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: March 2016

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1. Quantitative phosphoproteomics reveals Wee1 kinase as a therapeutic target in a model of proneural glioblastoma. Lescarbeau RS, Lei L, Bakken KK, Sims PA, Sarkaria JN, Canoll P, White FM. Mol Cancer Ther. pubmed:27009214;  doi:10.1158/1535-7163.MCT-15-0692

2. Isolation of potent neutralizing antibodies from a survivor of the 2014 Ebola virus outbreak. Bornholdt ZA, Turner HL, Murin CD, Li W, Sok D, Souders CA, Piper AE, Goff A, Shamblin JD, Wollen SE, Sprague TR, Fusco ML, Pommert KB, Cavacini LA, Smith HL, Klempner M, Reimann KA, Krauland E, Gerngross TU, Wittrup DK, Saphire EO, Burton DR, Glass PJ, Ward AB, Walker LM. Science. pubmed:26912366;  doi:10.1126/science.aad5788

3. Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota. Mimee M, Tucker AC, Voigt CA, Lu TK. Cell Syst. pubmed:27135367;  doi:10.1016/j.cels.2016.03.007

4. Beyond antigens and adjuvants: formulating future vaccines. Moyer TJ, Zmolek AC, Irvine DJ. J Clin Invest. pubmed:26928033;  doi:10.1172/JCI81083

5. Encoded Hydrogel Microparticles for Sensitive and Multiplex microRNA Detection Directly from Raw Cell Lysates. Lee H, Shapiro SJ, Chapin SC, Doyle PS. Anal Chem. pubmed:26863201;  doi:10.1021/acs.analchem.5b03902

6. Generation of fluorogen-activating designed ankyrin repeat proteins (FADAs) as versatile sensor tools. Schutz M, Batyuk A, Klenk C, Kummer L, de Picciotto S, Gulbakan B, Wu Y, Newby GA, Zosel F, Schoppe J, Sedlak E, Mittl PR, Zenobi R, Wittrup KD, Pluckthun A. J Mol Biol. pubmed:26812208;  doi:10.1016/j.jmb.2016.01.017

7. Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution. Zhao B, Sedlak JC, Srinivas R, Creixell P, Pritchard JR, Tidor B, Lauffenburger DA, Hemann MT. Cell. pubmed:26924578;  doi:10.1016/j.cell.2016.01.045

8. Characterization of the expression of the pro-metastatic Mena isoform during breast tumor progression. Oudin MJ, Hughes SK, Rohani N, Moufarrej MN, Jones JG, Condeelis JS, Lauffenburger DA, Gertler FB. Clin Exp Metastasis. pubmed:26680363;  doi:10.1007/s10585-015-9775-5

9. Early signaling dynamics of the epidermal growth factor receptor. Reddy RJ, Gajadhar AS, Swenson EJ, Rothenberg DA, Curran TG, White FM. Proc Natl Acad Sci U S A. pubmed:26929352;  doi:10.1073/pnas.1521288113

10. Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. Logan DJ, Shan J, Bhatia SN, Carpenter AE. Methods. pubmed:26687239;  doi:10.1016/j.ymeth.2015.12.002

11. 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

12. A Multi-RNAi Microsponge Platform for Simultaneous Controlled Delivery of Multiple Small Interfering RNAs. Roh YH, Deng JZ, Dreaden EC, Park JH, Yun DS, Shopsowitz KE, Hammond PT. Angew Chem Int Ed Engl. pubmed:26695874;  doi:10.1002/anie.201508978

13. Self-Assembled Wound Dressings Silence MMP-9 and Improve Diabetic Wound Healing In Vivo. Castleberry SA, Almquist BD, Li W, Reis T, Chow J, Mayner S, Hammond PT. Adv Mater. pubmed:26695434;  doi:10.1002/adma.201503565

14. Splenic progenitors aid in maintaining high neutrophil numbers at sites of sterile chronic inflammation. Jhunjhunwala S, Alvarez D, Aresta-DaSilva S, Tang K, Tang BC, Greiner DL, Newburger PE, von Andrian UH, Langer R, Anderson DG. J Leukoc Biol. pubmed:26965635;  doi:10.1189/jlb.1HI0615-248RR

15. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y, Wu Q, Park A, Yang J, Suresh S, Bizhanova A, Gupta A, Bolukbasi MF, Walsh S, Bogorad RL, Gao G, Weng Z, Dong Y, Koteliansky V, Wolfe SA, Langer R, Xue W, Anderson DG. Nat Biotechnol. pubmed:26829318;  doi:10.1038/nbt.3471

16. Long-term glycemic control using polymer-encapsulated human stem cell-derived beta cells in immune-competent mice. Vegas AJ, Veiseh O, Gurtler M, Millman JR, Pagliuca FW, Bader AR, Doloff JC, Li J, Chen M, Olejnik K, Tam HH, Jhunjhunwala S, Langan E, Aresta-Dasilva S, Gandham S, McGarrigle JJ, Bochenek MA, Hollister-Lock J, Oberholzer J, Greiner DL, Weir GC, Melton DA, Langer R, Anderson DG. Nat Med. pubmed:26808346;  doi:10.1038/nm.4030

17. Combinatorial hydrogel library enables identification of materials that mitigate the foreign body response in primates. Vegas AJ, Veiseh O, Doloff JC, Ma M, Tam HH, Bratlie K, Li J, Bader AR, Langan E, Olejnik K, Fenton P, Kang JW, Hollister-Locke J, Bochenek MA, Chiu A, Siebert S, Tang K, Jhunjhunwala S, Aresta-Dasilva S, Dholakia N, Thakrar R, Vietti T, Chen M, Cohen J, Siniakowicz K, Qi M, McGarrigle J, Lyle S, Harlan DM, Greiner DL, Oberholzer J, Weir GC, Langer R, Anderson DG. Nat Biotechnol. pubmed:26807527;  doi:10.1038/nbt.3462

18. Amino Acids Rather than Glucose Account for the Majority of Cell Mass in Proliferating Mammalian Cells. Hosios AM, Hecht VC, Danai LV, Johnson MO, Rathmell JC, Steinhauser ML, Manalis SR, Vander Heiden MG. Dev Cell. pubmed:26954548;  doi:10.1016/j.devcel.2016.02.012

19. Nanoemulsions: formation, properties and applications. Gupta A, Eral HB, Hatton TA, Doyle PS. Soft Matter. pubmed:26924445;  doi:10.1039/c5sm02958a

20. Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. Wong AS, Choi GC, Cui CH, Pregernig G, Milani P, Adam M, Perli SD, Kazer SW, Gaillard A, Hermann M, Shalek AK, Fraenkel E, Lu TK. Proc Natl Acad Sci U S A. pubmed:26864203;  doi:10.1073/pnas.1517883113

21. Voices of biotech. Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T. Nat Biotechnol. pubmed:26963549;  doi:10.1038/nbt.3502

22. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. Solomon KV, Haitjema CH, Henske JK, Gilmore SP, Borges-Rivera D, Lipzen A, Brewer HM, Purvine SO, Wright AT, Theodorou MK, Grigoriev IV, Regev A, Thompson DA, O'Malley MA. Science. pubmed:26912365;  doi:10.1126/science.aad1431

23. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA. Science. pubmed:26940867;  doi:10.1126/science.aad9024

24. Crystal structure of a substrate-engaged SecY protein-translocation channel. Li L, Park E, Ling J, Ingram J, Ploegh H, Rapoport TA. Nature. pubmed:26950603;  doi:10.1038/nature17163

25. Twenty-eight genetic loci associated with ST-T wave amplitudes of the electrocardiogram. Verweij N, Mateo Leach I, Isaacs A, Arking DE, Bis JC, Pers TH, van den Berg ME, Lyytikainen LP, Barnett P, Wang X, Soliman EZ, van Duijn CM, Kahonen M, van Veldhuisen DJ, Kors JA, Raitakari OT, Silva CT, Lehtimaki T, Hillege HL, Hirschhorn JN, Boyer LA, van Gilst WH, Alonso A, Sotoodehnia N, Eijgelsheim M, de Boer RA, de Bakker PI, Franke L, van der Harst P. Hum Mol Genet. pubmed:26962151;  doi:10.1093/hmg/ddw058

26. B Cells Promote Pancreatic Tumorigenesis. Roghanian A, Fraser C, Kleyman M, Chen J. Cancer Discov. pubmed:26951836;  doi:10.1158/2159-8290.CD-16-0100

27. Models of human core transcriptional regulatory circuitries. Saint-Andre V, Federation AJ, Lin CY, Abraham BJ, Reddy J, Lee TI, Bradner JE, Young RA. Genome Res. pubmed:26843070;  doi:10.1101/gr.197590.115

28. Distal Alternative Last Exons Localize mRNAs to Neural Projections. Taliaferro JM, Vidaki M, Oliveira R, Olson S, Zhan L, Saxena T, Wang ET, Graveley BR, Gertler FB, Swanson MS, Burge CB. Mol Cell. pubmed:26907613;  doi:10.1016/j.molcel.2016.01.020

29. Large-Scale Single Guide RNA Library Construction and Use for CRISPR-Cas9-Based Genetic Screens. Wang T, Lander ES, Sabatini DM. Cold Spring Harb Protoc. pubmed:26933254;  doi:10.1101/pdb.top086892

30. Viral Packaging and Cell Culture for CRISPR-Based Screens. Wang T, Lander ES, Sabatini DM. Cold Spring Harb Protoc. pubmed:26933250;  doi:10.1101/pdb.prot090811

31. Single Guide RNA Library Design and Construction. Wang T, Lander ES, Sabatini DM. Cold Spring Harb Protoc. pubmed:26933249;  doi:10.1101/pdb.prot090803

32. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Nat Methods. pubmed:26780094;  doi:10.1038/nmeth.3732

33. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Beyaz S, Mana MD, Roper J, Kedrin D, Saadatpour A, Hong SJ, Bauer-Rowe KE, Xifaras ME, Akkad A, Arias E, Pinello L, Katz Y, Shinagare S, Abu-Remaileh M, Mihaylova MM, Lamming DW, Dogum R, Guo G, Bell GW, Selig M, Nielsen GP, Gupta N, Ferrone CR, Deshpande V, Yuan GC, Orkin SH, Sabatini DM, Yilmaz OH. Nature. pubmed:26935695;  doi:10.1038/nature17173

34. Assessment of megabase-scale somatic copy number variation using single cell sequencing. Knouse KA, Wu J, Amon A. Genome Res. pubmed:26772196;  doi:10.1101/gr.198937.115

35. STAR syndrome-associated CDK10/Cyclin M regulates actin network architecture and ciliogenesis. Guen VJ, Gamble C, Perez DE, Bourassa S, Zappel H, Gartner J, Lees JA, Colas P. Cell Cycle. pubmed:27104747;  doi:10.1080/15384101.2016.1147632

36. The CASTOR Proteins Are Arginine Sensors for the mTORC1 Pathway. Chantranupong L, Scaria SM, Saxton RA, Gygi MP, Shen K, Wyant GA, Wang T, Harper JW, Gygi SP, Sabatini DM. Cell. pubmed:26972053;  doi:10.1016/j.cell.2016.02.035

37. Environment Impacts the Metabolic Dependencies of Ras-Driven Non-Small Cell Lung Cancer. Davidson SM, Papagiannakopoulos T, Olenchock BA, Heyman JE, Keibler MA, Luengo A, Bauer MR, Jha AK, O'Brien JP, Pierce KA, Gui DY, Sullivan LB, Wasylenko TM, Subbaraj L, Chin CR, Stephanopolous G, Mott BT, Jacks T, Clish CB, Vander Heiden MG. Cell Metab. pubmed:26853747;  doi:10.1016/j.cmet.2016.01.007

38. Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability. Pattabiraman DR, Bierie B, Kober KI, Thiru P, Krall JA, Zill C, Reinhardt F, Tam WL, Weinberg RA. Science. pubmed:26941323;  doi:10.1126/science.aad3680

39. The Next Generation of Platinum Drugs: Targeted Pt(II) Agents, Nanoparticle Delivery, and Pt(IV) Prodrugs. Johnstone TC, Suntharalingam K, Lippard SJ. Chem Rev. pubmed:26865551;  doi:10.1021/acs.chemrev.5b00597

40. Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Hung V, Udeshi ND, Lam SS, Loh KH, Cox KJ, Pedram K, Carr SA, Ting AY. Nat Protoc. pubmed:26866790;  doi:10.1038/nprot.2016.018

41. Progressive Saturation Improves the Encapsulation of Functional Proteins in Nanoscale Polymer Vesicles. Yewle J, Wattamwar P, Tao Z, Ostertag EM, Ghoroghchian PP. Pharm Res. pubmed:26508477;  doi:10.1007/s11095-015-1809-9