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: October 2015

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1. Degradable hydrogels derived from PEG-diacrylamide for hepatic tissue engineering. Stevens KR, Miller JS, Blakely BL, Chen CS, Bhatia SN. J Biomed Mater Res A. pubmed:25851120;  doi:10.1002/jbm.a.35478

2. A Novel Algorithm to Quantify Coronary Remodeling Using Inferred Normal Dimensions. Falcao BA, Falcao JL, Morais GR, Silva RC, Lopes AC, Soares PR, Mariani JJr, Kalil-Filho R, Edelman ER, Lemos PA. Arq Bras Cardiol. pubmed:26559986;  doi:10.5935/abc.20150098

3. Tracking of Drug Release and Material Fate for Naturally Derived Omega-3 Fatty Acid Biomaterials. Faucher KM, Artzi N, Beck M, Beckerman R, Moodie G, Albergo T, Conroy S, Dale A, Corbeil S, Martakos P, Edelman ER. Ann Biomed Eng. pubmed:26502170;  doi:10.1007/s10439-015-1489-y

4. Structural Mechanics Predictions Relating to Clinical Coronary Stent Fracture in a 5 Year Period in FDA MAUDE Database. Everett KD, Conway C, Desany GJ, Baker BL, Choi G, Taylor CA, Edelman ER. Ann Biomed Eng. pubmed:26467552;  doi:10.1007/s10439-015-1476-3

5. Tuning of Collagen Scaffold Properties Modulates Embedded Endothelial Cell Regulatory Phenotype in Repair of Vascular Injuries In Vivo. Unterman S, Freiman A, Beckerman M, Abraham E, Stanley JR, Levy E, Artzi N, Edelman E. Adv Healthc Mater. pubmed:26333178;  doi:10.1002/adhm.201500457

6. Biodegradable nano-films for capture and non-invasive release of circulating tumor cells. Li W, Reategui E, Park MH, Castleberry S, Deng JZ, Hsu B, Mayner S, Jensen AE, Sequist LV, Maheswaran S, Haber DA, Toner M, Stott SL, Hammond PT. Biomaterials. pubmed:26142780;  doi:10.1016/j.biomaterials.2015.06.036

7. Tumor-Targeted Synergistic Blockade of MAPK and PI3K From a Layer-by-Layer Nanoparticle. Dreaden EC, Kong YW, Morton SW, Correa S, Choi KY, Shopsowitz KE, Renggli K, Drapkin R, Yaffe MB, Hammond PT. Clin Cancer Res. pubmed:26034127;  doi:10.1158/1078-0432.CCR-15-0013

8. Ultrasound-mediated gastrointestinal drug delivery. Schoellhammer CM, Schroeder A, Maa R, Lauwers GY, Swiston A, Zervas M, Barman R, DiCiccio AM, Brugge WR, Anderson DG, Blankschtein D, Langer R, Traverso G. Sci Transl Med. pubmed:26491078;  doi:10.1126/scitranslmed.aaa5937

9. Cell-Substrate Interactions: Tuning of Collagen Scaffold Properties Modulates Embedded Endothelial Cell Regulatory Phenotype in Repair of Vascular Injuries In Vivo. Unterman S, Freiman A, Beckerman M, Abraham E, Stanley JR, Levy E, Artzi N, Edelman E. Adv Healthc Mater. pubmed:26503521;  doi:10.1002/adhm.201570087

10. A pH-responsive supramolecular polymer gel as an enteric elastomer for use in gastric devices. Zhang S, Bellinger AM, Glettig DL, Barman R, Lee YL, Zhu J, Cleveland C, Montgomery VA, Gu L, Nash LD, Maitland DJ, Langer R, Traverso G. Nat Mater. pubmed:26213897;  doi:10.1038/nmat4355

11. Mathematical framework for activity-based cancer biomarkers. Kwong GA, Dudani JS, Carrodeguas E, Mazumdar EV, Zekavat SM, Bhatia SN. Proc Natl Acad Sci U S A. pubmed:26417077;  doi:10.1073/pnas.1506925112

12. The soft palate is an important site of adaptation for transmissible influenza viruses. Lakdawala SS, Jayaraman A, Halpin RA, Lamirande EW, Shih AR, Stockwell TB, Lin X, Simenauer A, Hanson CT, Vogel L, Paskel M, Minai M, Moore I, Orandle M, Das SR, Wentworth DE, Sasisekharan R, Subbarao K. Nature. pubmed:26416728;  doi:10.1038/nature15379

13. Monocyte-endothelial cell interactions in the regulation of vascular sprouting and liver regeneration in mouse. Melgar-Lesmes P, Edelman ER. J Hepatol. pubmed:26022689;  doi:10.1016/j.jhep.2015.05.011

14. Synthetic Nanoparticles for Vaccines and Immunotherapy. Irvine DJ, Hanson MC, Rakhra K, Tokatlian T. Chem Rev. pubmed:26154342;  doi:10.1021/acs.chemrev.5b00109

15. A switchable yeast display/secretion system. Van Deventer JA, Kelly RL, Rajan S, Wittrup KD, Sidhu SS. Protein Eng Des Sel. pubmed:26333274;  doi:10.1093/protein/gzv043

16. Characterizing Cellular Biophysical Responses to Stress by Relating Density, Deformability, and Size. Byun S, Hecht VC, Manalis SR. Biophys J. pubmed:26488647;  doi:10.1016/j.bpj.2015.08.038

17. Reply to Lee: Downward bias in heritability estimation is not due to simplified linkage equilibrium SNP simulation. Golan D, Rosset S, Lander ES. Proc Natl Acad Sci U S A. pubmed:26417112;  doi:10.1073/pnas.1511370112

18. A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling. Patterson HC, Gerbeth C, Thiru P, Vogtle NF, Knoll M, Shahsafaei A, Samocha KE, Huang CX, Harden MM, Song R, Chen C, Kao J, Shi J, Salmon W, Shaul YD, Stokes MP, Silva JC, Bell GW, MacArthur DG, Ruland J, Meisinger C, Lodish HF. Proc Natl Acad Sci U S A. pubmed:26438848;  doi:10.1073/pnas.1517932112

19. Mutations driving CLL and their evolution in progression and relapse. Landau DA, Tausch E, Taylor-Weiner AN, Stewart C, Reiter JG, Bahlo J, Kluth S, Bozic I, Lawrence M, Bottcher S, Carter SL, Cibulskis K, Mertens D, Sougnez CL, Rosenberg M, Hess JM, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K, Gabriel S, Lander ES, Nowak MA, Dohner H, Hallek M, Neuberg D, Getz G, Stilgenbauer S, Wu CJ. Nature. pubmed:26466571;  doi:10.1038/nature15395

20. Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. Cell. pubmed:26422227;  doi:10.1016/j.cell.2015.09.038

21. Monitoring Dynamics of DNA Methylation at Single-Cell Resolution during Development and Disease. Stelzer Y, Jaenisch R. Cold Spring Harb Symp Quant Biol. pubmed:26432525;  doi:10.1101/sqb.2015.80.027334

22. Comprehensive assessment of cancer missense mutation clustering in protein structures. Kamburov A, Lawrence MS, Polak P, Leshchiner I, Lage K, Golub TR, Lander ES, Getz G. Proc Natl Acad Sci U S A. pubmed:26392535;  doi:10.1073/pnas.1516373112

23. Disruption of Sphingolipid Biosynthesis Blocks Phagocytosis of Candida albicans. Tafesse FG, Rashidfarrokhi A, Schmidt FI, Freinkman E, Dougan S, Dougan M, Esteban A, Maruyama T, Strijbis K, Ploegh HL. PLoS Pathog. pubmed:26431038;  doi:10.1371/journal.ppat.1005188

24. IGFBP3 and T1D: Systemic Factors in Colonic Stem Cell Function and Diabetic Enteropathy. Cheng CW, Yilmaz OH. Cell Stem Cell. pubmed:26431180;  doi:10.1016/j.stem.2015.09.008

25. Identification of an oncogenic RAB protein. Wheeler DB, Zoncu R, Root DE, Sabatini DM, Sawyers CL. Science. pubmed:26338797;  doi:10.1126/science.aaa4903

26. Aneuploidy-induced cellular stresses limit autophagic degradation. Santaguida S, Vasile E, White E, Amon A. Genes Dev. pubmed:26404941;  doi:10.1101/gad.269118.115

27. Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma. Mazur PK, Herner A, Mello SS, Wirth M, Hausmann S, Sanchez-Rivera FJ, Lofgren SM, Kuschma T, Hahn SA, Vangala D, Trajkovic-Arsic M, Gupta A, Heid I, Noel PB, Braren R, Erkan M, Kleeff J, Sipos B, Sayles LC, Heikenwalder M, Hessmann E, Ellenrieder V, Esposito I, Jacks T, Bradner JE, Khatri P, Sweet-Cordero EA, Attardi LD, Schmid RM, Schneider G, Sage J, Siveke JT. Nat Med. pubmed:26390243;  doi:10.1038/nm.3952

28. The multifaceted functions of sirtuins in cancer. Chalkiadaki A, Guarente L. Nat Rev Cancer. pubmed:26383140;  doi:10.1038/nrc3985

29. Regulated Formation of an Amyloid-like Translational Repressor Governs Gametogenesis. Berchowitz LE, Kabachinski G, Walker MR, Carlile TM, Gilbert WV, Schwartz TU, Amon A. Cell. pubmed:26411291;  doi:10.1016/j.cell.2015.08.060

30. Sensitivity-Enhanced NMR Reveals Alterations in Protein Structure by Cellular Milieus. Frederick KK, Michaelis VK, Corzilius B, Ong TC, Jacavone AC, Griffin RG, Lindquist S. Cell. pubmed:26456111;  doi:10.1016/j.cell.2015.09.024

31. A quantitative system for studying metastasis using transparent zebrafish. Heilmann S, Ratnakumar K, Langdon E, Kansler E, Kim I, Campbell NR, Perry E, McMahon A, Kaufman C, van Rooijen E, Lee W, Iacobuzio-Donahue C, Hynes R, Zon L, Xavier J, White RM. Cancer Res. pubmed:26282170;  doi:10.1158/0008-5472.CAN-14-3319

32. Solving 21st Century Problems in Biological Inorganic Chemistry Using Synthetic Models. Karlin KD, Lippard SJ, Valentine JS, Burrows CJ. Acc Chem Res. pubmed:26481328;  doi:10.1021/acs.accounts.5b00447