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: November 2018

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1. Creatine kinase pathway inhibition alters GSK3 and WNT signaling in EVI1-positive AML. Benajiba L, Alexe G, Su A, Raffoux E, Soulier J, Hemann MT, Hermine O, Itzykson R, Stegmaier K, Puissant A. Leukemia. pubmed:30390009;  doi:10.1038/s41375-018-0291-x

2. Intercepting Pancreatic Cancer: Our Dream Team's Resolve to Stop Pancreatic Cancer. Goggins MG, Lippman SM, Constantinou PE, Jacks T, Petersen GM, Syngal S, Maitra A. Pancreas. pubmed:30325853;  doi:10.1097/MPA.0000000000001165

3. Yap regulates glucose utilization and sustains nucleotide synthesis to enable organ growth. Cox AG, Tsomides A, Yimlamai D, Hwang KL, Miesfeld J, Galli GG, Fowl BH, Fort M, Ma KY, Sullivan MR, Hosios AM, Snay E, Yuan M, Brown KK, Lien EC, Chhangawala S, Steinhauser ML, Asara JM, Houvras Y, Link B, Vander Heiden MG, Camargo FD, Goessling W. EMBO J. pubmed:30348863;  doi:10.15252/embj.2018100294

4. Cytosolic Aspartate Availability Determines Cell Survival When Glutamine Is Limiting. Alkan HF, Walter KE, Luengo A, Madreiter-Sokolowski CT, Stryeck S, Lau AN, Al-Zoughbi W, Lewis CA, Thomas CJ, Hoefler G, Graier WF, Madl T, Vander Heiden MG, Bogner-Strauss JG. Cell Metab. pubmed:30122555;  doi:10.1016/j.cmet.2018.07.021

5. New insights into the mechanisms of epithelial-mesenchymal transition and implications for cancer. Dongre A, Weinberg RA. Nat Rev Mol Cell Biol. pubmed:30459476;  doi:10.1038/s41580-018-0080-4

6. Widespread Accumulation of Ribosome-Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain. Sudmant PH, Lee H, Dominguez D, Heiman M, Burge CB. Cell Rep. pubmed:30485811;  doi:10.1016/j.celrep.2018.10.094

7. Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region. Moffitt JR, Bambah-Mukku D, Eichhorn SW, Vaughn E, Shekhar K, Perez JD, Rubinstein ND, Hao J, Regev A, Dulac C, Zhuang X. Science. pubmed:30385464;  doi:10.1126/science.aau5324

8. Whole Genome Sequencing to Characterize Monogenic and Polygenic Contributions in Patients Hospitalized with Early-Onset Myocardial Infarction. Khera AV, Chaffin M, Zekavat SM, Collins RL, Roselli C, Natarajan P, Lichtman JH, D'Onofrio G, Mattera JA, Dreyer RP, Spertus JA, Taylor KD, Psaty BM, Rich SS, Post WS, Gupta N, Gabriel S, Lander E, Chen YI, Talkowski ME, Rotter JI, Krumholz HM, Kathiresan S. Circulation. pubmed:30586733;  doi:10.1161/CIRCULATIONAHA.118.035658

9. iRGD-guided tumor-penetrating nanocomplexes for therapeutic siRNA delivery to pancreatic cancer. Lo JH, Hao L, Muzumdar MD, Raghavan S, Kwon EJ, Pulver EM, Hsu F, Aguirre AJ, Wolpin BM, Fuchs CS, Hahn WC, Jacks T, Bhatia SN. Mol Cancer Ther. pubmed:30097486;  doi:10.1158/1535-7163.MCT-17-1090

10. Publisher Correction: 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:30279576;  doi:10.1038/s41586-018-0584-2

11. The Rb tumor suppressor regulates epithelial cell migration and polarity. Parisi T, Balsamo M, Gertler F, Lees JA. Mol Carcinog. pubmed:30084175;  doi:10.1002/mc.22886

12. SFXN1 is a mitochondrial serine transporter required for one-carbon metabolism. Kory N, Wyant GA, Prakash G, Uit de Bos J, Bottanelli F, Pacold ME, Chan SH, Lewis CA, Wang T, Keys HR, Guo YE, Sabatini DM. Science. pubmed:30442778;  doi:10.1126/science.aat9528

13. A SUBSET OF FIVE HUMAN MITOCHONDRIAL FORMYL PEPTIDES MIMICS BACTERIAL PEPTIDES AND FUNCTIONALLY DEACTIVATES HUMAN NEUETROPHILS. Kaczmarek E, Hauser CJ, Kwon WY, Rica I, Chen L, Sandler N, Otterbein LE, Campbell Y, Cook CH, Yaffe MB, Marusich M, Itagaki K. J Trauma Acute Care Surg. pubmed:29787548;  doi:10.1097/TA.0000000000001971

14. Potent in vivo lung cancer Wnt signaling inhibition via cyclodextrin-LGK974 inclusion complexes. Guimaraes PPG, Tan M, Tammela T, Wu K, Chung A, Oberli M, Wang K, Spektor R, Riley RS, Viana CTR, Jacks T, Langer R, Mitchell MJ. J Control Release. pubmed:30290244;  doi:10.1016/j.jconrel.2018.09.025

15. CRAD as a cytoskeletal tumour suppressor. Eng G, Braverman J, Yilmaz OH. Nat Cell Biol. pubmed:30361696;  doi:10.1038/s41556-018-0225-x

16. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ. Cell. pubmed:30392957;  doi:10.1016/j.cell.2018.10.008

17. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Canadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. Cell. pubmed:30388455;  doi:10.1016/j.cell.2018.09.006

18. Isolating mitotic and meiotic germ cells from male mice by developmental synchronization, staging, and sorting. Romer KA, de Rooij DG, Kojima ML, Page DC. Dev Biol. pubmed:30149006;  doi:10.1016/j.ydbio.2018.08.009

19. Evolution of weak cooperative interactions for biological specificity. Gao A, Shrinivas K, Lepeudry P, Suzuki HI, Sharp PA, Chakraborty AK. Proc Natl Acad Sci U S A. pubmed:30404915;  doi:10.1073/pnas.1815912115

20. Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses. Douam F, Ziegler CGK, Hrebikova G, Fant B, Leach R, Parsons L, Wang W, Gaska JM, Winer BY, Heller B, Shalek AK, Ploss A. Nat Commun. pubmed:30487575;  doi:10.1038/s41467-018-07478-2

21. Linking single-cell measurements of mass, growth rate, and gene expression. Kimmerling RJ, Prakadan SM, Gupta AJ, Calistri NL, Stevens MM, Olcum S, Cermak N, Drake RS, Pelton K, De Smet F, Ligon KL, Shalek AK, Manalis SR. Genome Biol. pubmed:30482222;  doi:10.1186/s13059-018-1576-0

22. Triply Loaded Nitroxide Brush-Arm Star Polymers Enable Metal-Free Millimetric Tumor Detection by Magnetic Resonance Imaging. Nguyen HV, Detappe A, Gallagher NM, Zhang H, Harvey P, Yan C, Mathieu C, Golder MR, Jiang Y, Ottaviani MF, Jasanoff A, Rajca A, Ghobrial I, Ghoroghchian PP, Johnson JA. ACS Nano. pubmed:30387988;  doi:10.1021/acsnano.8b06160

23. Arylation Chemistry for Bioconjugation. Pentelute B, Zhang C, Vinogradova E, Spokoyny A, Buchwald S. Angew Chem Int Ed Engl. pubmed:30399206;  doi:10.1002/anie.201806009

24. Cell and fluid sampling microneedle patches for monitoring skin-resident immunity. Mandal A, Boopathy AV, Lam LKW, Moynihan KD, Welch ME, Bennett NR, Turvey ME, Thai N, Van JH, Love JC, Hammond PT, Irvine DJ. Sci Transl Med. pubmed:30429353;  doi:10.1126/scitranslmed.aar2227

25. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. Choudhury AD, Werner L, Francini E, Wei XX, Ha G, Freeman SS, Rhoades J, Reed SC, Gydush G, Rotem D, Lo C, Taplin ME, Harshman LC, Zhang Z, O'Connor EP, Stover DG, Parsons HA, Getz G, Meyerson M, Love JC, Hahn WC, Adalsteinsson VA. JCI Insight. pubmed:30385733;  doi:10.1172/jci.insight.122109

26. Trisomy of a Down Syndrome Critical Region Globally Amplifies Transcription via HMGN1 Overexpression. Mowery CT, Reyes JM, Cabal-Hierro L, Higby KJ, Karlin KL, Wang JH, Kimmerling RJ, Cejas P, Lim K, Li H, Furusawa T, Long HW, Pellman D, Chapuy B, Bustin M, Manalis SR, Westbrook TF, Lin CY, Lane AA. Cell Rep. pubmed:30428356;  doi:10.1016/j.celrep.2018.10.061

27. A combined microfluidic-transcriptomic approach to characterize the extravasation potential of cancer cells. Bersini S, Miermont A, Pavesi A, Kamm RD, Thiery JP, Moretti M, Adriani G. Oncotarget. pubmed:30546831;  doi:10.18632/oncotarget.26306

28. Vaccine-Induced Protection from Homologous Tier 2 SHIV Challenge in Nonhuman Primates Depends on Serum-Neutralizing Antibody Titers. Pauthner MG, Nkolola JP, Havenar-Daughton C, Murrell B, Reiss SM, Bastidas R, Prevost J, Nedellec R, von Bredow B, Abbink P, Cottrell CA, Kulp DW, Tokatlian T, Nogal B, Bianchi M, Li H, Lee JH, Butera ST, Evans DT, Hangartner L, Finzi A, Wilson IA, Wyatt RT, Irvine DJ, Schief WR, Ward AB, Sanders RW, Crotty S, Shaw GM, Barouch DH, Burton DR. Immunity. pubmed:30552025;  doi:10.1016/j.immuni.2018.11.011

29. Microfluidic active loading of single cells enables analysis of complex clinical specimens. Calistri NL, Kimmerling RJ, Malinowski SW, Touat M, Stevens MM, Olcum S, Ligon KL, Manalis SR. Nat Commun. pubmed:30429479;  doi:10.1038/s41467-018-07283-x

30. Integrated mapping of pharmacokinetics and pharmacodynamics in a patient-derived xenograft model of glioblastoma. Randall EC, Emdal KB, Laramy JK, Kim M, Roos A, Calligaris D, Regan MS, Gupta SK, Mladek AC, Carlson BL, Johnson AJ, Lu FK, Xie XS, Joughin BA, Reddy RJ, Peng S, Abdelmoula WM, Jackson PR, Kolluri A, Kellersberger KA, Agar JN, Lauffenburger DA, Swanson KR, Tran NL, Elmquist WF, White FM, Sarkaria JN, Agar NYR. Nat Commun. pubmed:30464169;  doi:10.1038/s41467-018-07334-3

31. Encryption and steganography of synthetic gene circuits. Purcell O, Wang J, Siuti P, Lu TK. Nat Commun. pubmed:30467337;  doi:10.1038/s41467-018-07144-7

32. Enhancing Humoral Responses Against HIV Envelope Trimers via Nanoparticle Delivery with Stabilized Synthetic Liposomes. Tokatlian T, Kulp DW, Mutafyan AA, Jones CA, Menis S, Georgeson E, Kubitz M, Zhang MH, Melo MB, Silva M, Yun DS, Schief WR, Irvine DJ. Sci Rep. pubmed:30410003;  doi:10.1038/s41598-018-34853-2

33. A Mechanical Approach for Smooth Surface Fitting to Delineate Vessel Walls in Optical Coherence Tomography Images. Olender ML, Athanasiou LS, Hernandez JMT, Ben-Assa E, Nezami FR, Edelman ER. IEEE Trans Med Imaging. pubmed:30507499;  doi:10.1109/TMI.2018.2884142

34. Cartilage-penetrating nanocarriers improve delivery and efficacy of growth factor treatment of osteoarthritis. Geiger BC, Wang S, Padera RFJr, Grodzinsky AJ, Hammond PT. Sci Transl Med. pubmed:30487252;  doi:10.1126/scitranslmed.aat8800

35. Author Correction: A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity. Gam JJ, Babb J, Weiss R. Nat Commun. pubmed:30389927;  doi:10.1038/s41467-018-07158-1

36. Green fluorescent proteins engineered for cartilage-targeted drug delivery: Insights for transport into highly charged avascular tissues. Krishnan Y, Rees HA, Rossitto CP, Kim SE, Hung HK, Frank EH, Olsen BD, Liu DR, Hammond PT, Grodzinsky AJ. Biomaterials. pubmed:30173104;  doi:10.1016/j.biomaterials.2018.08.050

37. Small-molecule-based regulation of RNA-delivered circuits in mammalian cells. Wagner TE, Becraft JR, Bodner K, Teague B, Zhang X, Woo A, Porter E, Alburquerque B, Dobosh B, Andries O, Sanders NN, Beal J, Densmore D, Kitada T, Weiss R. Nat Chem Biol. pubmed:30327560;  doi:10.1038/s41589-018-0146-9

38. Bacteriophage Therapy Testing against Shigella flexneri in a Novel Human Intestinal Organoid-Derived Infection Model. Llanos-Chea A, Citorik RJ, Nickerson KP, Ingano L, Serena G, Senger S, Lu TK, Fasano A, Faherty CS. J Pediatr Gastroenterol Nutr. pubmed:30418409;  doi:10.1097/MPG.0000000000002203

39. Multifunctional Hierarchically-Assembled Hydrogel Particles with Pollen Grains via Pickering Suspension Polymerization. Park J, Doyle PS. Langmuir. pubmed:30400737;  doi:10.1021/acs.langmuir.8b02957

40. Design of Hydrogel Particle Morphology for Rapid Bioassays. Shapiro SJ, Dendukuri D, Doyle PS. Anal Chem. pubmed:30339359;  doi:10.1021/acs.analchem.8b03728

41. Combined HDAC and BET Inhibition Enhances Melanoma Vaccine Immunogenicity and Efficacy. Badamchi-Zadeh A, Moynihan KD, Larocca RA, Aid M, Provine NM, Iampietro MJ, Kinnear E, Penaloza-MacMaster P, Abbink P, Blass E, Tregoning JS, Irvine DJ, Barouch DH. J Immunol. pubmed:30249811;  doi:10.4049/jimmunol.1800885

42. Multilayer flow modulator enhances vital organ perfusion in patients with type B aortic dissection. Rikhtegar Nezami F, Athanasiou LS, Amrute JM, Edelman ER. Am J Physiol Heart Circ Physiol. pubmed:30095992;  doi:10.1152/ajpheart.00199.2018

43. Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics. Kumar MP, Du J, Lagoudas G, Jiao Y, Sawyer A, Drummond DC, Lauffenburger DA, Raue A. Cell Rep. pubmed:30404002;  doi:10.1016/j.celrep.2018.10.047

44. Translating Temporal Interference Brain Stimulation to Treat Neurological and Psychiatric Conditions. Grossman N, Okun MS, Boyden ES. JAMA Neurol. pubmed:30264149;  doi:10.1001/jamaneurol.2018.2760

45. Microtubule-Based Control of Motor-Clutch System Mechanics in Glioma Cell Migration. Prahl LS, Bangasser PF, Stopfer LE, Hemmat M, White FM, Rosenfeld SS, Odde DJ. Cell Rep. pubmed:30485822;  doi:10.1016/j.celrep.2018.10.101

46. A Proteomics Approach to Profiling the Temporal Translational Response to Stress and Growth. Rothenberg DA, Taliaferro JM, Huber SM, Begley TJ, Dedon PC, White FM. iScience. pubmed:30466063;  doi:10.1016/j.isci.2018.11.004

47. Drug loading augmentation in polymeric nanoparticles using a coaxial turbulent jet mixer: Yong investigator perspective. Lim JM, Cai T, Mandaric S, Chopra S, Han H, Jang S, Il Choi W, Langer R, Farokhzad OC, Karnik R. J Colloid Interface Sci. pubmed:30500466;  doi:10.1016/j.jcis.2018.11.029