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: April 2019

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1. Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood. Khera AV, Chaffin M, Wade KH, Zahid S, Brancale J, Xia R, Distefano M, Senol-Cosar O, Haas ME, Bick A, Aragam KG, Lander ES, Smith GD, Mason-Suares H, Fornage M, Lebo M, Timpson NJ, Kaplan LM, Kathiresan S. Cell. pubmed:31002795;  doi:10.1016/j.cell.2019.03.028

2. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ, Cleveland DW. Nat Genet. pubmed:30833795;  doi:10.1038/s41588-019-0360-8

3. Intergenerational epigenetic inheritance of cancer susceptibility in mammals. Lesch BJ, Tothova Z, Morgan EA, Liao Z, Bronson RT, Ebert BL, Page DC. Elife. pubmed:30963999;  doi:10.7554/eLife.39380

4. Mechanisms of Lymphoma Clearance Induced by High-Dose Alkylating Agents. Lossos C, Liu Y, Kolb KE, Christie AL, Van Scoyk A, Prakadan SM, Shigemori K, Stevenson KE, Morrow S, Plana OD, Fraser C, Jones KL, Liu H, Pallasch CP, Modiste R, Nguyen QD, Craig JW, Morgan EA, Vega F, Aster JC, Sarosiek KA, Shalek AK, Hemann MT, Weinstock DM. Cancer Discov. pubmed:31040105;  doi:10.1158/2159-8290.CD-18-1393

5. Gain-of-function mutation of microRNA-140 in human skeletal dysplasia. Grigelioniene G, Suzuki HI, Taylan F, Mirzamohammadi F, Borochowitz ZU, Ayturk UM, Tzur S, Horemuzova E, Lindstrand A, Weis MA, Grigelionis G, Hammarsjo A, Marsk E, Nordgren A, Nordenskjold M, Eyre DR, Warman ML, Nishimura G, Sharp PA, Kobayashi T. Nat Med. pubmed:30804514;  doi:10.1038/s41591-019-0353-2

6. Genome-wide CRISPR screen for Zika virus resistance in human neural cells. Li Y, Muffat J, Omer Javed A, Keys HR, Lungjangwa T, Bosch I, Khan M, Virgilio MC, Gehrke L, Sabatini DM, Jaenisch R. Proc Natl Acad Sci U S A. pubmed:31019072;  doi:10.1073/pnas.1900867116

7. CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation. Krajewska M, Dries R, Grassetti AV, Dust S, Gao Y, Huang H, Sharma B, Day DS, Kwiatkowski N, Pomaville M, Dodd O, Chipumuro E, Zhang T, Greenleaf AL, Yuan GC, Gray NS, Young RA, Geyer M, Gerber SA, George RE. Nat Commun. pubmed:30988284;  doi:10.1038/s41467-019-09703-y

8. Quantification of microenvironmental metabolites in murine cancers reveals determinants of tumor nutrient availability. Sullivan MR, Danai LV, Lewis CA, Chan SH, Gui DY, Kunchok T, Dennstedt EA, Vander Heiden MG, Muir A. Elife. pubmed:30990168;  doi:10.7554/eLife.44235

9. The Human Lung Cell Atlas - A high-resolution reference map of the human lung in health and disease. Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Vieira Braga F, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis FJ, Regev A, Kaminski N, Rajagopal J, Teichmann SA, Misharin AV, Nawijn MC. Am J Respir Cell Mol Biol. pubmed:30995076;  doi:10.1165/rcmb.2018-0416TR

10. Nanobody-based CAR T cells that target the tumor microenvironment inhibit the growth of solid tumors in immunocompetent mice. Xie YJ, Dougan M, Jailkhani N, Ingram J, Fang T, Kummer L, Momin N, Pishesha N, Rickelt S, Hynes RO, Ploegh H. Proc Natl Acad Sci U S A. pubmed:30936321;  doi:10.1073/pnas.1817147116

11. In-solution enrichment identifies peptide inhibitors of protein-protein interactions. Touti F, Gates ZP, Bandyopdhyay A, Lautrette G, Pentelute BL. Nat Chem Biol. pubmed:30886434;  doi:10.1038/s41589-019-0245-2

12. Visible-light-mediated, additive-free, and open-to-air controlled radical polymerization of acrylates and acrylamides. Lamb JR, Qin KP, Johnson JA. Polym Chem. pubmed:31057672;  doi:10.1039/C9PY00022D

13. Dynamic filopodial forces induce accumulation, damage, and plastic remodeling of 3D extracellular matrices. Malandrino A, Trepat X, Kamm RD, Mak M. PLoS Comput Biol. pubmed:30958816;  doi:10.1371/journal.pcbi.1006684

14. The Physics of Cancer. White FM, Gatenby RA, Fischbach C. Cancer Res. pubmed:31018939;  doi:10.1158/0008-5472.CAN-18-3937

15. PatcherBot: a single-cell electrophysiology robot for adherent cells and brain slices. Kolb I, Landry CR, Yip MC, Lewallen CF, Stoy WA, Lee J, Felouzis A, Yang B, Boyden ES, Rozell CJ, Forest CR. J Neural Eng. pubmed:30970335;  doi:10.1088/1741-2552/ab1834

16. Deep Learning Model to Assess Cancer Risk on the Basis of a Breast MR Image Alone. Portnoi T, Yala A, Schuster T, Barzilay R, Dontchos B, Lamb L, Lehman C. AJR Am J Roentgenol. pubmed:30933651;  doi:10.2214/AJR.18.20813

17. Oxytocin-dependent reopening of a social reward learning critical period with MDMA. Nardou R, Lewis EM, Rothhaas R, Xu R, Yang A, Boyden E, Dolen G. Nature. pubmed:30944474;  doi:10.1038/s41586-019-1075-9

18. Ultra-rapid drug delivery in the oral cavity using ultrasound. France MM, Del Rio T, Travers H, Raftery E, Xu K, Langer R, Traverso G, Lennerz JK, Schoellhammer CM. J Control Release. pubmed:31039376;  doi:10.1016/j.jconrel.2019.04.037

19. Engineering advanced cancer therapies with synthetic biology. Wu MR, Jusiak B, Lu TK. Nat Rev Cancer. pubmed:30837696;  doi:10.1038/s41568-019-0121-0

20. Multi-sensory Gamma Stimulation Ameliorates Alzheimer's-Associated Pathology and Improves Cognition. Martorell AJ, Paulson AL, Suk HJ, Abdurrob F, Drummond GT, Guan W, Young JZ, Kim DN, Kritskiy O, Barker SJ, Mangena V, Prince SM, Brown EN, Chung K, Boyden ES, Singer AC, Tsai LH. Cell. pubmed:30879788;  doi:10.1016/j.cell.2019.02.014

21. Tissue-specific oncogenic activity of K-RasA146T. Poulin EJ, Bera AK, Lu J, Lin YJ, Strasser SD, Paulo JA, Huang TQ, Morales C, Yan W, Cook J, Nowak JA, Brubaker DK, Joughin BA, Johnson CW, DeStefanis RA, Ghazi PC, Gondi S, Wales TE, Iacob RE, Bogdanova L, Gierut JJ, Li Y, Engen JR, Perez-Mancera PA, Braun BS, Gygi SP, Lauffenburger DA, Westover KD, Haigis KM. Cancer Discov. pubmed:30952657;  doi:10.1158/2159-8290.CD-18-1220

22. Steroid Hormone Function Controls Non-competitive Plasmodium Development in Anopheles. Werling K, Shaw WR, Itoe MA, Westervelt KA, Marcenac P, Paton DG, Peng D, Singh N, Smidler AL, South A, Deik AA, Mancio-Silva L, Demas AR, March S, Calvo E, Bhatia SN, Clish CB, Catteruccia F. Cell. pubmed:30929905;  doi:10.1016/j.cell.2019.02.036

23. Self-organization of hepatocyte morphogenesis depending on the size of collagen microbeads relative to hepatocytes. Ajoudanian M, Enomoto K, Tokunaga Y, Minami H, Chung S, Tanishita K, Kamm RD, Sudo R. Biofabrication. pubmed:31025629;  doi:10.1088/1758-5090/ab145d

24. A decade of Science Translational Medicine. Edelman ER, FitzGerald GA. Sci Transl Med. pubmed:31019024;  doi:10.1126/scitranslmed.aax4327

25. Microbial therapeutics: New opportunities for drug delivery. Jimenez M, Langer R, Traverso G. J Exp Med. pubmed:31028093;  doi:10.1084/jem.20190609

26. Self-assembly of droplets in three-dimensional microchannels. Parthiban P, Doyle PS, Hashimoto M. Soft Matter. pubmed:31016319;  doi:10.1039/c8sm02305k

27. Modular genetic design of multi-domain functional amyloids: insights into self-assembly and functional properties. Cui M, Qi Q, Gurry T, Zhao T, An B, Pu J, Gui X, Cheng AA, Zhang S, Xun D, Becce M, Briatico-Vangosa F, Liu C, Lu TK, Zhong C. Chem Sci. pubmed:31015941;  doi:10.1039/c9sc00208a

28. Remodeling of the Tumor Microenvironment by a Chemokine/Anti-PD-L1 Nanobody Fusion Protein. Fang T, Li R, Li Z, Cho J, Guzman JS, Kamm RD, Ploegh HL. Mol Pharm. pubmed:31013423;  doi:10.1021/acs.molpharmaceut.9b00078

29. Real-Time Single-Walled Carbon Nanotube-Based Fluorescence Imaging Improves Survival after Debulking Surgery in an Ovarian Cancer Model. Ceppi L, Bardhan NM, Na Y, Siegel A, Rajan N, Fruscio R, Del Carmen MG, Belcher AM, Birrer MJ. ACS Nano. pubmed:31009198;  doi:10.1021/acsnano.8b09829

30. A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation. Jarvenpaa M, Sater MRA, Lagoudas GK, Blainey PC, Miller LG, McKinnell JA, Huang SS, Grad YH, Marttinen P. PLoS Comput Biol. pubmed:31009452;  doi:10.1371/journal.pcbi.1006534

31. Temperature-responsive biometamaterials for gastrointestinal applications. Babaee S, Pajovic S, Kirtane AR, Shi J, Caffarel-Salvador E, Hess K, Collins JE, Tamang S, Wahane AV, Hayward AM, Mazdiyasni H, Langer R, Traverso G. Sci Transl Med. pubmed:30996082;  doi:10.1126/scitranslmed.aau8581

32. Solution Conditions Tune and Optimize Loading of Therapeutic Polyelectrolytes into Layer-by-Layer Functionalized Liposomes. Correa S, Boehnke N, Deiss-Yehiely E, Hammond PT. ACS Nano. pubmed:30986034;  doi:10.1021/acsnano.9b00792

33. Autonomous patch clamp robot for functional characterization of neurons in vivo: development and application to mouse visual cortex. Holst G, Stoy WA, Yang B, Kolb I, Kodandaramaiah SB, Li L, Knoblich U, Zeng H, Haider B, Boyden ES, Forest CR. J Neurophysiol. pubmed:30969898;  doi:10.1152/jn.00738.2018

34. Polymers for extended-release administration. Paolini MS, Fenton OS, Bhattacharya C, Andresen JL, Langer R. Biomed Microdevices. pubmed:30963297;  doi:10.1007/s10544-019-0386-9