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: January 2016

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1. New England harbor seal H3N8 influenza virus retains avian-like receptor specificity. Hussein IT, Krammer F, Ma E, Estrin M, Viswanathan K, Stebbins NW, Quinlan DS, Sasisekharan R, Runstadler J. Sci Rep. pubmed:26888262;  doi:10.1038/srep21428

2. Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6. Guye P, Ebrahimkhani MR, Kipniss N, Velazquez JJ, Schoenfeld E, Kiani S, Griffith LG, Weiss R. Nat Commun. pubmed:26732624;  doi:10.1038/ncomms10243

3. The era of synthetic biology and genome engineering: Where no man has gone before. Lu TK, Chandrasegaran S, Hodak H. J Mol Biol. pubmed:26827726;  doi:10.1016/j.jmb.2016.01.025

4. 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

5. Tumor cell-driven extracellular matrix remodeling enables haptotaxis during metastatic progression. Oudin MJ, Jonas O, Kosciuk T, Broye LC, Guido BC, Wyckoff J, Riquelme D, Lamar JM, Asokan SB, Whittaker C, Ma D, Langer R, Cima MJ, Wisinski KB, Hynes RO, Lauffenburger DA, Keely PJ, Bear JE, Gertler FB. Cancer Discov. pubmed:26811325;  doi:10.1158/2159-8290.CD-15-1183

6. Periodic-shRNA molecules are capable of gene silencing, cytotoxicity and innate immune activation in cancer cells. Shopsowitz KE, Wu C, Liu G, Dreaden EC, Hammond PT. Nucleic Acids Res. pubmed:26704983;  doi:10.1093/nar/gkv1488

7. Coronary Artery Disease and Diabetes Mellitus. Aronson D, Edelman ER. Heart Fail Clin. pubmed:26567979;  doi:10.1016/j.hfc.2015.08.010

8. 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

9. Distinct genital tract HIV-specific antibody profiles associated with tenofovir gel. Archary D, Seaton KE, Passmore JS, Werner L, Deal A, Dunphy LJ, Arnold KB, Yates NL, Lauffenburger DA, Bergin P, Liebenberg LJ, Samsunder N, Mureithi MW, Altfeld M, Garrett N, Abdool Karim Q, Abdool Karim S, Morris L, Tomaras GD. Mucosal Immunol. pubmed:26813340;  doi:10.1038/mi.2015.145

10. Time series modeling of live-cell shape dynamics for image-based phenotypic profiling. Gordonov S, Hwang MK, Wells A, Gertler FB, Lauffenburger DA, Bathe M. Integr Biol (Camb). pubmed:26658688;  doi:10.1039/c5ib00283d

11. Engineering nanolayered particles for modular drug delivery. Correa S, Dreaden EC, Gu L, Hammond PT. J Control Release. pubmed:26809005;  doi:10.1016/j.jconrel.2016.01.040

12. Measurement of Phosphorylated Peptides with Absolute Quantification. Reddy RJ, Curran TG, Zhang Y, White FM. Methods Mol Biol. pubmed:26867751;  doi:10.1007/978-1-4939-3524-6_17

13. Identification of Direct Kinase Substrates Using Analogue-Sensitive Alleles. Rothenberg DA, Gordon EA, White FM, Lourido S. Methods Mol Biol. pubmed:26584919;  doi:10.1007/978-1-4939-3049-4_5

14. 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

15. The Aryl Hydrocarbon Receptor is a Critical Regulator of Tissue Factor Stability and an Antithrombotic Target in Uremia. Shivanna S, Kolandaivelu K, Shashar M, Belghasim M, Al-Rabadi L, Balcells M, Zhang A, Weinberg J, Francis J, Pollastri MP, Edelman ER, Sherr DH, Chitalia VC. J Am Soc Nephrol. pubmed:26019318;  doi:10.1681/ASN.2014121241

16. Three-dimensional multilayered fibrous constructs for wound healing applications. Reis TC, Castleberry S, Rego AM, Aguiar-Ricardo A, Hammond PT. Biomater Sci. pubmed:26584183;  doi:10.1039/c5bm00211g

17. Live-cell protein labelling with nanometre precision by cell squeezing. Kollmannsperger A, Sharei A, Raulf A, Heilemann M, Langer R, Jensen KF, Wieneke R, Tampe R. Nat Commun. pubmed:26822409;  doi:10.1038/ncomms10372

18. 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

19. 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

20. Selective binding of C-6 OH sulfated hyaluronic acid to the angiogenic isoform of VEGF. Lim DK, Wylie RG, Langer R, Kohane DS. Biomaterials. pubmed:26588795;  doi:10.1016/j.biomaterials.2015.10.074

21. Engineering Stem Cell Organoids. Yin X, Mead BE, Safaee H, Langer R, Karp JM, Levy O. Cell Stem Cell. pubmed:26748754;  doi:10.1016/j.stem.2015.12.005

22. Emerging Frontiers in Drug Delivery. Tibbitt MW, Dahlman JE, Langer R. J Am Chem Soc. pubmed:26741786;  doi:10.1021/jacs.5b09974

23. High Throughput Layer-by-Layer Films for Extracting Film Forming Parameters and Modulating Film Interactions with Cells. Jaklenec A, Anselmo AC, Hong J, Vegas A, Kozminsky M, Langer R, Hammond PT, Anderson DG. ACS Appl Mater Interfaces. pubmed:26713554;  doi:10.1021/acsami.5b11081

24. Advances in tissue engineering. Langer R, Vacanti J. J Pediatr Surg. pubmed:26711689;  doi:10.1016/j.jpedsurg.2015.10.022

25. Injectable Self-Healing Glucose-Responsive Hydrogels with pH-Regulated Mechanical Properties. Yesilyurt V, Webber MJ, Appel EA, Godwin C, Langer R, Anderson DG. Adv Mater. pubmed:26540021;  doi:10.1002/adma.201502902

26. A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages. Kimmerling RJ, Lee Szeto G, Li JW, Genshaft AS, Kazer SW, Payer KR, de Riba Borrajo J, Blainey PC, Irvine DJ, Shalek AK, Manalis SR. Nat Commun. pubmed:26732280;  doi:10.1038/ncomms10220

27. Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs. Chen J, Shishkin AA, Zhu X, Kadri S, Maza I, Guttman M, Hanna JH, Regev A, Garber M. Genome Biol. pubmed:26838501;  doi:10.1186/s13059-016-0880-9

28. Parsing the Interferon Transcriptional Network and Its Disease Associations. Mostafavi S, Yoshida H, Moodley D, LeBoite H, Rothamel K, Raj T, Ye CJ, Chevrier N, Zhang SY, Feng T, Lee M, Casanova JL, Clark JD, Hegen M, Telliez JB, Hacohen N, De Jager PL, Regev A, Mathis D, Benoist C. Cell. pubmed:26824662;  doi:10.1016/j.cell.2015.12.032

29. 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

30. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Kaufman CK, Mosimann C, Fan ZP, Yang S, Thomas AJ, Ablain J, Tan JL, Fogley RD, van Rooijen E, Hagedorn EJ, Ciarlo C, White RM, Matos DA, Puller AC, Santoriello C, Liao EC, Young RA, Zon LI. Science. pubmed:26823433;  doi:10.1126/science.aad2197

31. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). 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Avantaggiati ML, Avrahami L, Awale S, Azad N, Bachetti T, Backer JM, Bae DH, Bae JS, Bae ON, Bae SH, Baehrecke EH, Baek SH, Baghdiguian S, Bagniewska-Zadworna A, Bai H, Bai J, Bai XY, Bailly Y, Balaji KN, Balduini W, Ballabio A, Balzan R, Banerjee R, Banhegyi G, Bao H, Barbeau B, Barrachina MD, Barreiro E, Bartel B, Bartolome A, Bassham DC, Bassi MT, Bast RCJr, Basu A, Batista MT, Batoko H, Battino M, Bauckman K, Baumgarner BL, Bayer KU, Beale R, Beaulieu JF, Beck GRJr, Becker C, Beckham JD, Bedard PA, Bednarski PJ, Begley TJ, Behl C, Behrends C, Behrens GM, Behrns KE, Bejarano E, Belaid A, Belleudi F, Benard G, Berchem G, Bergamaschi D, Bergami M, Berkhout B, Berliocchi L, Bernard A, Bernard M, Bernassola F, Bertolotti A, Bess AS, Besteiro S, Bettuzzi S, Bhalla S, Bhattacharyya S, Bhutia SK, Biagosch C, Bianchi MW, Biard-Piechaczyk M, Billes V, Bincoletto C, Bingol B, Bird SW, Bitoun M, Bjedov I, Blackstone C, Blanc L, Blanco GA, Blomhoff HK, Boada-Romero E, Bockler S, Boes M, 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Castro-Obregon S, Cavallini G, Ceccherini I, Cecconi F, Cederbaum AI, Cena V, Cenci S, Cerella C, Cervia D, Cetrullo S, Chaachouay H, Chae HJ, Chagin AS, Chai CY, Chakrabarti G, Chamilos G, Chan EY, Chan MT, Chandra D, Chandra P, Chang CP, Chang RC, Chang TY, Chatham JC, Chatterjee S, Chauhan S, Che Y, Cheetham ME, Cheluvappa R, Chen CJ, Chen G, Chen GC, Chen G, Chen H, Chen JW, Chen JK, Chen M, Chen M, Chen P, Chen Q, Chen Q, Chen SD, Chen S, Chen SS, Chen W, Chen WJ, Chen WQ, Chen W, Chen X, Chen YH, Chen YG, Chen Y, Chen Y, Chen Y, Chen YJ, Chen YQ, Chen Y, Chen Z, Chen Z, Cheng A, Cheng CH, Cheng H, Cheong H, Cherry S, Chesney J, Cheung CH, Chevet E, Chi HC, Chi SG, Chiacchiera F, Chiang HL, Chiarelli R, Chiariello M, Chieppa M, Chin LS, Chiong M, Chiu GN, Cho DH, Cho SG, Cho WC, Cho YY, Cho YS, Choi AM, Choi EJ, Choi EK, Choi J, Choi ME, Choi SI, Chou TF, Chouaib S, Choubey D, Choubey V, Chow KC, Chowdhury K, Chu CT, Chuang TH, Chun T, Chung H, Chung T, Chung YL, Chwae YJ, Cianfanelli V, Ciarcia R, Ciechomska IA, Ciriolo MR, Cirone M, Claerhout S, Clague MJ, Claria J, Clarke PG, Clarke R, Clementi E, Cleyrat C, Cnop M, Coccia EM, Cocco T, Codogno P, Coers J, Cohen EE, Colecchia D, Coletto L, Coll NS, Colucci-Guyon E, Comincini S, Condello M, Cook KL, Coombs GH, Cooper CD, Cooper JM, Coppens I, Corasaniti MT, Corazzari M, Corbalan R, Corcelle-Termeau E, Cordero MD, Corral-Ramos C, Corti O, Cossarizza A, Costelli P, Costes S, Cotman SL, Coto-Montes A, Cottet S, Couve E, Covey LR, Cowart LA, Cox JS, Coxon FP, Coyne CB, Cragg MS, Craven RJ, Crepaldi T, Crespo JL, Criollo A, Crippa V, Cruz MT, Cuervo AM, Cuezva JM, Cui T, Cutillas PR, Czaja MJ, Czyzyk-Krzeska MF, Dagda RK, Dahmen U, Dai C, Dai W, Dai Y, Dalby KN, Dalla Valle L, Dalmasso G, D'Amelio M, Damme M, Darfeuille-Michaud A, Dargemont C, Darley-Usmar VM, Dasarathy S, Dasgupta B, Dash S, Dass CR, Davey HM, Davids LM, Davila D, Davis RJ, Dawson TM, Dawson VL, Daza P, de Belleroche J, de Figueiredo P, de 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