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: May 2019

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1. Single Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations. Kalluri AS, Vellarikkal SK, Edelman ER, Nguyen L, Subramanian A, Ellinor PT, Regev A, Kathiresan S, Gupta RM. Circulation. pubmed:31146585;  doi:10.1161/CIRCULATIONAHA.118.038362

2. Functional screens identify coordinators of RNA molecule birth, life, and death as targetable cancer vulnerabilities. Braun CJ, Hemann MT. Curr Opin Genet Dev. pubmed:31121413;  doi:10.1016/j.gde.2019.04.003

3. Toward a comprehensive view of cancer immune responsiveness: a synopsis from the SITC workshop. Bedognetti D, Ceccarelli M, Galluzzi L, Lu R, Palucka K, Samayoa J, Spranger S, Warren S, Wong KK, Ziv E, Chowell D, Coussens LM, De Carvalho DD, DeNardo DG, Galon J, Kaufman HL, Kirchhoff T, Lotze MT, Luke JJ, Minn AJ, Politi K, Shultz LD, Simon R, Thorsson V, Weidhaas JB, Ascierto ML, Ascierto PA, Barnes JM, Barsan V, Bommareddy PK, Bot A, Church SE, Ciliberto G, De Maria A, Draganov D, Ho WS, McGee HM, Monette A, Murphy JF, Nistico P, Park W, Patel M, Quigley M, Radvanyi L, Raftopoulos H, Rudqvist NP, Snyder A, Sweis RF, Valpione S, Butterfield LH, Disis ML, Fox BA, Cesano A, Marincola FM. J Immunother Cancer. pubmed:31113486;  doi:10.1186/s40425-019-0602-4

4. Putting the K(+) in K(+)aloric Restriction. Lien EC, Lau AN, Vander Heiden MG. Immunity. pubmed:31117009;  doi:10.1016/j.immuni.2019.04.016

5. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs. van de Kooij B, Creixell P, van Vlimmeren A, Joughin BA, Miller CJ, Haider N, Simpson CD, Linding R, Stambolic V, Turk BE, Yaffe MB. Elife. pubmed:31124786;  doi:10.7554/eLife.44635

6. IKKbeta slows Huntington's disease progression in R6/1 mice. Ochaba J, Fote G, Kachemov M, Thein S, Yeung SY, Lau AL, Hernandez S, Lim RG, Casale M, Neel MJ, Monuki ES, Reidling J, Housman DE, Thompson LM, Steffan JS. Proc Natl Acad Sci U S A. pubmed:31088970;  doi:10.1073/pnas.1814246116

7. A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. Yang JH, Wright SN, Hamblin M, McCloskey D, Alcantar MA, Schrubbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC, Collins JJ. Cell. pubmed:31080069;  doi:10.1016/j.cell.2019.04.016

8. Noninvasive imaging of tumor progression, metastasis, and fibrosis using a nanobody targeting the extracellular matrix. Jailkhani N, Ingram JR, Rashidian M, Rickelt S, Tian C, Mak H, Jiang Z, Ploegh HL, Hynes RO. Proc Natl Acad Sci U S A. pubmed:31068469;  doi:10.1073/pnas.1817442116

9. Atlas Drugged. Chen JK, Yaffe MB. Cell. pubmed:31051104;  doi:10.1016/j.cell.2019.04.023

10. EMT and Cancer: More Than Meets the Eye. Derynck R, Weinberg RA. Dev Cell. pubmed:31063750;  doi:10.1016/j.devcel.2019.04.026

11. Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program. Kikani CK, Wu X, Fogarty S, Kang SAW, Dephoure N, Gygi SP, Sabatini DM, Rutter J. Proc Natl Acad Sci U S A. pubmed:31072927;  doi:10.1073/pnas.1804013116

12. Defining the core essential genome of Pseudomonas aeruginosa. Poulsen BE, Yang R, Clatworthy AE, White T, Osmulski SJ, Li L, Penaranda C, Lander ES, Shoresh N, Hung DT. Proc Natl Acad Sci U S A. pubmed:31036669;  doi:10.1073/pnas.1900570116

13. Counting loops in sidechain-crosslinked polymers from elastic solids to single-chain nanoparticles. Wang J, Wang R, Gu Y, Sourakov A, Olsen BD, Johnson JA. Chem Sci. pubmed:31191890;  doi:10.1039/c9sc01297d

14. Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection. Ndhlovu ZM, Kazer SW, Nkosi T, Ogunshola F, Muema DM, Anmole G, Swann SA, Moodley A, Dong K, Reddy T, Brockman MA, Shalek AK, Ndung'u T, Walker BD. Sci Transl Med. pubmed:31118290;  doi:10.1126/scitranslmed.aau0528

15. Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration. Pepe-Mooney BJ, Dill MT, Alemany A, Ordovas-Montanes J, Matsushita Y, Rao A, Sen A, Miyazaki M, Anakk S, Dawson PA, Ono N, Shalek AK, van Oudenaarden A, Camargo FD. Cell Stem Cell. pubmed:31080134;  doi:10.1016/j.stem.2019.04.004

16. CRISPR/Cas-based devices for mammalian synthetic biology. Kim T, Lu TK. Curr Opin Chem Biol. pubmed:31136835;  doi:10.1016/j.cbpa.2019.04.015

17. mRNA Delivery for Therapeutic Anti-HER2 Antibody Expression In Vivo. Rybakova Y, Kowalski PS, Huang Y, Gonzalez JT, Heartlein MW, DeRosa F, Delcassian D, Anderson DG. Mol Ther. pubmed:31160223;  doi:10.1016/j.ymthe.2019.05.012

18. Immunization expands B cells specific to HIV-1 V3 glycan in mice and macaques. Escolano A, Gristick HB, Abernathy ME, Merkenschlager J, Gautam R, Oliveira TY, Pai J, West APJr, Barnes CO, Cohen AA, Wang H, Golijanin J, Yost D, Keeffe JR, Wang Z, Zhao P, Yao KH, Bauer J, Nogueira L, Gao H, Voll AV, Montefiori DC, Seaman MS, Gazumyan A, Silva M, McGuire AT, Stamatatos L, Irvine DJ, Wells L, Martin MA, Bjorkman PJ, Nussenzweig MC. Nature. pubmed:31142836;  doi:10.1038/s41586-019-1250-z

19. Strategies, design, and chemistry in siRNA delivery systems. Dong Y, Siegwart DJ, Anderson DG. Adv Drug Deliv Rev. pubmed:31102606;  doi:10.1016/j.addr.2019.05.004

20. M13 Virus-Based Framework for High Fluorescence Enhancement. Huang S, Qi J, deQuilettes DW, Huang M, Lin CW, Bardhan NM, Dang X, Bulovic V, Belcher AM. Small. pubmed:31131998;  doi:10.1002/smll.201901233

21. Functional remodeling of an electrospun polydimethylsiloxane-based polyether urethane external vein graft support device in an ovine model. El-Kurdi M, Soletti L, McGrath J, Linhares S, Rousselle S, Greisler H, Edelman E, Schoen FJ. J Biomed Mater Res A. pubmed:31094084;  doi:10.1002/jbm.a.36724

22. Challenges in IBD Research: Novel Technologies. Dhyani M, Joshi N, Bemelman WA, Gee MS, Yajnik V, D'Hoore A, Traverso G, Donowitz M, Mostoslavsky G, Lu TK, Lineberry N, Niessen HG, Peer D, Braun J, Delaney CP, Dubinsky MC, Guillory AN, Pereira M, Shtraizent N, Honig G, Polk DB, Hurtado-Lorenzo A, Karp JM, Michelassi F. Inflamm Bowel Dis. pubmed:31095703;  doi:10.1093/ibd/izz077

23. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S. Cell. pubmed:31080066;  doi:10.1016/j.cell.2019.04.012

24. Architecting Discovery: A Model for How Engineers Can Help Invent Tools for Neuroscience. Boyden ES, Marblestone AH. Neuron. pubmed:31071286;  doi:10.1016/j.neuron.2019.03.023

25. In vitro evolution of enhanced RNA replicons for immunotherapy. Li Y, Teague B, Zhang Y, Su Z, Porter E, Dobosh B, Wagner T, Irvine DJ, Weiss R. Sci Rep. pubmed:31061426;  doi:10.1038/s41598-019-43422-0

26. Short Cationic Peptide Derived from Archaea with Dual Antibacterial Properties and Anti-Infective Potential. Candido ES, Cardoso MH, Chan LY, Torres MDT, Oshiro KGN, Porto WF, Ribeiro SM, Haney EF, Hancock REW, Lu TK, de la Fuente-Nunez C, Craik DJ, Franco OL. ACS Infect Dis. pubmed:31016969;  doi:10.1021/acsinfecdis.9b00073

27. Broad-Spectrum Proteome Editing with an Engineered Bacterial Ubiquitin Ligase Mimic. Ludwicki MB, Li J, Stephens EA, Roberts RW, Koide S, Hammond PT, DeLisa MP. ACS Cent Sci. pubmed:31139721;  doi:10.1021/acscentsci.9b00127

28. The Future of Layer-by-Layer Assembly: A Tribute to ACS Nano Associate Editor Helmuth Mohwald. Zhao S, Caruso F, Dahne L, Decher G, De Geest BG, Fan J, Feliu N, Gogotsi Y, Hammond PT, Hersam MC, Khademhosseini A, Kotov N, Leporatti S, Li Y, Lisdat F, Liz-Marzan LM, Moya S, Mulvaney P, Rogach AL, Roy S, Shchukin DG, Skirtach AG, Stevens MM, Sukhorukov GB, Weiss PS, Yue Z, Zhu D, Parak WJ. ACS Nano. pubmed:31124656;  doi:10.1021/acsnano.9b03326

29. Mammalian cell growth dynamics in mitosis. Miettinen TP, Kang JH, Yang LF, Manalis SR. Elife. pubmed:31063131;  doi:10.7554/eLife.44700

30. Reprogramming the microenvironment with tumor-selective angiotensin blockers enhances cancer immunotherapy. Chauhan VP, Chen IX, Tong R, Ng MR, Martin JD, Naxerova K, Wu MW, Huang P, Boucher Y, Kohane DS, Langer R, Jain RK. Proc Natl Acad Sci U S A. pubmed:31040208;  doi:10.1073/pnas.1819889116

31. A Combined Screening and In Silico Strategy for the Rapid Design of Integrated Downstream Processes for Process and Product-Related Impurity Removal. Vecchiarello N, Timmick SM, Goodwine C, Crowell LE, Love KR, Love JC, Cramer SM. Biotechnol Bioeng. pubmed:31081177;  doi:10.1002/bit.27018

32. Balance of mechanical forces drives endothelial gap formation and may facilitate cancer and immune-cell extravasation. Escribano J, Chen MB, Moeendarbary E, Cao X, Shenoy V, Garcia-Aznar JM, Kamm RD, Spill F. PLoS Comput Biol. pubmed:31048903;  doi:10.1371/journal.pcbi.1006395

33. Chondrogenic, hypertrophic, and osteochondral differentiation of human mesenchymal stem cells on three-dimensionally woven scaffolds. Larson BL, Yu SN, Park H, Estes BT, Moutos FT, Bloomquist CJ, Wu PB, Welter JF, Langer R, Guilak F, Freed LE. J Tissue Eng Regen Med. pubmed:31115161;  doi:10.1002/term.2899