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 2018

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1. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES. Nature. pubmed:30150775;  doi:10.1038/s41586-018-0453-z

2. Chromosome Segregation Fidelity in Epithelia Requires Tissue Architecture. Knouse KA, Lopez KE, Bachofner M, Amon A. Cell. pubmed:30146160;  doi:10.1016/j.cell.2018.07.042

3. Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma. McBrayer SK, Mayers JR, DiNatale GJ, Shi DD, Khanal J, Chakraborty AA, Sarosiek KA, Briggs KJ, Robbins AK, Sewastianik T, Shareef SJ, Olenchock BA, Parker SJ, Tateishi K, Spinelli JB, Islam M, Haigis MC, Looper RE, Ligon KL, Bernstein BE, Carrasco RD, Cahill DP, Asara JM, Metallo CM, Yennawar NH, Vander Heiden MG, Kaelin WGJr. Cell. pubmed:30220459;  doi:10.1016/j.cell.2018.08.038

4. Regulation of Cellular Heterogeneity and Rates of Symmetric and Asymmetric Divisions in Triple-Negative Breast Cancer. Granit RZ, Masury H, Condiotti R, Fixler Y, Gabai Y, Glikman T, Dalin S, Winter E, Nevo Y, Carmon E, Sella T, Sonnenblick A, Peretz T, Lehmann U, Paz K, Piccioni F, Regev A, Root DE, Ben-Porath I. Cell Rep. pubmed:30232005;  doi:10.1016/j.celrep.2018.08.053

5. Uveal melanoma driver mutations in GNAQ/11 yield numerous changes in melanocyte biology. Perez DE, Henle AM, Amsterdam A, Hagen HR, Lees JA. Pigment Cell Melanoma Res. pubmed:29570931;  doi:10.1111/pcmr.12700

6. Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry. Durbin AD, Zimmerman MW, Dharia NV, Abraham BJ, Iniguez AB, Weichert-Leahey N, He S, Krill-Burger JM, Root DE, Vazquez F, Tsherniak A, Hahn WC, Golub TR, Young RA, Look AT, Stegmaier K. Nat Genet. pubmed:30127528;  doi:10.1038/s41588-018-0191-z

7. Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations. Khera AV, Chaffin M, Aragam KG, Haas ME, Roselli C, Choi SH, Natarajan P, Lander ES, Lubitz SA, Ellinor PT, Kathiresan S. Nat Genet. pubmed:30104762;  doi:10.1038/s41588-018-0183-z

8. IL-1beta inflammatory response driven by primary breast cancer prevents metastasis-initiating cell colonization. Castano Z, San Juan BP, Spiegel A, Pant A, DeCristo MJ, Laszewski T, Ubellacker JM, Janssen SR, Dongre A, Reinhardt F, Henderson A, Del Rio AG, Gifford AM, Herbert ZT, Hutchinson JN, Weinberg RA, Chaffer CL, McAllister SS. Nat Cell Biol. pubmed:30154549;  doi:10.1038/s41556-018-0173-5

9. Elevated levels of Era GTPase improve growth, 16S rRNA processing, and 70S ribosome assembly of Escherichia coli lacking highly conserved multifunctional YbeY endoribonuclease. Ghosal A, Babu VMP, Walker GC. J Bacteriol. pubmed:29914987;  doi:10.1128/JB.00278-18

10. Ragulator and SLC38A9 activate the Rag GTPases through noncanonical GEF mechanisms. Shen K, Sabatini DM. Proc Natl Acad Sci U S A. pubmed:30181260;  doi:10.1073/pnas.1811727115

11. Enhancement of peptide vaccine immunogenicity by increasing lymphatic drainage and boosting serum stability. Moynihan KD, Holden RL, Mehta NK, Wang C, Karver MR, Dinter J, Liang S, Abraham W, Melo MB, Zhang AQ, Li N, Le Gall S, Pentelute B, Irvine DJ. Cancer Immunol Res. pubmed:29915023;  doi:10.1158/2326-6066.CIR-17-0607

12. Supramolecular Regulation of Anions Enhances Conductivity and Transference Number of Lithium in Liquid Electrolytes. Qiao B, Leverick GM, Zhao W, Flood AH, Johnson JA, Shao-Horn Y. J Am Chem Soc. pubmed:30014696;  doi:10.1021/jacs.8b05915

13. Identification of Novel Cryptic Multifunctional Antimicrobial Peptides from the Human Stomach Enabled by a Computational-Experimental Platform. Pane K, Cafaro V, Avitabile A, Torres MT, Vollaro A, De Gregorio E, Catania MR, Di Maro A, Bosso A, Gallo G, Zanfardino A, Varcamonti M, Pizzo E, Di Donato A, Lu TK, de la Fuente-Nunez C, Notomista E. ACS Synth Biol. pubmed:30124040;  doi:10.1021/acssynbio.8b00084

14. Phage-Based Applications in Synthetic Biology. Lemire S, Yehl KM, Lu TK. Annu Rev Virol. pubmed:30001182;  doi:10.1146/annurev-virology-092917-043544

15. Nonfouling, Encoded Hydrogel Microparticles for Multiplex MicroRNA Profiling Directly from Formalin-Fixed, Paraffin-Embedded Tissue. Nagarajan MB, Tentori AM, Zhang WC, Slack FJ, Doyle PS. Anal Chem. pubmed:30106558;  doi:10.1021/acs.analchem.8b02010

16. Oil Recovery from Micropatterned Triangular Troughs during a Surfactant Flood. Gupta A, Lee H, Doyle PS. Langmuir. pubmed:30124298;  doi:10.1021/acs.langmuir.8b02150

17. Cooperative Effects of Vascular Angiogenesis and Lymphangiogenesis. Osaki T, Serrano JC, Kamm RD. Regen Eng Transl Med. pubmed:30417074;  doi:10.1007/s40883-018-0054-2

18. Enhancing T cell therapy through TCR-signaling-responsive nanoparticle drug delivery. Tang L, Zheng Y, Melo MB, Mabardi L, Castano AP, Xie YQ, Li N, Kudchodkar SB, Wong HC, Jeng EK, Maus MV, Irvine DJ. Nat Biotechnol. pubmed:29985479;  doi:10.1038/nbt.4181

19. A Bayesian framework for high-throughput T cell receptor pairing. Holec PV, Berleant J, Bathe M, Birnbaum ME. Bioinformatics. pubmed:30215679;  doi:10.1093/bioinformatics/bty801

20. Fracture in drug-eluting stents increases focal intimal hyperplasia in the atherosclerosed rabbit iliac artery. Conway C, Desany GJ, Bailey LR, Keating JH, Baker BL, Edelman ER. Catheter Cardiovasc Interv. pubmed:30244502;  doi:10.1002/ccd.27726

21. B'reshith. Siegel RA, Brown L, Edelman ER, Linhardt RJ. J Control Release. pubmed:30078756;  doi:10.1016/j.jconrel.2018.07.005

22. Initiation of anti-retroviral therapy before pregnancy reduces the risk of infection-related hospitalization in HIV-exposed uninfected infants born in a high-income country. Goetghebuer T, Smolen KK, Adler C, Das J, McBride T, Smits G, Lecomte S, Haelterman E, Barlow P, Piedra PA, van der Klis F, Kollmann TR, Lauffenburger DA, Alter G, Levy J, Marchant A. Clin Infect Dis. pubmed:30215689;  doi:10.1093/cid/ciy673

23. Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues. Asano SM, Gao R, Wassie AT, Tillberg PW, Chen F, Boyden ES. Curr Protoc Cell Biol. pubmed:30070431;  doi:10.1002/cpcb.56

24. Publisher Correction: A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters. Piatkevich KD, Jung EE, Straub C, Linghu C, Park D, Suk HJ, Hochbaum DR, Goodwin D, Pnevmatikakis E, Pak N, Kawashima T, Yang CT, Rhoades JL, Shemesh O, Asano S, Yoon YG, Freifeld L, Saulnier JL, Riegler C, Engert F, Hughes T, Drobizhev M, Szabo B, Ahrens MB, Flavell SW, Sabatini BL, Boyden ES. Nat Chem Biol. pubmed:29520042;  doi:10.1038/s41589-018-0023-6

25. Genotype-targeted local therapy of glioma. Shankar GM, Kirtane AR, Miller JJ, Mazdiyasni H, Rogner J, Tai T, Williams EA, Higuchi F, Juratli TA, Tateishi K, Koerner MVA, Tummala SS, Fink AL, Penson T, Schmidt SP, Wojtkiewicz GR, Baig A, Francis JM, Rinne ML, Batten JM, Batchelor TT, Brastianos PK, Curry WTJr, Barker FG2nd, Jordan JT, Iafrate AJ, Chi AS, Lennerz JK, Meyerson M, Langer R, Wakimoto H, Traverso G, Cahill DP. Proc Natl Acad Sci U S A. pubmed:30082399;  doi:10.1073/pnas.1805751115

26. Classification of prostate cancer using a protease activity nanosensor library. Dudani JS, Ibrahim M, Kirkpatrick J, Warren AD, Bhatia SN. Proc Natl Acad Sci U S A. pubmed:30126988;  doi:10.1073/pnas.1805337115

27. Pathologic findings in reduction mammoplasty specimens: a surrogate for the population prevalence of breast cancer and high-risk lesions. Acevedo F, Armengol VD, Deng Z, Tang R, Coopey SB, Braun D, Yala A, Barzilay R, Li C, Colwell A, Guidi A, Cetrulo CLJr, Garber J, Smith BL, King T, Hughes KS. Breast Cancer Res Treat. pubmed:30238276;  doi:10.1007/s10549-018-4962-0