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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: September 2019

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1. Context is everything: aneuploidy in cancer. Ben-David U, Amon A. Nat Rev Genet. pubmed:31548659;  doi:10.1038/s41576-019-0171-x

2. Electrical and synaptic integration of glioma into neural circuits. Venkatesh HS, Morishita W, Geraghty AC, Silverbush D, Gillespie SM, Arzt M, Tam LT, Espenel C, Ponnuswami A, Ni L, Woo PJ, Taylor KR, Agarwal A, Regev A, Brang D, Vogel H, Hervey-Jumper S, Bergles DE, Suva ML, Malenka RC, Monje M. Nature. pubmed:31534222;  doi:10.1038/s41586-019-1563-y

3. Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis. Jackstadt R, van Hooff SR, Leach JD, Cortes-Lavaud X, Lohuis JO, Ridgway RA, Wouters VM, Roper J, Kendall TJ, Roxburgh CS, Horgan PG, Nixon C, Nourse C, Gunzer M, Clark W, Hedley A, Yilmaz OH, Rashid M, Bailey P, Biankin AV, Campbell AD, Adams DJ, Barry ST, Steele CW, Medema JP, Sansom OJ. Cancer Cell. pubmed:31526760;  doi:10.1016/j.ccell.2019.08.003

4. Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes. Zamudio AV, Dall'Agnese A, Henninger JE, Manteiga JC, Afeyan LK, Hannett NM, Coffey EL, Li CH, Oksuz O, Sabari BR, Boija A, Klein IA, Hawken SW, Spille JH, Decker TM, Cisse II, Abraham BJ, Lee TI, Taatjes DJ, Schuijers J, Young RA. Mol Cell. pubmed:31563432;  doi:10.1016/j.molcel.2019.08.016

5. Syndecan-mediated ligation of ECM proteins triggers proliferative arrest of disseminated tumor cells. Shibue T, Reinhardt F, Weinberg RA. Cancer Res. pubmed:31481497;  doi:10.1158/0008-5472.CAN-19-1165

6. Cellular redox state constrains serine synthesis and nucleotide production to impact cell proliferation. Diehl FF, Lewis CA, Fiske BP, Vander Heiden MG. Nat Metab. pubmed:31598584;  doi:10.1038/s42255-019-0108-x

7. Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance. Dalin S, Sullivan MR, Lau AN, Grauman-Boss B, Mueller HS, Kreidl E, Fenoglio S, Luengo A, Lees JA, Vander Heiden MG, Lauffenburger DA, Hemann MT. Cancer Res. pubmed:31484670;  doi:10.1158/0008-5472.CAN-19-0960

8. Proteomic analyses of ECM during pancreatic ductal adenocarcinoma progression reveal different contributions by tumor and stromal cells. Tian C, Clauser KR, Ohlund D, Rickelt S, Huang Y, Gupta M, Mani DR, Carr SA, Tuveson DA, Hynes RO. Proc Natl Acad Sci U S A. pubmed:31484774;  doi:10.1073/pnas.1908626116

9. Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene egl-1 in a Living Neuron Pair in Caenorhabditis elegans. Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT. G3 (Bethesda). pubmed:31519744;  doi:10.1534/g3.119.400654

10. PolyMOF Nanoparticles: Dual Roles of a Multivalent polyMOF Ligand in Size Control and Surface Functionalization. Gu Y, Huang M, Zhang W, Pearson MA, Johnson JA. Angew Chem Int Ed Engl. pubmed:31502339;  doi:10.1002/anie.201910542

11. Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. Tsankov AM, Wadsworth MH2nd, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A. Development. pubmed:31515224;  doi:10.1242/dev.174722

12. BigSMILES: A Structurally-Based Line Notation for Describing Macromolecules. Lin TS, Coley CW, Mochigase H, Beech HK, Wang W, Wang Z, Woods E, Craig SL, Johnson JA, Kalow JA, Jensen KF, Olsen BD. ACS Cent Sci. pubmed:31572779;  doi:10.1021/acscentsci.9b00476

13. Gene networks that compensate for crosstalk with crosstalk. Muller IE, Rubens JR, Jun T, Graham D, Xavier R, Lu TK. Nat Commun. pubmed:31492904;  doi:10.1038/s41467-019-12021-y

14. Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Wang J, Alvin Chew BL, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu CF, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC. Nucleic Acids Res. pubmed:31504804;  doi:10.1093/nar/gkz751

15. Application of Transmural Flow Across In Vitro Microvasculature Enables Direct Sampling of Interstitial Therapeutic Molecule Distribution. Offeddu GS, Possenti L, Loessberg-Zahl JT, Zunino P, Roberts J, Han X, Hickman D, Knutson CG, Kamm RD. Small. pubmed:31497931;  doi:10.1002/smll.201902393

16. Biomaterials for Personalized Cell Therapy. Facklam AL, Volpatti LR, Anderson DG. Adv Mater. pubmed:31495970;  doi:10.1002/adma.201902005

17. Predicting the broadly neutralizing antibody susceptibility of the HIV reservoir. Yu WH, Su D, Torabi J, Fennessey CM, Shiakolas A, Lynch R, Chun TW, Doria-Rose N, Alter G, Seaman MS, Keele BF, Lauffenburger DA, Julg B. JCI Insight. pubmed:31484826;  doi:10.1172/jci.insight.130153

18. Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes. Bao Y, Deng Z, Wang Y, Kim H, Armengol VD, Acevedo F, Ouardaoui N, Wang C, Parmigiani G, Barzilay R, Braun D, Hughes KS. JCO Clin Cancer Inform. pubmed:31545655;  doi:10.1200/CCI.19.00042

19. Endothelial TGF-beta signalling drives vascular inflammation and atherosclerosis. Chen PY, Qin L, Li G, Wang Z, Dahlman JE, Malagon-Lopez J, Gujja S, Kauffman KJ, Sun L, Sun H, Zhang X, Aryal B, Canfran-Duque A, Liu R, Kusters P, Sehgal A, Jiao Y, Anderson DG, Gulcher J, Fernandez-Hernando C, Lutgens E, Schwartz MA, Pober JS, Chittenden TW, Tellides G, Simons M. Nat Metab. pubmed:31572976;  doi:10.1038/s42255-019-0102-3

20. Quantitative screening of the effects of hyper-osmotic stress on cancer cells cultured in 2- or 3-dimensional settings. Miermont A, Lee SWL, Adriani G, Kamm RD. Sci Rep. pubmed:31551497;  doi:10.1038/s41598-019-50198-w

21. Tumor penetrating nanomedicine targeting both an oncomiR and an oncogene in pancreatic cancer. Gilles ME, Hao L, Brown K, Lim J, Bhatia SN, Slack FJ. Oncotarget. pubmed:31523393;  doi:10.18632/oncotarget.27160

22. Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation. Brubaker DK, Paulo JA, Sheth S, Poulin EJ, Popow O, Joughin BA, Strasser SD, Starchenko A, Gygi SP, Lauffenburger DA, Haigis KM. Cell Syst. pubmed:31521603;  doi:10.1016/j.cels.2019.07.006

23. Ventricular stroke work and vascular impedance refine the characterization of patients with aortic stenosis. Ben-Assa E, Brown J, Keshavarz-Motamed Z, de la Torre Hernandez JM, Leiden B, Olender M, Kallel F, Palacios IF, Inglessis I, Passeri JJ, Shah PB, Elmariah S, Leon MB, Edelman ER. Sci Transl Med. pubmed:31511424;  doi:10.1126/scitranslmed.aaw0181

24. Donor-Cell Engineering with GSK3 Inhibitor-Loaded Nanoparticles Enhances Engraftment Following in Utero Transplantation. Loukogeorgakis SP, Fachin CG, Santos Dias A, Li H, Tang L, Kim AG, Vrecenak JD, Stratigis J, Ahn NJ, Nissim I, Nissim I, Moron AF, Martins JL, Peranteau WH, De Coppi P, Irvine DJ, Flake AW. Blood. pubmed:31570489;  doi:10.1182/blood.2019001037

25. Delivery of mRNA vaccines with heterocyclic lipids increases anti-tumor efficacy by STING-mediated immune cell activation. Miao L, Li L, Huang Y, Delcassian D, Chahal J, Han J, Shi Y, Sadtler K, Gao W, Lin J, Doloff JC, Langer R, Anderson DG. Nat Biotechnol. pubmed:31570898;  doi:10.1038/s41587-019-0247-3

26. Expert recommendations on the assessment of wall shear stress in human coronary arteries: existing methodologies, technical considerations, and clinical applications. Gijsen F, Katagiri Y, Barlis P, Bourantas C, Collet C, Coskun U, Daemen J, Dijkstra J, Edelman E, Evans P, van der Heiden K, Hose R, Koo BK, Krams R, Marsden A, Migliavacca F, Onuma Y, Ooi A, Poon E, Samady H, Stone P, Takahashi K, Tang D, Thondapu V, Tenekecioglu E, Timmins L, Torii R, Wentzel J, Serruys P. Eur Heart J. pubmed:31566246;  doi:10.1093/eurheartj/ehz551

27. Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes. Guo SM, Veneziano R, Gordonov S, Li L, Danielson E, Perez de Arce K, Park D, Kulesa AB, Wamhoff EC, Blainey PC, Boyden ES, Cottrell JR, Bathe M. Nat Commun. pubmed:31558769;  doi:10.1038/s41467-019-12372-6

28. Development and Application of the Metalloprotease Activity Multi-plexed Bead-based Immunoassay (MAMBI). Ahrens CC, Chiswick EL, Ravindra KC, Miller MA, Ramseier J, Isaacson KB, Lauffenburger DA, Griffith LG. Biochemistry. pubmed:31474112;  doi:10.1021/acs.biochem.9b00584

29. Thermally robust solvent-free biofluids of M13 bacteriophage engineered for high compatibility with anhydrous ionic liquids. Brogan APS, Heldman N, Hallett JP, Belcher AM. Chem Commun (Camb). pubmed:31432818;  doi:10.1039/c9cc04909f

30. Renal clearable catalytic gold nanoclusters for in vivo disease monitoring. Loynachan CN, Soleimany AP, Dudani JS, Lin Y, Najer A, Bekdemir A, Chen Q, Bhatia SN, Stevens MM. Nat Nanotechnol. pubmed:31477801;  doi:10.1038/s41565-019-0527-6

31. Balance of interstitial flow magnitude and vascular endothelial growth factor concentration modulates three-dimensional microvascular network formation. Abe Y, Watanabe M, Chung S, Kamm RD, Tanishita K, Sudo R. APL Bioeng. pubmed:31431938;  doi:10.1063/1.5094735

32. A New Approach for Micro-fabrication of Printed Circuit Boards with Ultra-fine Traces. Mirvakili SM, Broderick K, Langer RS. ACS Appl Mater Interfaces. pubmed:31480839;  doi:10.1021/acsami.9b08761

33. Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P. Nat Biotechnol. pubmed:31427819;  doi:10.1038/s41587-019-0207-y