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: December 2015

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1. Materials for Non-viral intracellular delivery of messenger RNA therapeutics. Kauffman KJ, Webber MJ, Anderson DG. J Control Release. pubmed:26718856;  doi:10.1016/j.jconrel.2015.12.032

2. Micropatterned coculture of primary human hepatocytes and supportive cells for the study of hepatotropic pathogens. March S, Ramanan V, Trehan K, Ng S, Galstian A, Gural N, Scull MA, Shlomai A, Mota MM, Fleming HE, Khetani SR, Rice CM, Bhatia SN. Nat Protoc. pubmed:26584444;  doi:10.1038/nprot.2015.128

3. Sustained, low-dose intraperitoneal cisplatin improves treatment outcome in ovarian cancer mouse models. Ye H, Tanenbaum LM, Na YJ, Mantzavinou A, Fulci G, Del Carmen MG, Birrer MJ, Cima MJ. J Control Release. pubmed:26548976;  doi:10.1016/j.jconrel.2015.11.001

4. Intravascular fibrin molecular imaging improves the detection of unhealed stents assessed by optical coherence tomography in vivo. Hara T, Ughi GJ, McCarthy JR, Erdem SS, Mauskapf A, Lyon SC, Fard AM, Edelman ER, Tearney GJ, Jaffer FA. Eur Heart J. pubmed:26685129;  doi:10.1093/eurheartj/ehv677

5. The role of aortic compliance in determination of coarctation severity: Lumped parameter modeling, in vitro study and clinical evaluation. Keshavarz-Motamed Z, Edelman ER, Motamed PK, Garcia J, Dahdah N, Kadem L. J Biomech. pubmed:26596718;  doi:10.1016/j.jbiomech.2015.10.017

6. A Multi-RNAi Microsponge Platform for Simultaneous Controlled Delivery of Multiple Small Interfering RNAs. Roh YH, Deng JZ, Dreaden EC, Park JH, Yun DS, Shopsowitz KE, Hammond PT. Angew Chem Int Ed Engl. pubmed:26695874;  doi:10.1002/anie.201508978

7. Self-Assembled Wound Dressings Silence MMP-9 and Improve Diabetic Wound Healing In Vivo. Castleberry SA, Almquist BD, Li W, Reis T, Chow J, Mayner S, Hammond PT. Adv Mater. pubmed:26695434;  doi:10.1002/adma.201503565

8. Uncharged Helical Modular Polypeptide Hydrogels for Cellular Scaffolds. Ahrens CC, Welch ME, Griffith LG, Hammond PT. Biomacromolecules. pubmed:26461932;  doi:10.1021/acs.biomac.5b01076

9. Supramolecular biomaterials. Webber MJ, Appel EA, Meijer EW, Langer R. Nat Mater. pubmed:26681596;  doi:10.1038/nmat4474

10. Repeatable and adjustable on-demand sciatic nerve block with phototriggerable liposomes. Rwei AY, Lee JJ, Zhan C, Liu Q, Ok MT, Shankarappa SA, Langer R, Kohane DS. Proc Natl Acad Sci U S A. pubmed:26644576;  doi:10.1073/pnas.1518791112

11. Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC. Integr Biol (Camb). pubmed:26481611;  doi:10.1039/c5ib00169b

12. Automated pipeline for rapid production and screening of HIV-specific monoclonal antibodies using pichia pastoris. Shah KA, Clark JJ, Goods BA, Politano TJ, Mozdzierz NJ, Zimnisky RM, Leeson RL, Love JC, Love KR. Biotechnol Bioeng. pubmed:26032261;  doi:10.1002/bit.25663

13. Photoactivated Spatiotemporally-Responsive Nanosensors of in Vivo Protease Activity. Dudani JS, Jain PK, Kwong GA, Stevens KR, Bhatia SN. ACS Nano. pubmed:26565752;  doi:10.1021/acsnano.5b05946

14. The polymer physics of single DNA confined in nanochannels. Dai L, Renner CB, Doyle PS. Adv Colloid Interface Sci. pubmed:26782150;  doi:10.1016/j.cis.2015.12.002

15. Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA. Cong P, Dai L, Chen H, van der Maarel JR, Doyle PS, Yan J. Biophys J. pubmed:26636945;  doi:10.1016/j.bpj.2015.10.016

16. Synthesis of Cell-Adhesive Anisotropic Multifunctional Particles by Stop Flow Lithography and Streptavidin-Biotin Interactions. Bong KW, Kim JJ, Cho H, Lim E, Doyle PS, Irimia D. Langmuir. pubmed:26545155;  doi:10.1021/acs.langmuir.5b03501

17. Tenuous Tether. Edelman ER, Weber BN. N Engl J Med. pubmed:26630141;  doi:10.1056/NEJMp1509265

18. A Flow Cytometric Clonogenic Assay Reveals the Single-Cell Potency of Doxorubicin. Maass KF, Kulkarni C, Quadir MA, Hammond PT, Betts AM, Wittrup KD. J Pharm Sci. pubmed:26344409;  doi:10.1002/jps.24631

19. Biomaterial Strategies for Immunomodulation. Hotaling NA, Tang L, Irvine DJ, Babensee JE. Annu Rev Biomed Eng. pubmed:26421896;  doi:10.1146/annurev-bioeng-071813-104814

20. Single-injection vaccines: Progress, challenges, and opportunities. McHugh KJ, Guarecuco R, Langer R, Jaklenec A. J Control Release. pubmed:26254198;  doi:10.1016/j.jconrel.2015.07.029

21. Characterization of the expression of the pro-metastatic Mena isoform during breast tumor progression. Oudin MJ, Hughes SK, Rohani N, Moufarrej MN, Jones JG, Condeelis JS, Lauffenburger DA, Gertler FB. Clin Exp Metastasis. pubmed:26680363;  doi:10.1007/s10585-015-9775-5

22. Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. Gaublomme JT, Yosef N, Lee Y, Gertner RS, Yang LV, Wu C, Pandolfi PP, Mak T, Satija R, Shalek AK, Kuchroo VK, Park H, Regev A. Cell. pubmed:26607794;  doi:10.1016/j.cell.2015.11.009

23. A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians. Wurtzel O, Cote LE, Poirier A, Satija R, Regev A, Reddien PW. Dev Cell. pubmed:26651295;  doi:10.1016/j.devcel.2015.11.004

24. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS. Mol Cell. pubmed:26638175;  doi:10.1016/j.molcel.2015.11.013

25. CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity. Wang C, Yosef N, Gaublomme J, Wu C, Lee Y, Clish CB, Kaminski J, Xiao S, Zu Horste GM, Pawlak M, Kishi Y, Joller N, Karwacz K, Zhu C, Ordovas-Montanes M, Madi A, Wortman I, Miyazaki T, Sobel RA, Park H, Regev A, Kuchroo VK. Cell. pubmed:26607793;  doi:10.1016/j.cell.2015.10.068

26. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Kowalczyk MS, Tirosh I, Heckl D, Rao TN, Dixit A, Haas BJ, Schneider RK, Wagers AJ, Ebert BL, Regev A. Genome Res. pubmed:26430063;  doi:10.1101/gr.192237.115

27. Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, Anders L, Tian L, Zhang S, Wei JS, Khan J, Bramlett K, Rahman N, Capasso M, Iolascon A, Gerhard DS, Guidry Auvil JM, Young RA, Hakonarson H, Diskin SJ, Look AT, Maris JM. Nature. pubmed:26560027;  doi:10.1038/nature15540

28. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P. Cell Syst. pubmed:26771021;  doi:10.1016/j.cels.2015.12.004

29. Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. Brennand KJ, Marchetto MC, Benvenisty N, Brustle O, Ebert A, Izpisua Belmonte JC, Kaykas A, Lancaster MA, Livesey FJ, McConnell MJ, McKay RD, Morrow EM, Muotri AR, Panchision DM, Rubin LL, Sawa A, Soldner F, Song H, Studer L, Temple S, Vaccarino FM, Wu J, Vanderhaeghen P, Gage FH, Jaenisch R. Stem Cell Reports. pubmed:26610635;  doi:10.1016/j.stemcr.2015.10.011

30. Designing a broad-spectrum integrative approach for cancer prevention and treatment. Block KI, Gyllenhaal C, Lowe L, Amedei A, Amin AR, Amin A, Aquilano K, Arbiser J, Arreola A, Arzumanyan A, Ashraf SS, Azmi AS, Benencia F, Bhakta D, Bilsland A, Bishayee A, Blain SW, Block PB, Boosani CS, Carey TE, Carnero A, Carotenuto M, Casey SC, Chakrabarti M, Chaturvedi R, Chen GZ, Chen H, Chen S, Chen YC, Choi BK, Ciriolo MR, Coley HM, Collins AR, Connell M, Crawford S, Curran CS, Dabrosin C, Damia G, Dasgupta S, DeBerardinis RJ, Decker WK, Dhawan P, Diehl AM, Dong JT, Dou QP, Drew JE, Elkord E, El-Rayes B, Feitelson MA, Felsher DW, Ferguson LR, Fimognari C, Firestone GL, Frezza C, Fujii H, Fuster MM, Generali D, Georgakilas AG, Gieseler F, Gilbertson M, Green MF, Grue B, Guha G, Halicka D, Helferich WG, Heneberg P, Hentosh P, Hirschey MD, Hofseth LJ, Holcombe RF, Honoki K, Hsu HY, Huang GS, Jensen LD, Jiang WG, Jones LW, Karpowicz PA, Keith WN, Kerkar SP, Khan GN, Khatami M, Ko YH, Kucuk O, Kulathinal RJ, Kumar NB, Kwon BS, Le A, Lea MA, Lee HY, Lichtor T, Lin LT, Locasale JW, Lokeshwar BL, Longo VD, Lyssiotis CA, MacKenzie KL, Malhotra M, Marino M, Martinez-Chantar ML, Matheu A, Maxwell C, McDonnell E, Meeker AK, Mehrmohamadi M, Mehta K, Michelotti GA, Mohammad RM, Mohammed SI, Morre DJ, Muralidhar V, Muqbil I, Murphy MP, Nagaraju GP, Nahta R, Niccolai E, Nowsheen S, Panis C, Pantano F, Parslow VR, Pawelec G, Pedersen PL, Poore B, Poudyal D, Prakash S, Prince M, Raffaghello L, Rathmell JC, Rathmell WK, Ray SK, Reichrath J, Rezazadeh S, Ribatti D, Ricciardiello L, Robey RB, Rodier F, Rupasinghe HP, Russo GL, Ryan EP, Samadi AK, Sanchez-Garcia I, Sanders AJ, Santini D, Sarkar M, Sasada T, Saxena NK, Shackelford RE, Shantha Kumara HM, Sharma D, Shin DM, Sidransky D, Siegelin MD, Signori E, Singh N, Sivanand S, Sliva D, Smythe C, Spagnuolo C, Stafforini DM, Stagg J, Subbarayan PR, Sundin T, Talib WH, Thompson SK, Tran PT, Ungefroren H, Vander Heiden MG, Venkateswaran V, Vinay DS, Vlachostergios PJ, Wang Z, Wellen KE, Whelan RL, Yang ES, Yang H, Yang X, Yaswen P, Yedjou C, Yin X, Zhu J, Zollo M. Semin Cancer Biol. pubmed:26590477;  doi:10.1016/j.semcancer.2015.09.007

31. Dysregulated metabolism contributes to oncogenesis. Hirschey MD, DeBerardinis RJ, Diehl AM, Drew JE, Frezza C, Green MF, Jones LW, Ko YH, Le A, Lea MA, Locasale JW, Longo VD, Lyssiotis CA, McDonnell E, Mehrmohamadi M, Michelotti G, Muralidhar V, Murphy MP, Pedersen PL, Poore B, Raffaghello L, Rathmell JC, Sivanand S, Vander Heiden MG, Wellen KE. Semin Cancer Biol. pubmed:26454069;  doi:10.1016/j.semcancer.2015.10.002

32. Human C9ORF72 Hexanucleotide Expansion Reproduces RNA Foci and Dipeptide Repeat Proteins but Not Neurodegeneration in BAC Transgenic Mice. Peters OM, Cabrera GT, Tran H, Gendron TF, McKeon JE, Metterville J, Weiss A, Wightman N, Salameh J, Kim J, Sun H, Boylan KB, Dickson D, Kennedy Z, Lin Z, Zhang YJ, Daughrity L, Jung C, Gao FB, Sapp PC, Horvitz HR, Bosco DA, Brown SP, de Jong P, Petrucelli L, Mueller C, Brown RHJr. Neuron. pubmed:26637797;  doi:10.1016/j.neuron.2015.11.018

33. Rhizobial peptidase HrrP cleaves host-encoded signaling peptides and mediates symbiotic compatibility. Price PA, Tanner HR, Dillon BA, Shabab M, Walker GC, Griffitts JS. Proc Natl Acad Sci U S A. pubmed:26401024;  doi:10.1073/pnas.1417797112

34. E7449: A dual inhibitor of PARP1/2 and tankyrase1/2 inhibits growth of DNA repair deficient tumors and antagonizes Wnt signaling. McGonigle S, Chen Z, Wu J, Chang P, Kolber-Simonds D, Ackermann K, Twine NC, Shie JL, Miu JT, Huang KC, Moniz GA, Nomoto K. Oncotarget. pubmed:26513298;  doi:10.18632/oncotarget.5846

35. Loss of the Rap-1 effector RIAM results in leukocyte adhesion deficiency due to impaired beta2 integrin function in mice. Klapproth S, Sperandio M, Pinheiro EM, Prunster M, Soehnlein O, Gertler FB, Fassler R, Moser M. Blood. pubmed:26337492;  doi:10.1182/blood-2015-05-647453

36. Rap1 and its effector riam are required for lymphocyte trafficking. Su W, Wynne J, Pinheiro EM, Strazza M, Mor A, Montenont E, Berger J, Paul DS, Bergmeier W, Gertler FB, Philips MR. Blood. pubmed:26324702;  doi:10.1182/blood-2015-05-644104

37. AMPA receptor inhibition by synaptically released zinc. Kalappa BI, Anderson CT, Goldberg JM, Lippard SJ, Tzounopoulos T. Proc Natl Acad Sci U S A. pubmed:26647187;  doi:10.1073/pnas.1512296112

38. A Platinum(IV) Pro-drug Preferentially Targets IDO Providing Enhanced Ovarian Cancer Immuno-Chemotherapy. Awuah SG, Zheng YR, Bruno PM, Hemann MT, Lippard SJ. J Am Chem Soc. pubmed:26561720;  doi:10.1021/jacs.5b10182