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: November 2016

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1. Molecular Pathways: Receptor Ectodomain Shedding in Treatment, Resistance, and Monitoring of Cancer. Miller MA, Sullivan RJ, Lauffenburger DA. Clin Cancer Res. pubmed:27895032;  doi:10.1158/1078-0432.CCR-16-0869

2. 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

3. 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 Res. pubmed:27872091;  doi:10.1158/0008-5472.CAN-16-0442

4. Differential selective pressure alters rate of drug resistance acquisition in heterogeneous tumor populations. Sun D, Dalin S, Hemann MT, Lauffenburger DA, Zhao B. Sci Rep. pubmed:27819268;  doi:10.1038/srep36198

5. Base Excision Repair of N6-Deoxyadenosine Adducts of 1,3-Butadiene. Wickramaratne SS, Banda D, Ji S, Manlove AH, Malayappan B, Nunez NN, Samson LD, Campbell C, David SS, Tretyakova NY. Biochemistry. pubmed:27552084;  doi:10.1021/acs.biochem.6b00553

6. MicroRNA regulation of endothelial TREX1 reprograms the tumour microenvironment. Wilson R, Espinosa-Diez C, Kanner N, Chatterjee N, Ruhl R, Hipfinger C, Advani SJ, Li J, Khan OF, Franovic A, Weis SM, Kumar S, Coussens LM, Anderson DG, Chen CC, Cheresh DA, Anand S. Nat Commun. pubmed:27886180;  doi:10.1038/ncomms13597

7. TCT-391 Multiple drug coated balloon exposures increase arterial permeability and drug retention. Tzafriri R, Zani B, Alston S, Edelman E. J Am Coll Cardiol. pubmed:27969738;  doi:10.1016/j.jacc.2016.09.526

8. Oral, ultra-long-lasting drug delivery: Application toward malaria elimination goals. Bellinger AM, Jafari M, Grant TM, Zhang S, Slater HC, Wenger EA, Mo S, Lee YL, Mazdiyasni H, Kogan L, Barman R, Cleveland C, Booth L, Bensel T, Minahan D, Hurowitz HM, Tai T, Daily J, Nikolic B, Wood L, Eckhoff PA, Langer R, Traverso G. Sci Transl Med. pubmed:27856796;  doi:10.1126/scitranslmed.aag2374

9. Layer-by-Layer Encapsulation of Probiotics for Delivery to the Microbiome. Anselmo AC, McHugh KJ, Webster J, Langer R, Jaklenec A. Adv Mater. pubmed:27616140;  doi:10.1002/adma.201603270

10. Single-cell analysis at the threshold. Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV, Teichmann SA. Nat Biotechnol. pubmed:27824834;  doi:10.1038/nbt.3721

11. Drug sensitivity of single cancer cells is predicted by changes in mass accumulation rate. Stevens MM, Maire CL, Chou N, Murakami MA, Knoff DS, Kikuchi Y, Kimmerling RJ, Liu H, Haidar S, Calistri NL, Cermak N, Olcum S, Cordero NA, Idbaih A, Wen PY, Weinstock DM, Ligon KL, Manalis SR. Nat Biotechnol. pubmed:27723727;  doi:10.1038/nbt.3697

12. Kinetics of Change in Droplet Size during Nanoemulsion Formation. Gupta A, Narsimhan V, Hatton TA, Doyle PS. Langmuir. pubmed:27728762;  doi:10.1021/acs.langmuir.6b01862

13. Deciphering Combinatorial Genetics. Wong AS, Choi GC, Lu TK. Annu Rev Genet. pubmed:27732793;  doi:10.1146/annurev-genet-120215-034902

14. TGF-beta1 modulates microglial phenotype and promotes recovery after intracerebral hemorrhage. Taylor RA, Chang CF, Goods BA, Hammond MD, Grory BM, Ai Y, Steinschneider AF, Renfroe SC, Askenase MH, McCullough LD, Kasner SE, Mullen MT, Hafler DA, Love JC, Sansing LH. J Clin Invest. pubmed:27893460;  doi:10.1172/JCI88647

15. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang HC, Nussbacher JK, Broski SM, Kim HJ, Lardelli R, Sundararaman B, Donohue JP, Javaherian A, Lykke-Andersen J, Finkbeiner S, Bennett F, Ares MJr, Burge CB, Taylor JP, Rigo F, Yeo GW. Neuron. pubmed:27773581;  doi:10.1016/j.neuron.2016.09.050

16. Jointly reduced inhibition and excitation underlies circuit-wide changes in cortical processing in Rett syndrome. Banerjee A, Rikhye RV, Breton-Provencher V, Tang X, Li C, Li K, Runyan CA, Fu Z, Jaenisch R, Sur M. Proc Natl Acad Sci U S A. pubmed:27803317;  doi:10.1073/pnas.1615330113

17. Efficient derivation of microglia-like cells from human pluripotent stem cells. Muffat J, Li Y, Yuan B, Mitalipova M, Omer A, Corcoran S, Bakiasi G, Tsai LH, Aubourg P, Ransohoff RM, Jaenisch R. Nat Med. pubmed:27668937;  doi:10.1038/nm.4189

18. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, McDonel PE, Guttman M, Lander ES. Nature. pubmed:27783602;  doi:10.1038/nature20149

19. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM. Science. pubmed:27708057;  doi:10.1126/science.aag2445

20. Peripheral self-reactivity regulates antigen-specific CD8 T-cell responses and cell division under physiological conditions. Swee LK, Tan ZW, Sanecka A, Yoshida N, Patel H, Grotenbreg G, Frickel EM, Ploegh HL. Open Biol. pubmed:27881740;  doi:10.1098/rsob.160293

21. Transnuclear CD8 T cells specific for the immunodominant epitope Gra6 lower acute phase Toxoplasma gondii burden. Sanecka A, Yoshida N, Dougan SK, Jackson J, Shastri N, Ploegh H, Blanchard N, Frickel EM. Immunology. pubmed:27377596;  doi:10.1111/imm.12643

22. Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control. Hnisz D, Day DS, Young RA. Cell. pubmed:27863240;  doi:10.1016/j.cell.2016.10.024

23. JAK2 V617F stimulates proliferation of erythropoietin- dependent erythroid progenitors and delays their differentiation by activating Stat1 and other non-erythroid signaling pathways. Shi J, Yuan B, Hu W, Lodish H. Exp Hematol. pubmed:27473563;  doi:10.1016/j.exphem.2016.07.010

24. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, Neftel C, Desai N, Nyman J, Izar B, Luo CC, Francis JM, Patel AA, Onozato ML, Riggi N, Livak KJ, Gennert D, Satija R, Nahed BV, Curry WT, Martuza RL, Mylvaganam R, Iafrate AJ, Frosch MP, Golub TR, Rivera MN, Getz G, Rozenblatt-Rosen O, Cahill DP, Monje M, Bernstein BE, Louis DN, Regev A, Suva ML. Nature. pubmed:27806376;  doi:10.1038/nature20123

25. Revealing the vectors of cellular identity with single-cell genomics. Wagner A, Regev A, Yosef N. Nat Biotechnol. pubmed:27824854;  doi:10.1038/nbt.3711

26. Multiple mechanisms contribute to double-strand break repair at rereplication forks in Drosophila follicle cells. Alexander JL, Beagan K, Orr-Weaver TL, McVey M. Proc Natl Acad Sci U S A. pubmed:27849606;  doi:10.1073/pnas.1617110113

27. Altered metabolite levels in cancer: implications for tumour biology and cancer therapy. Sullivan LB, Gui DY, Vander Heiden MG. Nat Rev Cancer. pubmed:27658530;  doi:10.1038/nrc.2016.85

28. Environment Dictates Dependence on Mitochondrial Complex I for NAD+ and Aspartate Production and Determines Cancer Cell Sensitivity to Metformin. Gui DY, Sullivan LB, Luengo A, Hosios AM, Bush LN, Gitego N, Davidson SM, Freinkman E, Thomas CJ, Vander Heiden MG. Cell Metab. pubmed:27746050;  doi:10.1016/j.cmet.2016.09.006

29. The breast cancer stem cell potency of copper(ii) complexes bearing nonsteroidal anti-inflammatory drugs and their encapsulation using polymeric nanoparticles. Eskandari A, Boodram JN, Cressey PB, Lu C, Bruno PM, Hemann MT, Suntharalingam K. Dalton Trans. pubmed:27774561;  doi:10.1039/c6dt03811e

30. MenaINV dysregulates cortactin phosphorylation to promote invadopodium maturation. Weidmann MD, Surve CR, Eddy RJ, Chen X, Gertler FB, Sharma VP, Condeelis JS. Sci Rep. pubmed:27824079;  doi:10.1038/srep36142

31. PF4 Promotes Platelet Production and Lung Cancer Growth. Pucci F, Rickelt S, Newton AP, Garris C, Nunes E, Evavold C, Pfirschke C, Engblom C, Mino-Kenudson M, Hynes RO, Weissleder R, Pittet MJ. Cell Rep. pubmed:27829148;  doi:10.1016/j.celrep.2016.10.031

32. Phenanthriplatin Acts as a Covalent Poison of Topoisomerase II Cleavage Complexes. Riddell IA, Agama K, Park GY, Pommier Y, Lippard SJ. ACS Chem Biol. pubmed:27648475;  doi:10.1021/acschembio.6b00565

33. Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli. Vercruysse M, Kohrer C, Shen Y, Proulx S, Ghosal A, Davies BW, RajBhandary UL, Walker GC. MBio. pubmed:27834201;  doi:10.1128/mBio.01785-16

34. EMT, cell plasticity and metastasis. Chaffer CL, San Juan BP, Lim E, Weinberg RA. Cancer Metastasis Rev. pubmed:27878502;  doi:10.1007/s10555-016-9648-7