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 2019

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1. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Schiebinger G, Shu J, Tabaka M, Cleary B, Subramanian V, Solomon A, Gould J, Liu S, Lin S, Berube P, Lee L, Chen J, Brumbaugh J, Rigollet P, Hochedlinger K, Jaenisch R, Regev A, Lander ES. Cell. pubmed:30712874;  doi:10.1016/j.cell.2019.01.006

2. Acidification of tumor at stromal boundaries drives transcriptome alterations associated with aggressive phenotypes. Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. Cancer Res. pubmed:30755444;  doi:10.1158/0008-5472.CAN-18-1604

3. Squalene accumulation in cholesterol auxotrophic lymphomas prevents oxidative cell death. Garcia-Bermudez J, Baudrier L, Bayraktar EC, Shen Y, La K, Guarecuco R, Yucel B, Fiore D, Tavora B, Freinkman E, Chan SH, Lewis C, Min W, Inghirami G, Sabatini DM, Birsoy K. Nature. pubmed:30760928;  doi:10.1038/s41586-019-0945-5

4. ROS and Oxidative Stress Are Elevated in Mitosis during Asynchronous Cell Cycle Progression and Are Exacerbated by Mitotic Arrest. Patterson JC, Joughin BA, van de Kooij B, Lim DC, Lauffenburger DA, Yaffe MB. Cell Syst. pubmed:30797774;  doi:10.1016/j.cels.2019.01.005

5. Rate of Progression through a Continuum of Transit-Amplifying Progenitor Cell States Regulates Blood Cell Production. Li H, Natarajan A, Ezike J, Barrasa MI, Le Y, Feder ZA, Yang H, Ma C, Markoulaki S, Lodish HF. Dev Cell. pubmed:30827895;  doi:10.1016/j.devcel.2019.01.026

6. Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice. Kojima ML, de Rooij DG, Page DC. Elife. pubmed:30810530;  doi:10.7554/eLife.43738

7. Streamlined protocol for deep proteomic profiling of FAC-sorted cells and its application to freshly isolated murine immune cells. Myers SA, Rhoads A, Cocco AR, Peckner R, Haber A, Schweitzer LD, Krug K, Mani DR, Clauser KR, Rozenblatt-Rosen O, Hacohen N, Regev A, Carr SA. Mol Cell Proteomics. pubmed:30792265;  doi:10.1074/mcp.RA118.001259

8. Data on ultrabright fluorescent cellulose acetate nanoparticles for imaging tumors through systemic and topical applications. Peng B, Almeqdadi M, Laroche F, Palantavida S, Dokukin M, Roper J, Yilmaz OH, Feng H, Sokolov I. Data Brief. pubmed:30596135;  doi:10.1016/j.dib.2018.12.030

9. Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1. Frappier V, Jenson JM, Zhou J, Grigoryan G, Keating AE. Structure. pubmed:30773399;  doi:10.1016/j.str.2019.01.008

10. Arg-78 of Nprl2 catalyzes GATOR1-stimulated GTP hydrolysis by the Rag GTPases. Shen K, Valenstein ML, Gu X, Sabatini DM. J Biol Chem. pubmed:30651352;  doi:10.1074/jbc.AC119.007382

11. An ingestible self-orienting system for oral delivery of macromolecules. Abramson A, Caffarel-Salvador E, Khang M, Dellal D, Silverstein D, Gao Y, Frederiksen MR, Vegge A, Hubalek F, Water JJ, Friderichsen AV, Fels J, Kirk RK, Cleveland C, Collins J, Tamang S, Hayward A, Landh T, Buckley ST, Roxhed N, Rahbek U, Langer R, Traverso G. Science. pubmed:30733413;  doi:10.1126/science.aau2277

12. Human cathelicidin peptide LL-37 as a therapeutic antiviral targeting Venezuelan equine encephalitis virus infections. Ahmed A, Siman-Tov G, Keck F, Kortchak S, Bakovic A, Risner K, Lu TK, Bhalla N, de la Fuente-Nunez C, Narayanan A. Antiviral Res. pubmed:30738837;  doi:10.1016/j.antiviral.2019.02.002

13. BOLA3 Deficiency Controls Endothelial Metabolism and Glycine Homeostasis in Pulmonary Hypertension. Yu Q, Tai YY, Tang Y, Zhao J, Negi V, Culley MK, Pilli J, Sun W, Brugger K, Mayr J, Saggar R, Saggar R, Wallace WD, Ross DJ, Waxman AB, Wendell SG, Mullett SJ, Sembrat J, Rojas M, Khan OF, Dahlman JE, Sugahara M, Kagiyama N, Satoh T, Zhang M, Feng N, Gorcsan Iii J, Vargas SO, Haley KJ, Kumar R, Graham BB, Langer R, Anderson DG, Wang B, Shiva S, Bertero T, Chan SY. Circulation. pubmed:30759996;  doi:10.1161/CIRCULATIONAHA.118.035889

14. Platelet decoys inhibit thrombosis and prevent metastatic tumor formation in preclinical models. Papa AL, Jiang A, Korin N, Chen MB, Langan ET, Waterhouse A, Nash E, Caroff J, Graveline A, Vernet A, Mammoto A, Mammoto T, Jain A, Kamm RD, Gounis MJ, Ingber DE. Sci Transl Med. pubmed:30760580;  doi:10.1126/scitranslmed.aau5898

15. Delivering the Messenger: Advances in Technologies for Therapeutic mRNA Delivery. Kowalski PS, Rudra A, Miao L, Anderson DG. Mol Ther. pubmed:30846391;  doi:10.1016/j.ymthe.2019.02.012

16. Casting a wider net: Immunosurveillance by nonclassical MHC molecules. D'Souza MP, Adams E, Altman JD, Birnbaum ME, Boggiano C, Casorati G, Chien YH, Conley A, Eckle SBG, Fruh K, Gondre-Lewis T, Hassan N, Huang H, Jayashankar L, Kasmar AG, Kunwar N, Lavelle J, Lewinsohn DM, Moody B, Picker L, Ramachandra L, Shastri N, Parham P, McMichael AJ, Yewdell JW. PLoS Pathog. pubmed:30789961;  doi:10.1371/journal.ppat.1007567

17. Chasing the Paradigm: Clinical Translation of 25 Years of Tissue Engineering. Hoffman T, Khademhosseini A, Langer RS. Tissue Eng Part A. pubmed:30727841;  doi:10.1089/ten.TEA.2019.0032

18. Detection of amyloid beta oligomers toward early diagnosis of Alzheimer's disease. Hwang SS, Chan H, Sorci M, Van Deventer J, Wittrup D, Belfort G, Walt D. Anal Biochem. pubmed:30267709;  doi:10.1016/j.ab.2018.09.011

19. Noninvasive monitoring of single-cell mechanics by acoustic scattering. Kang JH, Miettinen TP, Chen L, Olcum S, Katsikis G, Doyle PS, Manalis SR. Nat Methods. pubmed:30742041;  doi:10.1038/s41592-019-0326-x