafy S, Jenney A, Du G, Nonami A, Griffin JD, Lauffenburger DA, Westover KD, Sorger PK, Gray NS. Bioorg Med Chempubmed:28038940;  doi:10.1016/j.bmc.2016.11.034

6. Molecular Pathways: Receptor Ectodomain Shedding in Treatment, Resistance, and Monitoring of Cancer. Miller MA, Sullivan RJ, Lauffenburger DA. Clin Cancer Res.pubmed:27895032;  doi:10.1158/1078-0432.CCR-16-0869

7. Enhanced Cell Capture on Functionalized Graphene Oxide Nanosheets through Oxygen Clustering. Bardhan NM, Kumar PV, Li Z, Ploegh HL, Grossman JC, Belcher AM, Chen GY. ACS Nano.pubmed:28085249;  doi:10.1021/acsnano.6b06979

8. A three dimensional in vitro glial scar model to investigate the local strain effects from micromotion around neural implants. Spencer KC, Sy JC, Falcon-Banchs R, Cima MJ. Lab Chip.pubmed:28119969;  doi:10.1039/c6lc01411a

9. Clonal Expansion of Lgr5-Positive Cells from Mammalian Cochlea and High-Purity Generation of Sensory Hair Cells. McLean WJ, Yin X, Lu L, Lenz DR, McLean D, Langer R, Karp JM, Edge AS. Cell Reppubmed:28228258;  doi:10.1016/j.celrep.2017.01.066

10. Barcoded nanoparticles for high throughput in vivo discovery of targeted therapeutics. Dahlman JE, Kauffman KJ, Xing Y, Shaw TE, Mir FF, Dlott CC, Langer R, Anderson DG, Wang ET. Proc Natl Acad Sci U S Apubmed:28167778;  doi:10.1073/pnas.1620874114

11. In vitro 3D model and miRNA drug delivery to target calcific aortic valve disease. van der Ven CF, Wu PJ, Tibbitt MW, van Mil A, Sluijter JP, Langer R, Aikawa E. Clin Sci (Lond).pubmed:28057890;  doi:10.1042/CS20160378

12. Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors. Davidson SM, Jonas O, Keibler MA, Hou HW, Luengo A, Mayers JR, Wyckoff J, Del Rosario AM, Whitman M, Chin CR, Condon KJ, Lammers A, Kellersberger KA, Stall BK, Stephanopoulos G, Bar-Sagi D, Han J, Rabinowitz JD, Cima MJ, Langer R, Vander Heiden MG. Nat Med.pubmed:28024083;  doi:10.1038/nm.4256

13. A Facile and Versatile Method to Endow Biomaterial Devices with Zwitterionic Surface Coatings. Yesilyurt V, Veiseh O, Doloff JC, Li J, Bose S, Xie X, Bader AR, Chen M, Webber MJ, Vegas AJ, Langer R, Anderson DG. Adv Healthc Materpubmed:27976536;  doi:10.1002/adhm.201601091

14. Stretchable living materials and devices with hydrogel-elastomer hybrids hosting programmed cells. Liu X, Tang TC, Tham E, Yuk H, Lin S, Lu TK, Zhao X. Proc Natl Acad Sci U S A.pubmed:28202725;  doi:10.1073/pnas.1618307114

15. Synthetic biology: Synthetic gene networks that smell. Farzadfard F, Lu TK. Nat Chem Biolpubmed:28199298;  doi:10.1038/nchembio.2315

16. A novel Bxb1 integrase RMCE system for high fidelity site-specific integration of mAb expression cassette in CHO cells. Inniss MC, Bandara K, Jusiak B, Lu TK, Weiss R, Wroblewska L, Zhang L. Biotechnol Bioengpubmed:28186334;  doi:10.1002/bit.26268

17. CRISPR-Cas9 technology: applications in genome engineering, development of sequence-specific antimicrobials, and future prospects. de la Fuente-Nunez C, Lu TK. Integr Biol (Camb).pubmed:28045163;  doi:10.1039/c6ib00140h

18. Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity. Seker UO, Chen AY, Citorik RJ, Lu TK. ACS Synth Biol.pubmed:27794590;  doi:10.1021/acssynbio.6b00166

19. 3D printing of self-assembling thermoresponsive nanoemulsions into hierarchical mesostructured hydrogels. Hsiao LC, Badruddoza AZ, Cheng LC, Doyle PS. Soft Matter.pubmed:28094392;  doi:10.1039/c6sm02208a

20. Noninvasive imaging of human immune responses in a human xenograft model of graft-versus-host disease. Van Elssen CH, Rashidian M, Vrbanac V, Wucherpfennig KW, El Habre Z, Sticht J, Freund C, Jacobsen J, Cragnolini J, Ingram J, Plaisier L, Spierings E, Tager AM, Ploegh H. J Nucl Medpubmed:28209904;  doi:10.2967/jnumed.116.186007

21. Systematic dissection of genomic features determining transcription factor binding and enhancer function. Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES. Proc Natl Acad Sci U S Apubmed:28137873;  doi:10.1073/pnas.1621150114

22. Integrated genomic analyses of de novo pathways underlying atypical meningiomas. Harmanci AS, Youngblood MW, Clark VE, Coskun S, Henegariu O, Duran D, Erson-Omay EZ, Kaulen LD, Lee TI, Abraham BJ, Simon M, Krischek B, Timmer M, Goldbrunner R, Omay SB, Baranoski J, Baran B, Carrion-Grant G, Bai H, Mishra-Gorur K, Schramm J, Moliterno J, Vortmeyer AO, Bilguvar K, Yasuno K, Young RA, Gunel M. Nat Communpubmed:28195122;  doi:10.1038/ncomms14433

23. Transcriptional Addiction in Cancer. Bradner JE, Hnisz D, Young RA. Cellpubmed:28187285;  doi:10.1016/j.cell.2016.12.013

24. Small genomic insertions form enhancers that misregulate oncogenes. Abraham BJ, Hnisz D, Weintraub AS, Kwiatkowski N, Li CH, Li Z, Weichert-Leahey N, Rahman S, Liu Y, Etchin J, Li B, Shen S, Lee TI, Zhang J, Look AT, Mansour MR, Young RA. Nat Communpubmed:28181482;  doi:10.1038/ncomms14385

25. Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras. Wang T, Yu H, Hughes NW, Liu B, Kendirli A, Klein K, Chen WW, Lander ES, Sabatini DM. Cellpubmed:28162770;  doi:10.1016/j.cell.2017.01.013

26. Drug discovery for Diamond-Blackfan anemia using reprogrammed hematopoietic progenitors. Doulatov S, Vo LT, Macari ER, Wahlster L, Kinney MA, Taylor AM, Barragan J, Gupta M, McGrath K, Lee HY, Humphries JM, DeVine A, Narla A, Alter BP, Beggs AH, Agarwal S, Ebert BL, Gazda HT, Lodish HF, Sieff CA, Schlaeger TM, Zon LI, Daley GQ. Sci Transl Med.pubmed:28179501;  doi:10.1126/scitranslmed.aah5645

27. A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltran W, Piechocka-Trocha A, Krogan NJ, Marson A, Sabatini DM, Lander ES, Hacohen N, Walker BD. Nat Genetpubmed:27992415;  doi:10.1038/ng.3741

28. The awakening of the CDK10/Cyclin M protein kinase. Guen VJ, Gamble C, Lees JA, Colas P. Oncotargetpubmed:28178678;  doi:10.18632/oncotarget.15024

29. Single-chromosome Gains Commonly Function as Tumor Suppressors. Sheltzer JM, Ko JH, Replogle JM, Habibe Burgos NC, Chung ES, Meehl CM, Sayles NM, Passerini V, Storchova Z, Amon A. Cancer Cellpubmed:28089890;  doi:10.1016/j.ccell.2016.12.004

30. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase. Looke M, Maloney MF, Bell SP. Genes Devpubmed:28270517;  doi:10.1101/gad.291336.116

31. HSP90 Shapes the Consequences of Human Genetic Variation. Karras GI, Yi S, Sahni N, Fischer M, Xie J, Vidal M, D'Andrea AD, Whitesell L, Lindquist S. Cellpubmed:28215707;  doi:10.1016/j.cell.2017.01.023

32. Genome-Scale Networks Link Neurodegenerative Disease Genes to alpha-Synuclein through Specific Molecular Pathways. Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schondorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S. Cell Systpubmed:28131822;  doi:10.1016/j.cels.2016.12.011

33. Understanding the Intersections between Metabolism and Cancer Biology. Vander Heiden MG, DeBerardinis RJ. Cellpubmed:28187287;  doi:10.1016/j.cell.2016.12.039

34. In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons. Chung CY, Khurana V, Yi S, Sahni N, Loh KH, Auluck PK, Baru V, Udeshi ND, Freyzon Y, Carr SA, Hill DE, Vidal M, Ting AY, Lindquist S. Cell Systpubmed:28131823;  doi:10.1016/j.cels.2017.01.002

35. Fasting-Mimicking Diet Promotes Ngn3-Driven beta-Cell Regeneration to Reverse Diabetes. Cheng CW, Villani V, Buono R, Wei M, Kumar S, Yilmaz OH, Cohen P, Sneddon JB, Perin L, Longo VD. Cellpubmed:28235195;  doi:10.1016/j.cell.2017.01.040

36. The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Beyaz S, Kim JH, Pinello L, Xifaras ME, Hu Y, Huang J, Kerenyi MA, Das PP, Barnitz RA, Herault A, Dogum R, Haining WN, Yilmaz OH, Passegue E, Yuan GC, Orkin SH, Winau F. Nat Immunolpubmed:27992400;  doi:10.1038/ni.3644

37. Cancer cells exhibit clonal diversity in phenotypic plasticity. Mathis RA, Sokol ES, Gupta PB. Open Biolpubmed:28202626;  doi:10.1098/rsob.160283

38. Emerging Biological Principles of Metastasis. Lambert AW, Pattabiraman DR, Weinberg RA. Cellpubmed:28187288;  doi:10.1016/j.cell.2016.11.037