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 2018

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1. A model of dormant-emergent metastatic breast cancer progression enabling exploration of biomarker signatures. Clark AM, Kumar M, Wheeler S, Young C, Venkataramanan R, Stolz D, Griffith L, Lauffenburger DA, Wells A. Mol Cell Proteomicspubmed:29353230;  doi:10.1074/mcp.RA117.000370

2. Circulating Magnetic Microbubbles for Localized Real-Time Control of Drug Delivery by Ultrasonography-Guided Magnetic Targeting and Ultrasound. Chertok B, Langer R. Theranosticspubmed:29290812;  doi:10.7150/thno.20781

3. Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes. Gee MH, Han A, Lofgren SM, Beausang JF, Mendoza JL, Birnbaum ME, Bethune MT, Fischer S, Yang X, Gomez-Eerland R, Bingham DB, Sibener LV, Fernandes RA, Velasco A, Baltimore D, Schumacher TN, Khatri P, Quake SR, Davis MM, Garcia KC. Cellpubmed:29275860;  doi:10.1016/j.cell.2017.11.043

4. Functional Genomics Approach Identifies Novel Signaling Regulators of TGFalpha Ectodomain Shedding. Wilson JL, Kefalogianni E, Stopfer L, Harrison C, Sabbisetti VS, Fraenkel E, Lauffenburger DA, Herrlich A. Mol Cancer Respubmed:29018056;  doi:10.1158/1541-7786.MCR-17-0140

5. Quantitative Analysis of Tyrosine Kinase Signaling Across Differentially Embedded Human Glioblastoma Tumors. Johnson H, White FM. Methods Mol Biolpubmed:29344889;  doi:10.1007/978-1-4939-7493-1_8

6. Src Homology 2 domains enhance tyrosine phosphorylation in vivo by protecting binding sites in their target proteins from dephosphorylation. Jadwin JA, Curran TG, Lafontaine AT, White FM, Mayer BJ. J Biol Chempubmed:29162725;  doi:10.1074/jbc.M117.794412

7. Rapamycin activates TGF receptor independently of its ligand: implications for endothelial dysfunction. Miyakawa AA, Girao-Silva T, Krieger JE, Edelman ER. Clin Sci (Lond)pubmed:29343616;  doi:10.1042/CS20171457

8. Inhibiting Integrin alpha5 Cytoplasmic Domain Signaling Reduces Atherosclerosis and Promotes Arteriogenesis. Budatha M, Zhang J, Zhuang ZW, Yun S, Dahlman JE, Anderson DG, Schwartz MA. J Am Heart Assocpubmed:29382667;  doi:10.1161/JAHA.117.007501

9. Engineered 3D-printed artificial axons. Espinosa-Hoyos D, Jagielska A, Homan KA, Du H, Busbee T, Anderson DG, Fang NX, Lewis JA, Van Vliet KJ. Sci Reppubmed:29323240;  doi:10.1038/s41598-017-18744-6

10. Engineered Livers for Infectious Diseases. Gural N, Mancio-Silva L, He J, Bhatia SN. Cell Mol Gastroenterol Hepatolpubmed:29322086;  doi:10.1016/j.jcmgh.2017.11.005

11. Catheter-based renal denervation in hypertension: heading for new shores. Mahfoud F, Bohm M, Edelman ER. J Hypertenspubmed:29210859;  doi:10.1097/HJH.0000000000001614

12. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Yin H, Song CQ, Suresh S, Kwan SY, Wu Q, Walsh S, Ding J, Bogorad RL, Zhu LJ, Wolfe SA, Koteliansky V, Xue W, Langer R, Anderson DG. Nat Chem Biolpubmed:29377001;  doi:10.1038/nchembio.2559

13. Miniaturized neural system for chronic, local intracerebral drug delivery. Dagdeviren C, Ramadi KB, Joe P, Spencer K, Schwerdt HN, Shimazu H, Delcasso S, Amemori KI, Nunez-Lopez C, Graybiel AM, Cima MJ, Langer R. Sci Transl Medpubmed:29367347;  doi:10.1126/scitranslmed.aan2742

14. Development of an oral once-weekly drug delivery system for HIV antiretroviral therapy. Kirtane AR, Abouzid O, Minahan D, Bensel T, Hill AL, Selinger C, Bershteyn A, Craig M, Mo SS, Mazdiyasni H, Cleveland C, Rogner J, Lee YL, Booth L, Javid F, Wu SJ, Grant T, Bellinger AM, Nikolic B, Hayward A, Wood L, Eckhoff PA, Nowak MA, Langer R, Traverso G. Nat Communpubmed:29317618;  doi:10.1038/s41467-017-02294-6

15. Molecular rotors for universal quantitation of nanoscale hydrophobic interfaces in microplate format. Bisso PW, Tai M, Katepalli H, Bertrand N, Blankschtein D, Langer R. Nano Lettpubmed:29244511;  doi:10.1021/acs.nanolett.7b04877

16. Prediction of Broad-spectrum Pathogen Attachment to Coating Materials for Biomedical Devices. Mikulskis P, Hook AL, Dundas A, Irvine DJ, Sanni O, Anderson DG, Langer R, Alexander MR, Williams P, Winkler DA. ACS Appl Mater Interfacespubmed:29191009;  doi:10.1021/acsami.7b14197

17. The development of bioresorbable composite polymeric implants with high mechanical strength. Sharma U, Concagh D, Core L, Kuang Y, You C, Pham Q, Zugates G, Busold R, Webber S, Merlo J, Langer R, Whitesides GM, Palasis M. Nat Materpubmed:29180778;  doi:10.1038/nmat5016

18. Sex differences in the outcomes of stent implantation in mini-swine model. Kunio M, Wong G, Markham PM, Edelman ER. PLoS Onepubmed:29377941;  doi:10.1371/journal.pone.0192004

19. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, Choudhury AD, Gydush G, Reed SC, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TR, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. J Clin Oncolpubmed:29298117;  doi:10.1200/JCO.2017.76.0033

20. Cover Image, Volume 115, Number 1, January 2018. Matthews CB, Kuo A, Love KR, Love JC. Biotechnol Bioengpubmed:29165792;  doi:10.1002/bit.26409

21. Development of a general defined medium for Pichia pastoris. Matthews CB, Kuo A, Love KR, Love JC. Biotechnol Bioengpubmed:28865117;  doi:10.1002/bit.26440

22. Targeting minimal residual disease: a path to cure?. Luskin MR, Murakami MA, Manalis SR, Weinstock DM. Nat Rev Cancerpubmed:29376520;  doi:10.1038/nrc.2017.125

23. Versatile and on-demand biologics co-production in yeast. Cao J, Perez-Pinera P, Lowenhaupt K, Wu MR, Purcell O, de la Fuente-Nunez C, Lu TK. Nat Communpubmed:29311542;  doi:10.1038/s41467-017-02587-w

24. 3D Printing of Living Responsive Materials and Devices. Liu X, Yuk H, Lin S, Parada GA, Tang TC, Tham E, de la Fuente-Nunez C, Lu TK, Zhao X. Adv Materpubmed:29205532;  doi:10.1002/adma.201704821

25. Expansion microscopy: development and neuroscience applications. Karagiannis ED, Boyden ES. Curr Opin Neurobiolpubmed:29316506;  doi:10.1016/j.conb.2017.12.012

26. Multi-neuron intracellular recording in vivo via interacting autopatching robots. Kodandaramaiah SB, Flores FJ, Holst GL, Singer AC, Han X, Brown EN, Boyden ES, Forest CR. Elifepubmed:29297466;  doi:10.7554/eLife.24656

27. Glyoxal as an alternative fixative to formaldehyde in immunostaining and super-resolution microscopy. Richter KN, Revelo NH, Seitz KJ, Helm MS, Sarkar D, Saleeb RS, D'Este E, Eberle J, Wagner E, Vogl C, Lazaro DF, Richter F, Coy-Vergara J, Coceano G, Boyden ES, Duncan RR, Hell SW, Lauterbach MA, Lehnart SE, Moser T, Outeiro T, Rehling P, Schwappach B, Testa I, Zapiec B, Rizzoli SO. EMBO Jpubmed:29146773;  doi:10.15252/embj.201695709

28. Machine learning to parse breast pathology reports in Chinese. Tang R, Ouyang L, Li C, He Y, Griffin M, Taghian A, Smith B, Yala A, Barzilay R, Hughes K. Breast Cancer Res Treatpubmed:29380208;  doi:10.1007/s10549-018-4668-3

29. A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers. Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG. Genome Biolpubmed:29378643;  doi:10.1186/s13059-017-1385-x

30. Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells. Gaya M, Barral P, Burbage M, Aggarwal S, Montaner B, Warren Navia A, Aid M, Tsui C, Maldonado P, Nair U, Ghneim K, Fallon PG, Sekaly RP, Barouch DH, Shalek AK, Bruckbauer A, Strid J, Batista FD. Cellpubmed:29249358;  doi:10.1016/j.cell.2017.11.036

31. Reduction of Nonspecificity Motifs in Synthetic Antibody Libraries. Kelly RL, Le D, Zhao J, Wittrup KD. J Mol Biolpubmed:29183788;  doi:10.1016/j.jmb.2017.11.008

32. Nanoparticle anchoring targets immune agonists to tumors enabling anti-cancer immunity without systemic toxicity. Zhang Y, Li N, Suh H, Irvine DJ. Nat Communpubmed:29295974;  doi:10.1038/s41467-017-02251-3

33. Intratumoral CD8+ T-Cell Apoptosis is a Major Component of T Cell Dysfunction and Impedes Anti-Tumor Immunity. Horton BL, Williams JB, Cabanov A, Spranger S, Gajewski TF. Cancer Immunol Respubmed:29097422;  doi:10.1158/2326-6066.CIR-17-0249

34. Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP. Chiu AC, Suzuki HI, Wu X, Mahat DB, Kriz AJ, Sharp PA. Mol Cellpubmed:29398447;  doi:10.1016/j.molcel.2018.01.006

35. Suppression of Adaptive Responses to Targeted Cancer Therapy by Transcriptional Repression. Rusan M, Li K, Li Y, Christensen CL, Abraham BJ, Kwiatkowski N, Buczkowski KA, Bockorny B, Chen T, Li S, Rhee K, Zhang H, Chen W, Terai H, Tavares T, Leggett AL, Li T, Wang Y, Zhang T, Kim TJ, Hong SH, Poudel-Neupane N, Silkes M, Mudianto T, Tan L, Shimamura T, Meyerson M, Bass AJ, Watanabe H, Gray NS, Young RA, Wong KK, Hammerman PS. Cancer Discovpubmed:29054992;  doi:10.1158/2159-8290.CD-17-0461

36. Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow. Murphy PA, Butty VL, Boutz PL, Begum S, Kimble AL, Sharp PA, Burge CB, Hynes RO. Elifepubmed:29293084;  doi:10.7554/eLife.29494

37. Impact of oncogenic pathways on evasion of antitumour immune responses. Spranger S, Gajewski TF. Nat Rev Cancerpubmed:29326431;  doi:10.1038/nrc.2017.117

38. The redox requirements of proliferating mammalian cells. Hosios AM, Vander Heiden MG. J Biol Chempubmed:29339555;  doi:10.1074/jbc.TM117.000239

39. A homozygous deleterious CDK10 mutation in a patient with agenesis of corpus callosum, retinopathy, and deafness. Guen VJ, Edvardson S, Fraenkel ND, Fattal-Valevski A, Jalas C, Anteby I, Shaag A, Dor T, Gillis D, Kerem E, Lees JA, Colas P, Elpeleg O. Am J Med Genet Apubmed:29130579;  doi:10.1002/ajmg.a.38506

40. Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018. Galluzzi L, Vitale I, Aaronson SA, Abrams JM, Adam D, Agostinis P, Alnemri ES, Altucci L, Amelio I, Andrews DW, Annicchiarico-Petruzzelli M, Antonov AV, Arama E, Baehrecke EH, Barlev NA, Bazan NG, Bernassola F, Bertrand MJM, Bianchi K, Blagosklonny MV, Blomgren K, Borner C, Boya P, Brenner C, Campanella M, Candi E, Carmona-Gutierrez D, Cecconi F, Chan FK, Chandel NS, Cheng EH, Chipuk JE, Cidlowski JA, Ciechanover A, Cohen GM, Conrad M, Cubillos-Ruiz JR, Czabotar PE, D'Angiolella V, Dawson TM, Dawson VL, De Laurenzi V, De Maria R, Debatin KM, DeBerardinis RJ, Deshmukh M, Di Daniele N, Di Virgilio F, Dixit VM, Dixon SJ, Duckett CS, Dynlacht BD, El-Deiry WS, Elrod JW, Fimia GM, Fulda S, Garcia-Saez AJ, Garg AD, Garrido C, Gavathiotis E, Golstein P, Gottlieb E, Green DR, Greene LA, Gronemeyer H, Gross A, Hajnoczky G, Hardwick JM, Harris IS, Hengartner MO, Hetz C, Ichijo H, Jaattela M, Joseph B, Jost PJ, Juin PP, Kaiser WJ, Karin M, Kaufmann T, Kepp O, Kimchi A, Kitsis RN, Klionsky DJ, Knight RA, Kumar S, Lee SW, Lemasters JJ, Levine B, Linkermann A, Lipton SA, Lockshin RA, Lopez-Otin C, Lowe SW, Luedde T, Lugli E, MacFarlane M, Madeo F, Malewicz M, Malorni W, Manic G, Marine JC, Martin SJ, Martinou JC, Medema JP, Mehlen P, Meier P, Melino S, Miao EA, Molkentin JD, Moll UM, Munoz-Pinedo C, Nagata S, Nunez G, Oberst A, Oren M, Overholtzer M, Pagano M, Panaretakis T, Pasparakis M, Penninger JM, Pereira DM, Pervaiz S, Peter ME, Piacentini M, Pinton P, Prehn JHM, Puthalakath H, Rabinovich GA, Rehm M, Rizzuto R, Rodrigues CMP, Rubinsztein DC, Rudel T, Ryan KM, Sayan E, Scorrano L, Shao F, Shi Y, Silke J, Simon HU, Sistigu A, Stockwell BR, Strasser A, Szabadkai G, Tait SWG, Tang D, Tavernarakis N, Thorburn A, Tsujimoto Y, Turk B, Vanden Berghe T, Vandenabeele P, Vander Heiden MG, Villunger A, Virgin HW, Vousden KH, Vucic D, Wagner EF, Walczak H, Wallach D, Wang Y, Wells JA, Wood W, Yuan J, Zakeri Z, Zhivotovsky B, Zitvogel L, Melino G, Kroemer G. Cell Death Differpubmed:29362479;  doi:10.1038/s41418-017-0012-4

41. RNA-Peptide nanoplexes drug DNA damage pathways in high-grade serous ovarian tumors. Dreaden EC, Kong YW, Quadir MA, Correa S, Suarez-Lopez L, Barberio AE, Hwang MK, Shi AC, Oberlton B, Gallagher PN, Shopsowitz KE, Elias KM, Yaffe MB, Hammond PT. Bioeng Transl Medpubmed:29376131;  doi:10.1002/btm2.10086

42. Premature polyadenylation of MAGI3 is associated with diminished N(6)-methyladenosine in its large internal exon. Ni TK, Elman JS, Jin DX, Gupta PB, Kuperwasser C. Sci Reppubmed:29362392;  doi:10.1038/s41598-018-19916-8

43. Predicting the future of signaling for 2018. Yaffe MB. Sci Signalpubmed:29295956;  doi:10.1126/scisignal.aar7429

44. Discovery of a 29-amino-acid reactive abiotic peptide for selective cysteine arylation. Evans ED, Pentelute BL. ACS Chem Biolpubmed:29283243;  doi:10.1021/acschembio.7b00520