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 2018

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1. Peptide design by optimization on a data-parameterized protein interaction landscape. Jenson JM, Xue V, Stretz L, Mandal T, Reich LL, Keating AE. Proc Natl Acad Sci U S A. pubmed:30322927;  doi:10.1073/pnas.1812939115

2. JAK2/IDH-mutant-driven myeloproliferative neoplasm is sensitive to combined targeted inhibition. McKenney AS, Lau AN, Somasundara AVH, Spitzer B, Intlekofer AM, Ahn J, Shank K, Rapaport FT, Patel MA, Papalexi E, Shih AH, Chiu A, Freinkman E, Akbay EA, Steadman M, Nagaraja R, Yen K, Teruya-Feldstein J, Wong KK, Rampal R, Vander Heiden MG, Thompson CB, Levine RL. J Clin Invest. pubmed:30222137;  doi:10.1172/JCI124920

3. Serine Synthesis via PHGDH Is Essential for Heme Production in Endothelial Cells. Vandekeere S, Dubois C, Kalucka J, Sullivan MR, Garcia-Caballero M, Goveia J, Chen R, Diehl FF, Bar-Lev L, Souffreau J, Pircher A, Kumar S, Vinckier S, Hirabayashi Y, Furuya S, Schoonjans L, Eelen G, Ghesquiere B, Keshet E, Li X, Vander Heiden MG, Dewerchin M, Carmeliet P. Cell Metab. pubmed:30017355;  doi:10.1016/j.cmet.2018.06.009

4. Antibodies and methods for immunohistochemistry of extracellular matrix proteins. Rickelt S, Hynes RO. Matrix Biol. pubmed:29730502;  doi:10.1016/j.matbio.2018.04.011

5. Rapid CLIP dissociation from MHC II promotes an unusual antigen presentation pathway in autoimmunity. Ito Y, Ashenberg O, Pyrdol J, Luoma AM, Rozenblatt-Rosen O, Hofree M, Christian E, Ferrari de Andrade L, Tay RE, Teyton L, Regev A, Dougan SK, Wucherpfennig KW. J Exp Med. pubmed:30185635;  doi:10.1084/jem.20180300

6. Stem Cells, Genome Editing, and the Path to Translational Medicine. Soldner F, Jaenisch R. Cell. pubmed:30340033;  doi:10.1016/j.cell.2018.09.010

7. Microcephaly Modeling of Kinetochore Mutation Reveals a Brain-Specific Phenotype. Omer Javed A, Li Y, Muffat J, Su KC, Cohen MA, Lungjangwa T, Aubourg P, Cheeseman IM, Jaenisch R. Cell Rep. pubmed:30304678;  doi:10.1016/j.celrep.2018.09.032

8. One-step generation of monoclonal B cell receptor mice capable of isotype switching and somatic hypermutation. Jacobsen JT, Mesin L, Markoulaki S, Schiepers A, Cavazzoni CB, Bousbaine D, Jaenisch R, Victora GD. J Exp Med. pubmed:30181412;  doi:10.1084/jem.20172064

9. Author Correction: Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Whyte WA, Bilodeau S, Orlando DA, Hoke HA, Frampton GM, Foster CT, Cowley SM, Young RA. Nature. pubmed:30209401;  doi:10.1038/s41586-018-0487-2

10. Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway. Ye W, Chew M, Hou J, Lai F, Leopold SJ, Loo HL, Ghose A, Dutta AK, Chen Q, Ooi EE, White NJ, Dondorp AM, Preiser P, Chen J. PLoS Pathog. pubmed:30286211;  doi:10.1371/journal.ppat.1007298

11. Recall by genotype and cascade screening for familial hypercholesterolemia in a population-based biobank from Estonia. Alver M, Palover M, Saar A, Lall K, Zekavat SM, Tonisson N, Leitsalu L, Reigo A, Nikopensius T, Ainla T, Kals M, Magi R, Gabriel SB, Eha J, Lander ES, Irs A, Philippakis A, Marandi T, Natarajan P, Metspalu A, Kathiresan S, Esko T. Genet Med. pubmed:30270359;  doi:10.1038/s41436-018-0311-2

12. Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Creixell P, Pandey JP, Palmeri A, Bhattacharyya M, Creixell M, Ranganathan R, Pincus D, Yaffe MB. Cell Syst. pubmed:30243563;  doi:10.1016/j.cels.2018.08.008

13. Histidine N(tau)-cyclized macrocycles as a new genre of polo-like kinase 1 polo-box domain-binding inhibitors. Hymel D, Grant RA, Tsuji K, Yaffe MB, Burke TRJr. Bioorg Med Chem Lett. pubmed:30174151;  doi:10.1016/j.bmcl.2018.08.018

14. Leaving Groups as Traceless Topological Modifiers for the Synthesis of Topologically Isomeric Polymer Networks. Gu Y, Schauenburg D, Bode JW, Johnson JA. J Am Chem Soc. pubmed:30335993;  doi:10.1021/jacs.8b07967

15. Antibody-Bactericidal Macrocyclic Peptide Conjugates to Target Gram Negative Bacteria. Touti F, Lautrette G, Johnson K, Delaney J, Wollacott A, Tissire H, Viswanathan K, Shriver Z, Mong S, Mijalis A, Plante O, Pentelute B. Chembiochem. pubmed:29984452;  doi:10.1002/cbic.201800295

16. In vivo detection of drug-induced apoptosis in tumors using Raman spectroscopy. Jonas O, Kang JW, Singh SP, Lammers A, Nguyen FT, Dasari RR, So PTC, Langer R, Cima MJ. Analyst. pubmed:30070266;  doi:10.1039/c8an00913a

17. Optimization of a Degradable Polymer-Lipid Nanoparticle for Potent Systemic Delivery of mRNA to the Lung Endothelium and Immune Cells. Kaczmarek JC, Kauffman KJ, Fenton OS, Sadtler K, Patel AK, Heartlein MW, DeRosa F, Anderson DG. Nano Lett. pubmed:30211557;  doi:10.1021/acs.nanolett.8b02917

18. Engineering protein-protein devices for multilayered regulation of mRNA translation using orthogonal proteases in mammalian cells. Cella F, Wroblewska L, Weiss R, Siciliano V. Nat Commun. pubmed:30349044;  doi:10.1038/s41467-018-06825-7

19. 3D microfluidic ex vivo culture of organotypic tumor spheroids to model immune checkpoint blockade. Aref AR, Campisi M, Ivanova E, Portell A, Larios D, Piel BP, Mathur N, Zhou C, Coakley RV, Bartels A, Bowden M, Herbert Z, Hill S, Gilhooley S, Carter J, Canadas I, Thai TC, Kitajima S, Chiono V, Paweletz CP, Barbie DA, Kamm RD, Jenkins RW. Lab Chip. pubmed:30183789;  doi:10.1039/c8lc00322j

20. New observations in neuroscience using superresolution microscopy. Igarashi M, Nozumi M, Wu LG, Cella Zanacchi F, Katona I, Barna L, Xu P, Zhang M, Xue F, Boyden E. J Neurosci. pubmed:30381437;  doi:10.1523/JNEUROSCI.1678-18.2018

21. Customizable Lipid Nanoparticle Materials for the Delivery of siRNAs and mRNAs. Fenton O, Kauffman K, McClellan R, Kaczmarek J, Zeng M, Andresen J, Rhym L, Heartlein M, DeRosa F, Anderson DG. Angew Chem Int Ed Engl. pubmed:30112821;  doi:10.1002/anie.201809056

22. Synthetic Charge-Invertible Polymer for Rapid and Complete Implantation of Layer-by-Layer Microneedle Drug Films for Enhanced Transdermal Vaccination. He Y, Hong C, Li J, Howard MT, Li Y, Turvey ME, Uppu DSSM, Martin JR, Zhang K, Irvine DJ, Hammond PT. ACS Nano. pubmed:30272942;  doi:10.1021/acsnano.8b05373

23. Artificial Repeat-Structured siRNA Precursors as Tunable Regulators for Saccharomyces cerevisiae. Purcell O, Cao J, Muller IE, Chen YC, Lu TK. ACS Synth Biol. pubmed:30176724;  doi:10.1021/acssynbio.8b00185

24. Emerging Paradigms for Synthetic Design of Functional Amyloids. Wang Y, Pu J, An B, Lu TK, Zhong C. J Mol Biol. pubmed:29702108;  doi:10.1016/j.jmb.2018.04.012

25. Microphysiological 3D model of amyotrophic lateral sclerosis (ALS) from human iPS-derived muscle cells and optogenetic motor neurons. Osaki T, Uzel SGM, Kamm RD. Sci Adv. pubmed:30324134;  doi:10.1126/sciadv.aat5847

26. Construction of continuous capillary networks stabilized by pericyte-like perivascular cells. Yamamoto K, Tanimura K, Watanabe M, Sano H, Uwamori H, Mabuchi Y, Matsuzaki Y, Chung S, Kamm R, Tanishita K, Sudo R. Tissue Eng Part A. pubmed:30234439;  doi:10.1089/ten.TEA.2018.0186

27. Route of immunization defines multiple mechanisms of vaccine-mediated protection against SIV. Ackerman ME, Das J, Pittala S, Broge T, Linde C, Suscovich TJ, Brown EP, Bradley T, Natarajan H, Lin S, Sassic JK, O'Keefe S, Mehta N, Goodman D, Sips M, Weiner JA, Tomaras GD, Haynes BF, Lauffenburger DA, Bailey-Kellogg C, Roederer M, Alter G. Nat Med. pubmed:30177821;  doi:10.1038/s41591-018-0161-0

28. Author Correction: Gamma frequency entrainment attenuates amyloid load and modifies microglia. Iaccarino HF, Singer AC, Martorell AJ, Rudenko A, Gao F, Gillingham TZ, Mathys H, Seo J, Kritskiy O, Abdurrob F, Adaikkan C, Canter RG, Rueda R, Brown EN, Boyden ES, Tsai LH. Nature. pubmed:30046102;  doi:10.1038/s41586-018-0351-4

29. The yeast stands alone: the future of protein biologic production. Love KR, Dalvie NC, Love JC. Curr Opin Biotechnol. pubmed:29277062;  doi:10.1016/j.copbio.2017.12.010

30. A fluorescence-based imaging approach to pharmacokinetic analysis of intracochlear drug delivery. Ayoob AM, Peppi M, Tandon V, Langer R, Borenstein JT. Hear Res. pubmed:29661614;  doi:10.1016/j.heares.2018.03.026

31. On-demand manufacturing of clinical-quality biopharmaceuticals. Crowell LE, Lu AE, Love KR, Stockdale A, Timmick SM, Wu D, Wang YA, Doherty W, Bonnyman A, Vecchiarello N, Goodwine C, Bradbury L, Brady JR, Clark JJ, Colant NA, Cvetkovic A, Dalvie NC, Liu D, Liu Y, Mascarenhas CA, Matthews CB, Mozdzierz NJ, Shah KA, Wu SL, Hancock WS, Braatz RD, Cramer SM, Love JC. Nat Biotechnol. pubmed:30272677;  doi:10.1038/nbt.4262

32. 3D self-organized microvascular model of the human blood-brain barrier with endothelial cells, pericytes and astrocytes. Campisi M, Shin Y, Osaki T, Hajal C, Chiono V, Kamm RD. Biomaterials. pubmed:30032046;  doi:10.1016/j.biomaterials.2018.07.014