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: March 2017

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1. Genital-Systemic Chemokine Gradients and the Risk of HIV Acquisition in Women. Liebenberg LJ, Masson L, Arnold KB, Mckinnon LR, Werner L, Proctor E, Archary D, Mansoor LE, Lauffenburger DA, Abdool Karim Q, Abdool Karim SS, Passmore JS. J Acquir Immune Defic Syndrpubmed:28187085;  doi:10.1097/QAI.0000000000001218

2. Delivery technologies for genome editing. Yin H, Kauffman KJ, Anderson DG. Nat Rev Drug Discovpubmed:28337020;  doi:10.1038/nrd.2016.280

3. An RNA nanoparticle vaccine against Zika virus elicits antibody and CD8+ T cell responses in a mouse model. Chahal JS, Fang T, Woodham AW, Khan OF, Ling J, Anderson DG, Ploegh HL. Sci Reppubmed:28325910;  doi:10.1038/s41598-017-00193-w

4. Microfluidic Fabrication of Colloidal Nanomaterials-Encapsulated Microcapsules for Biomolecular Sensing. Xie X, Zhang W, Abbaspourrad A, Ahn J, Bader A, Bose S, Vegas A, Lin J, Tao J, Hang T, Lee H, Iverson N, Bisker G, Li L, Strano MS, Weitz DA, Anderson DG. Nano Lettpubmed:28152589;  doi:10.1021/acs.nanolett.7b00026

5. Towards a Humanized Mouse Model of Liver Stage Malaria Using Ectopic Artificial Livers. Ng S, March S, Galstian A, Gural N, Stevens KR, Mota MM, Bhatia SN. Sci Rep.pubmed:28361899;  doi:10.1038/srep45424

6. A Modular Toolkit for Generating Pichia pastoris Secretion Libraries. Obst U, Lu TK, Sieber V. ACS Synth Biolpubmed:28252957;  doi:10.1021/acssynbio.6b00337

7. Hydrogel Nanocomposites with Independently Tunable Rheology and Mechanics. Unterman S, Charles LF, Strecker SE, Kramarenko D, Pivovarchik D, Edelman ER, Artzi N. ACS Nano.pubmed:28221760;  doi:10.1021/acsnano.6b06730

8. Local remodeling of synthetic extracellular matrix microenvironments by co-cultured endometrial epithelial and stromal cells enables long-term dynamic physiological function. Cook CD, Hill AS, Guo M, Stockdale L, Papps JP, Isaacson KB, Lauffenburger DA, Griffith LG. Integr Biol (Camb)pubmed:28317948;  doi:10.1039/c6ib00245e

9. Multi-functional scaling methodology for translational pharmacokinetic and pharmacodynamic applications using integrated microphysiological systems (MPS). Maass C, Stokes CL, Griffith LG, Cirit M. Integr Biol (Camb)pubmed:28267162;  doi:10.1039/c6ib00243a

10. A process engineering approach to increase organoid yield. Arora N, Alsous JI, Guggenheim JW, Mak M, Munera J, Wells JM, Kamm RD, Asada HH, Shvartsman SY, Griffith LG. Development.pubmed:28174251;  doi:10.1242/dev.142919

11. Ligand-decorated click polypeptide derived nanoparticles for targeted drug delivery applications. Quadir MA, Morton SW, Mensah LB, Shopsowitz K, Dobbelaar J, Effenberger N, Hammond PT. Nanomedicinepubmed:28263813;  doi:10.1016/j.nano.2017.02.010

12. Colony stimulating factor-1 receptor is a central component of the foreign body response to biomaterial implants in rodents and non-human primates. Doloff JC, Veiseh O, Vegas AJ, Tam HH, Farah S, Ma M, Li J, Bader A, Chiu A, Sadraei A, Aresta-Dasilva S, Griffin M, Jhunjhunwala S, Webber M, Siebert S, Tang K, Chen M, Langan E, Dholokia N, Thakrar R, Qi M, Oberholzer J, Greiner DL, Langer R, Anderson DG. Nat Materpubmed:28319612;  doi:10.1038/nmat4866

13. Polymeric mechanical amplifiers of immune cytokine-mediated apoptosis. Mitchell MJ, Webster J, Chung A, Guimaraes PP, Khan OF, Langer R. Nat Commun.pubmed:28317839;  doi:10.1038/ncomms14179

14. Mixed Reversible Covalent Crosslink Kinetics Enable Precise, Hierarchical Mechanical Tuning of Hydrogel Networks. Yesilyurt V, Ayoob AM, Appel EA, Borenstein JT, Langer R, Anderson DG. Adv Materpubmed:28295624;  doi:10.1002/adma.201605947

15. Subcellular probes for neurochemical recording from multiple brain sites. Schwerdt HN, Kim MJ, Amemori S, Homma D, Yoshida T, Shimazu H, Yerramreddy H, Karasan E, Langer R, Graybiel AM, Cima MJ. Lab Chippubmed:28233001;  doi:10.1039/c6lc01398h

16. Direct single-cell biomass estimates for marine bacteria via Archimedes' principle. Cermak N, Becker JW, Knudsen SM, Chisholm SW, Manalis SR, Polz MF. ISME J.pubmed:27922599;  doi:10.1038/ismej.2016.161

17. Effect of internal architecture on microgel deformation in microfluidic constrictions. Chen L, Wang KX, Doyle PS. Soft Matterpubmed:28186522;  doi:10.1039/c6sm02674e

18. Structurally Programmed Assembly of Translation Initiation Nanoplex for Superior mRNA Delivery. Li J, Wang W, He Y, Li Y, Yan EZ, Zhang K, Irvine DJ, Hammond PT. ACS Nano.pubmed:28157292;  doi:10.1021/acsnano.6b08447

19. Investigating the cellular specificity in tumors of a surface converting nanoparticle by multimodal imaging. Fay F, Hansen L, Hectors SJ, Sanchez-Gaytan BL, Zhao Y, Tang J, Munitz J, Alaarg A, Braza MS, Gianella A, Aaronson SA, Reiner T, Kjems J, Langer R, Hoeben FJ, Janssen HM, Calcagno C, Strijkers GJ, Fayad ZA, Perez-Medina C, Mulder WJ. Bioconjug Chem.pubmed:28316241;  doi:10.1021/acs.bioconjchem.7b00086

20. Lipid Nanoparticle Assisted mRNA Delivery for Potent Cancer Immunotherapy. Oberli MA, Reichmuth AM, Dorkin JR, Mitchell MJ, Fenton OS, Jaklenec A, Anderson DG, Langer R, Blankschtein D. Nano Lettpubmed:28273716;  doi:10.1021/acs.nanolett.6b03329

21. Enhancing Adoptive Cell Therapy of Cancer through Targeted Delivery of Small-Molecule Immunomodulators to Internalizing or Non-Internalizing Receptors. Zheng Y, Tang L, Mabardi L, Kumari S, Irvine DJ. ACS Nanopubmed:28231431;  doi:10.1021/acsnano.7b00078

22. Smart Radiation Therapy Biomaterials. Ngwa W, Boateng F, Kumar R, Irvine DJ, Formenti S, Ngoma T, Herskind C, Veldwijk MR, Hildenbrand GL, Hausmann M, Wenz F, Hesser J. Int J Radiat Oncol Biol Physpubmed:28126309;  doi:10.1016/j.ijrobp.2016.10.034

23. US immigration order strikes against biotech. Levin JM, Holtzman SH, Maraganore J, Hastings PJ, Cohen R, Dahiyat B, Adams J, Adams C, Ahrens B, Albers J, Aspinall MG, Audia JE, Babler M, Barrett P, Barry Z, Bermingham N, Bloch S, Blum RI, Bolno PB, Bonney MW, Booth B, Bradbury DM, Brauer SK, Byers B, Cagnoni PJ, Cali BM, Ciechanover I, Clark C, Clayman MD, Cleland JL, Cobb P, Cooper R, Currie MG, Diekman J, Dobmeier EL, Doerfler D, Donley EL, Dunsire D, During M, Eckstein JW, Elenko E, Exter NA, Fleming JJ, Flesher GJ, Formela JF, Forrester R, Francois C, Franklin H, Freeman MW, Furst H, Gage LP, Galakatos N, Gallagher BM, Geraghty JA, Gill S, Goeddel DV, Goldsmith MA, Gowen M, Goyal V, Graney T, Grayzel D, Greene B, Grint P, Gutierrez-Ramos JC, Haney B, Ha-Ngoc T, Harris T, Hasnain F, Hata YS, Hecht P, Henshaw L, Heyman R, Hoppenot H, Horvitz HR, Hughes TE, Hutton WS, Isaacs ST, Jenkins A, Jonker J, Kaplan J, Karsen P, Keiper J, Kim J, Kindler J, King R, King V, Kjellson N, Koenig S, Koenig G, Kolchinsky P, Laikind P, Langer RB, Lee JJ, Leff JS, Leicher BA, Leschly N, Levin A, Levin M, Levine AJ, Levy A, Liu DR, Lodish HF, Lopatin U, Love TW, Macdonald G, Maderis GJ, Mahadevia A, Mahanthappa NK, Martin JF, Martin A, Martucci WE, McArthur JG, McCann CM, McCarthy SA, McDonough CG, Mendlein J, Miller L, Miralles D, Moch KI, More B, Myers AG, Narachi MA, Nashat A, Nelson W, Newell WJ, Olle B, Osborn JE, Owens JC, Pande A, Papadopoulos S, Parker HS, Parmar KM, Patterson MR, Paul SM, Perez R, Perry M, Pfeffer CG, Powell M, Pruzanski M, Purcell DJ, Rakhit A, Ramamoorthi K, Rastetter W, Rawcliffe AA, Reid LE, Renaud RC, Rhodes JP, Rieflin WJ, Robins C, Rocklage SM, Rosenblatt M, Rosin JG, Rutter WJ, Saha S, Samuels C, Sato VL, Scangos G, Scarlett JA, Schenkein D, Schreiber SL, Schwab A, Sekhri P, Shah R, Shenk T, Siegall CB, Simon NJ, Simonian N, Stein J, Su M, Szela MT, Taglietti M, Tandon N, Termeer H, Thornberry NA, Tolar M, Ulevitch R, Vaishnaw AK, VanLent A, Varsavsky M, Vlasuk GP, Vounatsos M, Waksal SG, Warma N, Watts RJ, Werber Y, Westphal C, Wierenga W, Williams DE, Williams LR, Xanthopoulos KG, Zohar D, Zweifach SS. Nat Biotechnolpubmed:28267733;  doi:10.1038/nbt.3824

24. 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

25. A Phase Separation Model for Transcriptional Control. Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA. Cellpubmed:28340338;  doi:10.1016/j.cell.2017.02.007

26. Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis. Suzuki HI, Young RA, Sharp PA. Cellpubmed:28283057;  doi:10.1016/j.cell.2017.02.015

27. Activation of the LMO2 oncogene through a somatically acquired neomorphic promoter in T-cell acute lymphoblastic leukemia. Rahman S, Magnussen M, Leon TE, Farah N, Li Z, Abraham BJ, Alapi KZ, Mitchell RJ, Naughton T, Fielding AK, Pizzey A, Bustraan S, Allen C, Popa T, Pike-Overzet K, Garcia-Perez L, Gale RE, Linch DC, Staal FJ, Young RA, Look AT, Mansour MR. Blood.pubmed:28270453;  doi:10.1182/blood-2016-09-742148

28. Genome Sequencing Technologies and Nursing: What Are the Roles of Nurses and Nurse Scientists? Taylor JY, Wright ML, Hickey KT, Housman DE. Nurs Res.pubmed:28252579;  doi:10.1097/NNR.0000000000000211

29. Engineered erythrocytes covalently linked to antigenic peptides can protect against autoimmune disease. Pishesha N, Bilate AM, Wibowo MC, Huang NJ, Li Z, Dhesycka R, Bousbaine D, Li H, Patterson HC, Dougan SK, Maruyama T, Lodish HF, Ploegh HL. Proc Natl Acad Sci U S Apubmed:28270614;  doi:10.1073/pnas.1701746114

30. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Venteicher AS, Tirosh I, Hebert C, Yizhak K, Neftel C, Filbin MG, Hovestadt V, Escalante LE, Shaw ML, Rodman C, Gillespie SM, Dionne D, Luo CC, Ravichandran H, Mylvaganam R, Mount C, Onozato ML, Nahed BV, Wakimoto H, Curry WT, Iafrate AJ, Rivera MN, Frosch MP, Golub TR, Brastianos PK, Getz G, Patel AP, Monje M, Cahill DP, Rozenblatt-Rosen O, Louis DN, Bernstein BE, Regev A, Suva ML. Sciencepubmed:28360267;  doi:10.1126/science.aai8478

31. Purine synthesis promotes maintenance of brain tumor initiating cells in glioma. Wang X, Yang K, Xie Q, Wu Q, Mack SC, Shi Y, Kim LJ, Prager BC, Flavahan WA, Liu X, Singer M, Hubert CG, Miller TE, Zhou W, Huang Z, Fang X, Regev A, Suva ML, Hwang TH, Locasale JW, Bao S, Rich JN. Nat Neuroscipubmed:28346452;  doi:10.1038/nn.4537

32. Rapid capture and labeling of cells on single domain antibodies-functionalized flow cell. Chen GY, Li Z, Duarte JN, Esteban A, Cheloha RW, Theile CS, Fink GR, Ploegh HL. Biosens Bioelectron.pubmed:27816596;  doi:10.1016/j.bios.2016.10.015

33. Induction of Expansion and Folding in Human Cerebral Organoids. Li Y, Muffat J, Omer A, Bosch I, Lancaster MA, Sur M, Gehrke L, Knoblich JA, Jaenisch R. Cell Stem Cell.pubmed:28041895;  doi:10.1016/j.stem.2016.11.017

34. ANGPTL3 Deficiency and Protection Against Coronary Artery Disease. Stitziel NO, Khera AV, Wang X, Bierhals AJ, Vourakis AC, Sperry AE, Natarajan P, Klarin D, Emdin CA, Zekavat SM, Nomura A, Erdmann J, Schunkert H, Samani NJ, Kraus WE, Shah SH, Yu B, Boerwinkle E, Rader DJ, Gupta N, Frossard PM, Rasheed A, Danesh J, Lander ES, Gabriel S, Saleheen D, Musunuru K, Kathiresan S. J Am Coll Cardiolpubmed:28385496;  doi:10.1016/j.jacc.2017.02.030

35. Functional Selectivity in Cytokine Signaling Revealed Through a Pathogenic EPO Mutation. Kim AR, Ulirsch JC, Wilmes S, Unal E, Moraga I, Karakukcu M, Yuan D, Kazerounian S, Abdulhay NJ, King DS, Gupta N, Gabriel SB, Lander ES, Patiroglu T, Ozcan A, Ozdemir MA, Garcia KC, Piehler J, Gazda HT, Klein DE, Sankaran VG. Cellpubmed:28283061;  doi:10.1016/j.cell.2017.02.026

36. Association of Rare and Common Variation in the Lipoprotein Lipase Gene With Coronary Artery Disease. Khera AV, Won HH, Peloso GM, O'Dushlaine C, Liu D, Stitziel NO, Natarajan P, Nomura A, Emdin CA, Gupta N, Borecki IB, Asselta R, Duga S, Merlini PA, Correa A, Kessler T, Wilson JG, Bown MJ, Hall AS, Braund PS, Carey DJ, Murray MF, Kirchner HL, Leader JB, Lavage DR, Manus JN, Hartzel DN, Samani NJ, Schunkert H, Marrugat J, Elosua R, McPherson R, Farrall M, Watkins H, Lander ES, Rader DJ, Danesh J, Ardissino D, Gabriel S, Willer C, Abecasis GR, Saleheen D, Dewey FE, Kathiresan S. JAMApubmed:28267856;  doi:10.1001/jama.2017.0972

37. Maximizing Synergistic Activity When Combining RNAi and Platinum-Based Anticancer Agents. Xiao H, Qi R, Li T, Awuah SG, Zheng Y, Wei W, Kang X, Song H, Wang Y, Yu Y, Bird MA, Jing X, Yaffe MB, Birrer MJ, Ghoroghchian PP. J Am Chem Socpubmed:28166401;  doi:10.1021/jacs.6b12108

38. 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

39. Mutations that Allow SIR2 Orthologs to Function in a NAD+-Depleted Environment. Ondracek CR, Frappier V, Ringel AE, Wolberger C, Guarente L. Cell Rep.pubmed:28273448;  doi:10.1016/j.celrep.2017.02.031

40. Nucleosomes influence multiple steps during replication initiation. Azmi IF, Watanabe S, Maloney MF, Kang S, Belsky JA, MacAlpine DM, Peterson CL, Bell SP. Elife.pubmed:28322723;  doi:10.7554/eLife.22512

41. Mechanism and timing of Mcm2-7 ring closure during DNA replication origin licensing. Ticau S, Friedman LJ, Champasa K, Correa IRJr, Gelles J, Bell SP. Nat Struct Mol Biol.pubmed:28191892;  doi:10.1038/nsmb.3375

42. The CDK8 Complex and Proneural Proteins Together Drive Neurogenesis from a Mesodermal Lineage. Luo S, Horvitz HR. Curr Biolpubmed:28238659;  doi:10.1016/j.cub.2017.01.056

43. Insulin-like signalling to the maternal germline controls progeny response to osmotic stress. Burton NO, Furuta T, Webster AK, Kaplan RE, Baugh LR, Arur S, Horvitz HR. Nat Cell Biol.pubmed:28166192;  doi:10.1038/ncb3470

44. mTOR Signaling in Growth, Metabolism, and Disease. Saxton RA, Sabatini DM. Cellpubmed:28283069;  doi:10.1016/j.cell.2017.02.004

45. KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1. Wolfson RL, Chantranupong L, Wyant GA, Gu X, Orozco JM, Shen K, Condon KJ, Petri S, Kedir J, Scaria SM, Abu-Remaileh M, Frankel WN, Sabatini DM. Naturepubmed:28199306;  doi:10.1038/nature21423

46. Mex3a Marks a Slowly Dividing Subpopulation of Lgr5+ Intestinal Stem Cells. Barriga FM, Montagni E, Mana M, Mendez-Lago M, Hernando-Momblona X, Sevillano M, Guillaumet-Adkins A, Rodriguez-Esteban G, Buczacki SJ, Gut M, Heyn H, Winton DJ, Yilmaz OH, Attolini CS, Gut I, Batlle E. Cell Stem Cellpubmed:28285904;  doi:10.1016/j.stem.2017.02.007

47. The creatine kinase pathway is a metabolic vulnerability in EVI1-positive acute myeloid leukemia. Fenouille N, Bassil CF, Ben-Sahra I, Benajiba L, Alexe G, Ramos A, Pikman Y, Conway AS, Burgess MR, Li Q, Luciano F, Auberger P, Galinsky I, DeAngelo DJ, Stone RM, Zhang Y, Perkins AS, Shannon K, Hemann MT, Puissant A, Stegmaier K. Nat Med.pubmed:28191887;  doi:10.1038/nm.4283

48. Cutting Edge: Loss of T Cell RIAM Precludes Conjugate Formation with APC and Prevents Immune-Mediated Diabetes. Lagarrigue F, Gertler FB, Ginsberg MH, Cantor JM. J Immunol.pubmed:28348273;  doi:10.4049/jimmunol.1601743

49. Evolving policy with science. Charo RA, Hynes RO. Sciencepubmed:28254888;  doi:10.1126/science.aan0509

50. 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

51. 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

52. LACTB is a tumour suppressor that modulates lipid metabolism and cell state. Keckesova Z, Donaher JL, De Cock J, Freinkman E, Lingrell S, Bachovchin DA, Bierie B, Tischler V, Noske A, Okondo MC, Reinhardt F, Thiru P, Golub TR, Vance JE, Weinberg RA. Naturepubmed:28329758;  doi:10.1038/nature21408

53. Integrin-beta4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells. Bierie B, Pierce SE, Kroeger C, Stover DG, Pattabiraman DR, Thiru P, Liu Donaher J, Reinhardt F, Chaffer CL, Keckesova Z, Weinberg RA. Proc Natl Acad Sci U S Apubmed:28270621;  doi:10.1073/pnas.1618298114

54. Science Signaling Podcast for 14 March 2017: The Cancer Moonshot. Yaffe MB, VanHook AM. Sci Signalpubmed:28292953;  doi:10.1126/scisignal.aan1418