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: July 2020

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1. Biomolecular Condensates in the Nucleus. Sabari BR, Dall'Agnese A, Young RA. Trends Biochem Sci. pubmed:32684431;  doi:10.1016/j.tibs.2020.06.007

2. The environmental stress response causes ribosome loss in aneuploid yeast cells. Terhorst A, Sandikci A, Keller A, Whittaker CA, Dunham MJ, Amon A. Proc Natl Acad Sci U S A. pubmed:32632008;  doi:10.1073/pnas.2005648117

3. Dissecting cell type-specific metabolism in pancreatic ductal adenocarcinoma. Lau AN, Li Z, Danai LV, Westermark AM, Darnell AM, Ferreira R, Gocheva V, Sivanand S, Lien EC, Sapp KM, Mayers JR, Biffi G, Chin CR, Davidson SM, Tuveson DA, Jacks T, Matheson NJ, Yilmaz O, Vander Heiden MG. Elife. pubmed:32648540;  doi:10.7554/eLife.56782

4. Mapping and characterization of structural variation in 17,795 human genomes. Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S, Matise TC, Muzny DM, Zody MC, Lander ES, Dutcher SK, Stitziel NO, Hall IM. Nature. pubmed:32460305;  doi:10.1038/s41586-020-2371-0

5. A large-scale binding and functional map of human RNA-binding proteins. Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, McGurk MP, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD, Lecuyer E, Burge CB, Graveley BR, Yeo GW. Nature. pubmed:32728246;  doi:10.1038/s41586-020-2077-3

6. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lecuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigo R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Nature. pubmed:32728249;  doi:10.1038/s41586-020-2493-4

7. Rapid activation of distinct members of multigene families in Plasmodium spp. Omelianczyk RI, Loh HP, Chew M, Hoo R, Baumgarten S, Renia L, Chen J, Preiser PR. Commun Biol. pubmed:32620892;  doi:10.1038/s42003-020-1081-3

8. DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors. Mikedis MM, Fan Y, Nicholls PK, Endo T, Jackson EK, Cobb SA, de Rooij DG, Page DC. Elife. pubmed:32686646;  doi:10.7554/eLife.56523

9. A somatic evolutionary model of the dynamics of aneuploid cells during hematopoietic reconstitution. Rozhok AI, Silberman RE, Higa KC, Liggett LA, Amon A, DeGregori J. Sci Rep. pubmed:32699207;  doi:10.1038/s41598-020-68729-1

10. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Li B, Gould J, Yang Y, Sarkizova S, Tabaka M, Ashenberg O, Rosen Y, Slyper M, Kowalczyk MS, Villani AC, Tickle T, Hacohen N, Rozenblatt-Rosen O, Regev A. Nat Methods. pubmed:32719530;  doi:10.1038/s41592-020-0905-x

11. Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma. Gojo J, Englinger B, Jiang L, Hubner JM, Shaw ML, Hack OA, Madlener S, Kirchhofer D, Liu I, Pyrdol J, Hovestadt V, Mazzola E, Mathewson ND, Trissal M, Lotsch D, Dorfer C, Haberler C, Halfmann A, Mayr L, Peyrl A, Geyeregger R, Schwalm B, Mauermann M, Pajtler KW, Milde T, Shore ME, Geduldig JE, Pelton K, Czech T, Ashenberg O, Wucherpfennig KW, Rozenblatt-Rosen O, Alexandrescu S, Ligon KL, Pfister SM, Regev A, Slavc I, Berger W, Suva ML, Kool M, Filbin MG. Cancer Cell. pubmed:32663469;  doi:10.1016/j.ccell.2020.06.004

12. LIN28B regulates transcription and potentiates MYCN-induced neuroblastoma through binding to ZNF143 at target gene promotors. Tao T, Shi H, Mariani L, Abraham BJ, Durbin AD, Zimmerman MW, Powers JT, Missios P, Ross KN, Perez-Atayde AR, Bulyk ML, Young RA, Daley GQ, Look AT. Proc Natl Acad Sci U S A. pubmed:32601179;  doi:10.1073/pnas.1922692117

13. Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma. LaFave LM, Kartha VK, Ma S, Meli K, Del Priore I, Lareau C, Naranjo S, Westcott PMK, Duarte FM, Sankar V, Chiang Z, Brack A, Law T, Hauck H, Okimoto A, Regev A, Buenrostro JD, Jacks T. Cancer Cell. pubmed:32707078;  doi:10.1016/j.ccell.2020.06.006

14. BRG1 loss predisposes lung cancers to replicative stress and ATR dependency. Gupta M, Concepcion CP, Fahey CG, Keshishian H, Bhutkar A, Brainson CF, Sanchez-Rivera FJ, Pessina P, Kim JY, Simoneau A, Paschini M, Beytagh MC, Stanclift CR, Schenone M, Mani DR, Li C, Oh A, Li F, Hu H, Karatza A, Bronson RT, Shaw AT, Hata AN, Wong KK, Zou L, Carr SA, Jacks T, Kim CF. Cancer Res. pubmed:32690724;  doi:10.1158/0008-5472.CAN-20-1744

15. MeCP2 links heterochromatin condensates and neurodevelopmental disease. Li CH, Coffey EL, Dall'Agnese A, Hannett NM, Tang X, Henninger JE, Platt JM, Oksuz O, Zamudio AV, Afeyan LK, Schuijers J, Liu XS, Markoulaki S, Lungjangwa T, LeRoy G, Svoboda DS, Wogram E, Lee TI, Jaenisch R, Young RA. Nature. pubmed:32698189;  doi:N/A

16. Dihydroxyacetone phosphate signals glucose availability to mTORC1. Orozco JM, Krawczyk PA, Scaria SM, Cangelosi AL, Chan SH, Kunchok T, Lewis CA, Sabatini DM. Nat Metab. pubmed:32719541;  doi:N/A

17. Acquired FGFR and FGF alterations confer resistance to estrogen receptor (ER) targeted therapy in ER+ metastatic breast cancer. Mao P, Cohen O, Kowalski KJ, Kusiel J, Buendia-Buendia JE, Cuoco MS, Exman P, Wander SA, Waks AG, Nayar U, Chung JH, Freeman SS, Rozenblatt-Rosen O, Miller VA, Piccioni F, Root DE, Regev A, Winer EP, Lin NU, Wagle N. Clin Cancer Res. pubmed:32723837;  doi:N/A

18. Tranexamic acid is associated with reduced complement activation in trauma patients with hemorrhagic shock and hyperfibrinolysis on thromboelastography. Barrett CD, Vigneshwar N, Moore HB, Ghasabyan A, Chandler J, Moore EE, Yaffe MB. Blood Coagul Fibrinolysis. pubmed:32732500;  doi:N/A

19. Regenerative Reprogramming of the Intestinal Stem Cell State via Hippo Signaling Suppresses Metastatic Colorectal Cancer. Cheung P, Xiol J, Dill MT, Yuan WC, Panero R, Roper J, Osorio FG, Maglic D, Li Q, Gurung B, Calogero RA, Yilmaz OH, Mao J, Camargo FD. Cell Stem Cell. pubmed:32730753;  doi:N/A

20. A Platinum(IV) Prodrug-Perfluoroaryl Macrocyclic Peptide Conjugate Enhances Platinum Uptake in the Brain. Fadzen CM, Wolfe JM, Zhou W, Cho CF, von Spreckelsen N, Hutchinson KT, Lee YC, Chiocca EA, Lawler SE, Yilmaz OH, Lippard SJ, Pentelute BL. J Med Chem. pubmed:32410451;  doi:N/A

21. Safety Assessment of High-Purity, Synthetic Nicotinamide Riboside (NR-E) in a 90-Day Repeated Dose Oral Toxicity Study, With a 28-Day Recovery Arm. Marinescu AG, Chen J, Holmes HE, Guarente L, Mendes O, Morris M, Dellinger RW. Int J Toxicol. pubmed:32715855;  doi:N/A

22. NEK10 tyrosine phosphorylates p53 and controls its transcriptional activity. Haider N, Dutt P, van de Kooij B, Ho J, Palomero L, Pujana MA, Yaffe M, Stambolic V. Oncogene. pubmed:32561851;  doi:N/A

23. Redox priming promotes Aurora A activation during mitosis. Lim DC, Joukov V, Rettenmaier TJ, Kumagai A, Dunphy WG, Wells JA, Yaffe MB. Sci Signal. pubmed:32694171;  doi:N/A

24. Inducible de novo expression of neoantigens in tumor cells and mice. Damo M, Fitzgerald B, Lu Y, Nader M, William I, Cheung JF, Connolly KA, Foster GG, Akama-Garren E, Lee DY, Chang GP, Gocheva V, Schmidt LM, Boileve A, Wilson JH, Cui C, Monroy I, Gokare P, Cabeceiras P, Jacks T, Joshi NS. Nat Biotechnol. pubmed:32719479;  doi:N/A

25. Emergence of a High-Plasticity Cell State during Lung Cancer Evolution. Marjanovic ND, Hofree M, Chan JE, Canner D, Wu K, Trakala M, Hartmann GG, Smith OC, Kim JY, Evans KV, Hudson A, Ashenberg O, Porter CBM, Bejnood A, Subramanian A, Pitter K, Yan Y, Delorey T, Phillips DR, Shah N, Chaudhary O, Tsankov A, Hollmann T, Rekhtman N, Massion PP, Poirier JT, Mazutis L, Li R, Lee JH, Amon A, Rudin CM, Jacks T, Regev A, Tammela T. Cancer Cell. pubmed:32707077;  doi:N/A

26. Quantitative Mapping of Molecular Substituents to Macroscopic Properties Enables Predictive Design of Oligoethylene Glycol-Based Lithium Electrolytes. Qiao B, Mohapatra S, Lopez J, Leverick GM, Tatara R, Shibuya Y, Jiang Y, France-Lanord A, Grossman JC, Gomez-Bombarelli R, Johnson JA, Shao-Horn Y. ACS Cent Sci. pubmed:32724846;  doi:10.1021/acscentsci.0c00475

27. Conformational Dynamics in Extended RGD-Containing Peptides. Lindemann WR, Mijalis AJ, Alonso JL, Borbat PP, Freed JH, Arnaout MA, Pentelute BL, Ortony JH. Biomacromolecules. pubmed:32469507;  doi:10.1021/acs.biomac.0c00506

28. Cleavable comonomers enable degradable, recyclable thermoset plastics. Shieh P, Zhang W, Husted KEL, Kristufek SL, Xiong B, Lundberg DJ, Lem J, Veysset D, Sun Y, Nelson KA, Plata DL, Johnson JA. Nature. pubmed:32699399;  doi:10.1038/s41586-020-2495-2

29. Modeling, design, and machine learning-based framework for optimal injectability of microparticle-based drug formulations. Sarmadi M, Behrens AM, McHugh KJ, Contreras HTM, Tochka ZL, Lu X, Langer R, Jaklenec A. Sci Adv. pubmed:32923598;  doi:10.1126/sciadv.abb6594

30. In vivo microscopy reveals macrophage polarization locally promotes coherent microtubule dynamics in migrating cancer cells. Luthria G, Li R, Wang S, Prytyskach M, Kohler RH, Lauffenburger DA, Mitchison TJ, Weissleder R, Miller MA. Nat Commun. pubmed:32665556;  doi:10.1038/s41467-020-17147-y

31. Cancer Cell Coating Nanoparticles for Optimal Tumor-Specific Cytokine Delivery. Barberio AE, Smith SG, Correa S, Nguyen C, Nhan B, Melo M, Tokatlian T, Suh H, Irvine DJ, Hammond PT. ACS Nano. pubmed:32692155;  doi:10.1021/acsnano.0c03109

32. Single-shot Ad26 vaccine protects against SARS-CoV-2 in rhesus macaques. Mercado NB, Zahn R, Wegmann F, Loos C, Chandrashekar A, Yu J, Liu J, Peter L, McMahan K, Tostanoski LH, He X, Martinez DR, Rutten L, Bos R, van Manen D, Vellinga J, Custers J, Langedijk JP, Kwaks T, Bakkers MJG, Zuijdgeest D, Huber SKR, Atyeo C, Fischinger S, Burke JS, Feldman J, Hauser BM, Caradonna TM, Bondzie EA, Dagotto G, Gebre MS, Hoffman E, Jacob-Dolan C, Kirilova M, Li Z, Lin Z, Mahrokhian SH, Maxfield LF, Nampanya F, Nityanandam R, Nkolola JP, Patel S, Ventura JD, Verrington K, Wan H, Pessaint L, Ry AV, Blade K, Strasbaugh A, Cabus M, Brown R, Cook A, Zouantchangadou S, Teow E, Andersen H, Lewis MG, Cai Y, Chen B, Schmidt AG, Reeves RK, Baric RS, Lauffenburger DA, Alter G, Stoffels P, Mammen M, Hoof JV, Schuitemaker H, Barouch DH. Nature. pubmed:32731257;  doi:10.1038/s41586-020-2607-z

33. Polymer Nanocomposite Microactuators for On-Demand Chemical Release via High-Frequency Magnetic Field Excitation. Mirvakili SM, Ngo QP, Langer R. Nano Lett. pubmed:32479730;  doi:10.1021/acs.nanolett.0c00648

34. An Ultra-Sensitive Step-Function Opsin for Minimally Invasive Optogenetic Stimulation in Mice and Macaques. Gong X, Mendoza-Halliday D, Ting JT, Kaiser T, Sun X, Bastos AM, Wimmer RD, Guo B, Chen Q, Zhou Y, Pruner M, Wu CW, Park D, Deisseroth K, Barak B, Boyden ES, Miller EK, Halassa MM, Fu Z, Bi G, Desimone R, Feng G. Neuron. pubmed:32353253;  doi:10.1016/j.neuron.2020.03.032

35. Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona. Blume JE, Manning WC, Troiano G, Hornburg D, Figa M, Hesterberg L, Platt TL, Zhao X, Cuaresma RA, Everley PA, Ko M, Liou H, Mahoney M, Ferdosi S, Elgierari EM, Stolarczyk C, Tangeysh B, Xia H, Benz R, Siddiqui A, Carr SA, Ma P, Langer R, Farias V, Farokhzad OC. Nat Commun. pubmed:32699280;  doi:10.1038/s41467-020-17033-7

36. Mass measurements during lymphocytic leukemia cell polyploidization decouple cell cycle- and cell size-dependent growth. Mu L, Kang JH, Olcum S, Payer KR, Calistri NL, Kimmerling RJ, Manalis SR, Miettinen TP. Proc Natl Acad Sci U S A. pubmed:32581119;  doi:10.1073/pnas.1922197117

37. Calcium-triggered fusion of lipid membranes is enabled by amphiphilic nanoparticles. Tahir MA, Guven ZP, Arriaga LR, Tinao B, Yang YS, Bekdemir A, Martin JT, Bhanji AN, Irvine D, Stellacci F, Alexander-Katz A. Proc Natl Acad Sci U S A. pubmed:32690682;  doi:10.1073/pnas.1902597117

38. Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity. Mendoza JL, Fischer S, Gee MH, Lam LH, Brackenridge S, Powrie FM, Birnbaum M, McMichael AJ, Garcia KC, Gillespie GM. Elife. pubmed:32716298;  doi:10.7554/eLife.58128

39. Randomized trials of invasive cardiovascular interventions that include a placebo control: a systematic review and meta-analysis. Lauder L, da Costa BR, Ewen S, Scholz SS, Wijns W, Luscher TF, Serruys PW, Edelman ER, Capodanno D, Bohm M, Juni P, Mahfoud F. Eur Heart J. pubmed:32666097;  doi:10.1093/eurheartj/ehaa495

40. Paclitaxel Drug-Coated Balloon Angioplasty Suppresses Progression and Inflammation of Experimental Atherosclerosis in Rabbits. Chowdhury MM, Singh K, Albaghdadi MS, Khraishah H, Mauskapf A, Kessinger CW, Osborn EA, Kellnberger S, Piao Z, Lino Cardenas CL, Grau MS, Jaff MR, Rosenfield K, Libby P, Edelman ER, Lindsay ME, Tearney GJ, Jaffer FA. JACC Basic Transl Sci. pubmed:32760856;  doi:10.1016/j.jacbts.2020.04.007

41. Delivery of Tissue-Targeted Scalpels: Opportunities and Challenges for In Vivo CRISPR/Cas-Based Genome Editing. Wei T, Cheng Q, Farbiak L, Anderson DG, Langer R, Siegwart DJ. ACS Nano. pubmed:32697075;  doi:N/A

42. Simultaneous recording and marking of brain microstructures. Ramadi KB, Dagdeviren C, Bhagchandani P, Nunez-Lopez C, Kim MJ, Langer R, Graybiel AM, Cima MJ. J Neural Eng. pubmed:32604074;  doi:N/A

43. Approaches to Modulate the Chronic Wound Environment Using Localized Nucleic Acid Delivery. Berger AG, Chou JJ, Hammond PT. Adv Wound Care (New Rochelle). pubmed:32496978;  doi:N/A

44. Uncertainty Quantification using Neural Networks for Molecular Property Prediction. Hirschfeld L, Swanson K, Yang K, Barzilay R, Coley CW. J Chem Inf Model. pubmed:32702986;  doi:N/A

45. Phase 1 Trial of a Therapeutic Anti-Yellow Fever Virus Human Antibody. Low JG, Ng JHJ, Ong EZ, Kalimuddin S, Wijaya L, Chan YFZ, Ng DHL, Tan HC, Baglody A, Chionh YH, Lee DCP, Budigi Y, Sasisekharan R, Ooi EE. N Engl J Med. pubmed:32726531;  doi:N/A

46. Resistance to PD1 blockade in the absence of metalloprotease-mediated LAG3 shedding. Andrews LP, Somasundaram A, Moskovitz JM, Szymczak-Workman AL, Liu C, Cillo AR, Lin H, Normolle DP, Moynihan KD, Taniuchi I, Irvine DJ, Kirkwood JM, Lipson EJ, Ferris RL, Bruno TC, Workman CJ, Vignali DAA. Sci Immunol. pubmed:32680952;  doi:N/A

47. Microbes as Biosensors. Inda ME, Lu TK. Annu Rev Microbiol. pubmed:32660390;  doi:N/A

48. 3D aggregation of cells in packed microgel media. Morley CD, Tordoff J, O'Bryan CS, Weiss R, Angelini TE. Soft Matter. pubmed:32589183;  doi:N/A

49. Engineering synthetic breath biomarkers for respiratory disease. Chan LW, Anahtar MN, Ong TH, Hern KE, Kunz RR, Bhatia SN. Nat Nanotechnol. pubmed:32690884;  doi:N/A

50. A novel method to interpret early phase trials shows how the narrowing of the coronary sinus concordantly improves symptoms, functional status and quality of life in refractory angina. Jolicoeur EM, Verheye S, Henry TD, Joseph L, Doucet S, White CJ, Edelman E, Banai S. Heart. pubmed:32719097;  doi:N/A

51. A Computational Fluid Dynamics Study of the Extracorporeal Membrane Oxygenation-Failing Heart Circulation. Nezami FR, Khodaee F, Edelman ER, Keller SP. ASAIO J. pubmed:32909976;  doi:N/A

52. Mapping functional humoral correlates of protection against malaria challenge following RTS,S/AS01 vaccination. Suscovich TJ, Fallon JK, Das J, Demas AR, Crain J, Linde CH, Michell A, Natarajan H, Arevalo C, Broge T, Linnekin T, Kulkarni V, Lu R, Slein MD, Luedemann C, Marquette M, March S, Weiner J, Gregory S, Coccia M, Flores-Garcia Y, Zavala F, Ackerman ME, Bergmann-Leitner E, Hendriks J, Sadoff J, Dutta S, Bhatia SN, Lauffenburger DA, Jongert E, Wille-Reece U, Alter G. Sci Transl Med. pubmed:32718991;  doi:N/A