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 2017

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1. Ultrasound-Mediated Delivery of RNA to Colonic Mucosa of Live Mice. Schoellhammer CM, Lauwers GY, Goettel JA, Oberli MA, Cleveland C, Park JY, Minahan D, Chen Y, Anderson DG, Jaklenec A, Snapper SB, Langer R, Traverso G. Gastroenterology. pubmed:28088460 doi:10.1053/j.gastro.2017.01.002

2. A three dimensional in vitro glial scar model to investigate the local strain effects from micromotion around neural implants. Spencer KC, Sy JC, Falcon-Banchs R, Cima MJ. Lab Chip.pubmed:28119969;  doi:10.1039/c6lc01411a

3. DNA repair capacity in multiple pathways predicts chemoresistance in glioblastoma multiforme. Nagel ZD, Kitange GJ, Gupta SK, Joughin BA, Chaim IA, Mazzucato P, Lauffenburger DA, Sarkaria JN, Samson LD. Cancer Respubmed:27793847;  doi:10.1158/0008-5472.CAN-16-1151

4. Porous microwells for geometry-selective, large-scale microparticle arrays. Kim JJ, Bong KW, Reategui E, Irimia D, Doyle PS. Nat Materpubmed:27595351;  doi:10.1038/nmat4747

5. Synthesis of Lymph Node-Targeting Adjuvants. Hanson MC, Irvine DJ. Methods Mol Biolpubmed:27718191;  doi:10.1007/978-1-4939-6445-1_10

6. High-throughput quantitation of inorganic nanoparticle biodistribution at the single-cell level using mass cytometry. Yang YS, Atukorale PU, Moynihan KD, Bekdemir A, Rakhra K, Tang L, Stellacci F, Irvine DJ. Nat Communpubmed:28094297;  doi:10.1038/ncomms14069

7. CRISPR-Cas9 technology: applications in genome engineering, development of sequence-specific antimicrobials, and future prospects. de la Fuente-Nunez C, Lu TK. Integr Biol (Camb).pubmed:28045163;  doi:10.1039/c6ib00140h

8. Advances in the quantification of mitochondrial function in primary human immune cells through extracellular flux analysis. Nicholas D, Proctor EA, Raval FM, Ip BC, Habib C, Ritou E, Grammatopoulos TN, Steenkamp D, Dooms H, Apovian CM, Lauffenburger DA, Nikolajczyk BS. PLoS Onepubmed:28178278;  doi:10.1371/journal.pone.0170975

9. Macrophage-secreted TNFalpha and TGFbeta1 Influence Migration Speed and Persistence of Cancer Cells in 3D Tissue Culture via Independent Pathways. Li R, Hebert JD, Lee TA, Xing H, Boussommier-Calleja A, Hynes RO, Lauffenburger DA, Kamm RD. Cancer Respubmed:27872091;  doi:10.1158/0008-5472.CAN-16-0442

10. Mena confers resistance to Paclitaxel in triple-negative breast cancer. Oudin MJ, Barbier L, Schafer C, Kosciuk T, Miller MA, Han S, Jonas O, Lauffenburger DA, Gertler FB. Mol Cancer Ther.pubmed:27811011;  doi:10.1158/1535-7163.MCT-16-0413

11. Profiling drugs for rheumatoid arthritis that inhibit synovial fibroblast activation. Jones DS, Jenney AP, Swantek JL, Burke JM, Lauffenburger DA, Sorger PK. Nat Chem Biol.pubmed:27820799;  doi:10.1038/nchembio.2211

12. Lipidoid mRNA Nanoparticles for Myocardial Delivery in Rodents. Turnbull IC, Eltoukhy AA, Anderson DG, Costa KD. Methods Mol Biolpubmed:27910047;  doi:10.1007/978-1-4939-6588-5_10

13. A Chiral Pentagonal Polyhedral Framework for Characterizing Virus Capsid Structures. Raguram A, Sasisekharan V, Sasisekharan R.  Trends Microbiol. pubmed:28094093doi:10.1016/j.tim.2016.12.007

14. Enhanced Cell Capture on Functionalized Graphene Oxide Nanosheets through Oxygen Clustering. Bardhan NM, Kumar PV, Li Z, Ploegh HL, Grossman JC, Belcher AM, Chen GY. ACS Nano.pubmed:28085249;  doi:10.1021/acsnano.6b06979

15. Biocompatibility, bone healing, and safety evaluation in rabbits with an IlluminOss bone stabilization system. McSweeney AL, Zani BG, Baird R, Stanley JR, Hayward A, Markham PM, Kopia GA, Edelman ER, Rabiner R. J Orthop Respubmed:28135014;  doi:10.1002/jor.23532

16. Single-molecule detection of protein efflux from microorganisms using fluorescent single-walled carbon nanotube sensor arrays. Landry MP, Ando H, Chen AY, Cao J, Kottadiel VI, Chio L, Yang D, Dong J, Lu TK, Strano MS.Nat Nanotechnol.pubmed:28114298;  doi:10.1038/nnano.2016.284

17. A novel role for transcription-coupled nucleotide excision repair for the in vivo repair of 3,N4-ethenocytosine. Chaim IA, Gardner A, Wu J, Iyama T, Wilson DM3rd, Samson LD. Nucleic Acids Res.pubmed:28115629;  doi:10.1093/nar/gkx015

18. Cocapture of cognate and bystander antigens can activate autoreactive B cells. Sanderson NS, Zimmermann M, Eilinger L, Gubser C, Schaeren-Wiemers N, Lindberg RL, Dougan SK, Ploegh HL, Kappos L, Derfuss T. Proc Natl Acad Sci U S Apubmed:28057865;  doi:10.1073/pnas.1614472114

19. Hepta-Mutant Staphylococcus aureus Sortase A (SrtA7m) as a Tool for in Vivo Protein Labeling in Caenorhabditis elegans. Wu Q, Ploegh HL, Truttmann MC. ACS Chem Biol.pubmed:28098972;  doi:10.1021/acschembio.6b00998

20. Differentiation of Club Cells to Alveolar Epithelial Cells In Vitro. Zheng D, Soh BS, Yin L, Hu G, Chen Q, Choi H, Han J, Chow VT, Chen J. Sci Reppubmed:28128362;  doi:10.1038/srep41661

21. Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation. Sahakyan A, Kim R, Chronis C, Sabri S, Bonora G, Theunissen TW, Kuoy E, Langerman J, Clark AT, Jaenisch R, Plath K. Cell Stem Cellpubmed:27989770;  doi:10.1016/j.stem.2016.10.006

22. A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo TH, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RMJr, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL. Cell Rep.pubmed:28099853;  doi:10.1016/j.celrep.2016.12.063

23. Selective Y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining. Ly P, Teitz LS, Kim DH, Shoshani O, Skaletsky H, Fachinetti D, Page DC, Cleveland DW. Nat Cell Biolpubmed:27918550;  doi:10.1038/ncb3450

24. Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms. Guo MH, Nandakumar SK, Ulirsch JC, Zekavat SM, Buenrostro JD, Natarajan P, Salem RM, Chiarle R, Mitt M, Kals M, Parn K, Fischer K, Milani L, Magi R, Palta P, Gabriel SB, Metspalu A, Lander ES, Kathiresan S, Hirschhorn JN, Esko T, Sankaran VG. Proc Natl Acad Sci U S A.pubmed:28031487;  doi:10.1073/pnas.1619052114

25. Unrestrained AMPylation targets cytosolic chaperones and activates the heat shock response. Truttmann MC, Zheng X, Hanke L, Damon JR, Grootveld M, Krakowiak J, Pincus D, Ploegh HL. Proc Natl Acad Sci U S Apubmed:28031489;  doi:10.1073/pnas.1619234114

26. Scaling single-cell genomics from phenomenology to mechanism. Tanay A, Regev A. Naturepubmed:28102262;  doi:10.1038/nature21350

27. Tet1 in Nucleus Accumbens Opposes Depression- and Anxiety-Like Behaviors. Feng J, Pena CJ, Purushothaman I, Engmann O, Walker D, Brown AN, Issler O, Doyle M, Harrigan E, Mouzon E, Vialou V, Shen L, Dawlaty MM, Jaenisch R, Nestler EJ. Neuropsychopharmacologypubmed:28074830;  doi:10.1038/npp.2017.6

28. Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Bellott DW, Skaletsky H, Cho TJ, Brown L, Locke D, Chen N, Galkina S, Pyntikova T, Koutseva N, Graves T, Kremitzki C, Warren WC, Clark AG, Gaginskaya E, Wilson RK, Page DC. Nat Genetpubmed:28135246;  doi:10.1038/ng.3778

29. Critical Functions of the Lysosome in Cancer Biology. Davidson SM, Vander Heiden MG. Annu Rev Pharmacol Toxicolpubmed:27732799;  doi:10.1146/annurev-pharmtox-010715-103101

30. The unexpected role of mTORC1 in intestinal stem cells during calorie restriction. Igarashi M, Guarente L. Cell Cyclepubmed:27592731;  doi:10.1080/15384101.2016.1221210

31. Starving leukemia to induce differentiation. Cheng CW, Yilmaz OH. Nat Medpubmed:28060803;  doi:10.1038/nm.4259

32. Suppression of 19S proteasome subunits marks emergence of an altered cell state in diverse cancers. Tsvetkov P, Sokol E, Jin D, Brune Z, Thiru P, Ghandi M, Garraway LA, Gupta PB, Santagata S, Whitesell L, Lindquist S. Proc Natl Acad Sci U S Apubmed:28028240;  doi:10.1073/pnas.1619067114

33. Rethinking origin licensing. Bell SP. Elifepubmed:28102819;  doi:10.7554/eLife.24052

34. In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons. Chung CY, Khurana V, Yi S, Sahni N, Loh KH, Auluck PK, Baru V, Udeshi ND, Freyzon Y, Carr SA, Hill DE, Vidal M, Ting AY, Lindquist S. Cell Systpubmed:28131823;  doi:10.1016/j.cels.2017.01.002

35. Genome-Scale Networks Link Neurodegenerative Disease Genes to alpha-Synuclein through Specific Molecular Pathways. Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schondorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S. Cell Systpubmed:28131822;  doi:10.1016/j.cels.2016.12.011

36. Endothelial Cells Get beta-ox-ed In to Support Lymphangiogenesis. Hosios AM, Vander Heiden MG. Dev Cellpubmed:28118598;  doi:10.1016/j.devcel.2017.01.004

37. Mobile zinc increases rapidly in the retina after optic nerve injury and regulates ganglion cell survival and optic nerve regeneration. Li Y, Andereggen L, Yuki K, Omura K, Yin Y, Gilbert HY, Erdogan B, Asdourian MS, Shrock C, de Lima S, Apfel UP, Zhuo Y, Hershfinkel M, Lippard SJ, Rosenberg PA, Benowitz L. Proc Natl Acad Sci U S Apubmed:28049831;  doi:10.1073/pnas.1616811114

38. Integrin PSI domain has endogenous thiol isomerase function and is a novel target for anti-platelet therapy. Zhu G, Zhang Q, Reddy EC, Carrim N, Chen Y, Xu XR, Xu M, Wang Y, Hou Y, Ma L, Li Y, Rui M, Petruzziello T, Lavalle C, Stratton TW, Lei X, Reheman A, Chen P, Zhu C, Wilkins JA, Hynes RO, Freedman J, Ni H. Bloodpubmed:28122739;  doi:10.1182/blood-2016-07-729400

39. Repair shielding of platinum-DNA lesions in testicular germ cell tumors by high-mobility group box protein 4 imparts cisplatin hypersensitivity. Awuah SG, Riddell IA, Lippard SJ. Proc Natl Acad Sci U S Apubmed:28096358;  doi:10.1073/pnas.1615327114

40. Targeting the Epithelial-to-Mesenchymal Transition: The Case for Differentiation-Based Therapy. Pattabiraman DR, Weinberg RA. Cold Spring Harb Symp Quant Biol.pubmed:28057845;  doi:10.1101/sqb.2016.81.030957

41. C21orf57 is a human homologue of bacterial YbeY proteins. Ghosal A, Kohrer C, Babu VM, Yamanaka K, Davies BW, Jacob AI, Ferullo DJ, Gruber CC, Vercruysse M, Walker GC. Biochem Biophys Res Communpubmed:28153719;  doi:10.1016/j.bbrc.2017.01.149

42. Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression. Naba A, Clauser KR, Mani DR, Carr SA, Hynes RO. Sci Rep.pubmed:28071719;  doi:10.1038/srep40495