If you can spare a few minutes, please help us improve our website by completing this survey.

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: August 2019

Return to Progress index

1. H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration. Ben-Yair R, Butty VL, Busby M, Qiu Y, Levine SS, Goren A, Boyer LA, Burns CG, Burns CE. Development. pubmed:31427288;  doi:10.1242/dev.178632

2. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cheng CW, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, Moreno-Serrano M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, Yilmaz OH. Cell. pubmed:31442404;  doi:10.1016/j.cell.2019.07.048

3. Enhancer Features that Drive Formation of Transcriptional Condensates. Shrinivas K, Sabari BR, Coffey EL, Klein IA, Boija A, Zamudio AV, Schuijers J, Hannett NM, Sharp PA, Young RA, Chakraborty AK. Mol Cell. pubmed:31398323;  doi:10.1016/j.molcel.2019.07.009

4. Pol II phosphorylation regulates a switch between transcriptional and splicing condensates. Guo YE, Manteiga JC, Henninger JE, Sabari BR, Dall'Agnese A, Hannett NM, Spille JH, Afeyan LK, Zamudio AV, Shrinivas K, Abraham BJ, Boija A, Decker TM, Rimel JK, Fant CB, Lee TI, Cisse II, Sharp PA, Taatjes DJ, Young RA. Nature. pubmed:31391587;  doi:10.1038/s41586-019-1464-0

5. Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs. Song Y, van den Berg PR, Markoulaki S, Soldner F, Dall'Agnese A, Henninger JE, Drotar J, Rosenau N, Cohen MA, Young RA, Semrau S, Stelzer Y, Jaenisch R. Mol Cell. pubmed:31422875;  doi:10.1016/j.molcel.2019.06.045

6. Immuno-PET identifies the myeloid compartment as a key contributor to the outcome of the antitumor response under PD-1 blockade. Rashidian M, LaFleur MW, Verschoor VL, Dongre A, Zhang Y, Nguyen TH, Kolifrath S, Aref AR, Lau CJ, Paweletz CP, Bu X, Freeman GJ, Barrasa MI, Weinberg RA, Sharpe AH, Ploegh HL. Proc Natl Acad Sci U S A. pubmed:31375632;  doi:10.1073/pnas.1905005116

7. Cholangiolar pattern and albumin in situ hybridisation enable a diagnosis of intrahepatic cholangiocarcinoma. Brackett DG, Neyaz A, Arora K, Masia R, Mattia A, Zukerberg L, Misdraji J, Goyal L, Zhu AX, Ferrone CR, Yilmaz OH, Deshpande V. J Clin Pathol. pubmed:31422372;  doi:10.1136/jclinpath-2019-206055

8. MYC promotes tryptophan uptake and metabolism by the kynurenine pathway in colon cancer. Venkateswaran N, Lafita-Navarro MC, Hao YH, Kilgore JA, Perez-Castro L, Braverman J, Borenstein-Auerbach N, Kim M, Lesner NP, Mishra P, Brabletz T, Shay JW, DeBerardinis RJ, Williams NS, Yilmaz OH, Conacci-Sorrell M. Genes Dev. pubmed:31416966;  doi:10.1101/gad.327056.119

9. Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1. Khor B, Conway KL, Omar AS, Biton M, Haber AL, Rogel N, Baxt LA, Begun J, Kuballa P, Gagnon JD, Lassen KG, Regev A, Xavier RJ. J Immunol. pubmed:31451676;  doi:10.4049/jimmunol.1800419

10. Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells. Reitman ZJ, Paolella BR, Bergthold G, Pelton K, Becker S, Jones R, Sinai CE, Malkin H, Huang Y, Grimmet L, Herbert ZT, Sun Y, Weatherbee JL, Alberta JA, Daley JF, Rozenblatt-Rosen O, Condurat AL, Qian K, Khadka P, Segal RA, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles CD, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R. Nat Commun. pubmed:31427603;  doi:10.1038/s41467-019-11493-2

11. High-fat diet in a mouse insulin-resistant model induces widespread rewiring of the phosphotyrosine signaling network. Dittmann A, Kennedy NJ, Soltero NL, Morshed N, Mana MD, Yilmaz OH, Davis RJ, White FM. Mol Syst Biol. pubmed:31464373;  doi:10.15252/msb.20198849

12. A dynamic view of chemotherapy effectiveness. Liu Y, Hemann MT. Nature. pubmed:31406309;  doi:10.1038/d41586-019-02336-7

13. Resolving medulloblastoma cellular architecture by single-cell genomics. Hovestadt V, Smith KS, Bihannic L, Filbin MG, Shaw ML, Baumgartner A, DeWitt JC, Groves A, Mayr L, Weisman HR, Richman AR, Shore ME, Goumnerova L, Rosencrance C, Carter RA, Phoenix TN, Hadley JL, Tong Y, Houston J, Ashmun RA, DeCuypere M, Sharma T, Flasch D, Silkov A, Ligon KL, Pomeroy SL, Rivera MN, Rozenblatt-Rosen O, Rusert JM, Wechsler-Reya RJ, Li XN, Peyrl A, Gojo J, Kirchhofer D, Lotsch D, Czech T, Dorfer C, Haberler C, Geyeregger R, Halfmann A, Gawad C, Easton J, Pfister SM, Regev A, Gajjar A, Orr BA, Slavc I, Robinson GW, Bernstein BE, Suva ML, Northcott PA. Nature. pubmed:31341285;  doi:10.1038/s41586-019-1434-6

14. BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells. Debruyne DN, Dries R, Sengupta S, Seruggia D, Gao Y, Sharma B, Huang H, Moreau L, McLane M, Day DS, Marco E, Chen T, Gray NS, Wong KK, Orkin SH, Yuan GC, Young RA, George RE. Nature. pubmed:31391581;  doi:10.1038/s41586-019-1472-0

15. Enhanced adaptive immune responses in lung adenocarcinoma through natural killer cell stimulation. Schmidt L, Eskiocak B, Kohn R, Dang C, Joshi NS, DuPage M, Lee DY, Jacks T. Proc Natl Acad Sci U S A. pubmed:31409707;  doi:10.1073/pnas.1904253116

16. A dominant-negative effect drives selection of TP53 missense mutations in myeloid malignancies. Boettcher S, Miller PG, Sharma R, McConkey M, Leventhal M, Krivtsov AV, Giacomelli AO, Wong W, Kim J, Chao S, Kurppa KJ, Yang X, Milenkowic K, Piccioni F, Root DE, Rucker FG, Flamand Y, Neuberg D, Lindsley RC, Janne PA, Hahn WC, Jacks T, Dohner H, Armstrong SA, Ebert BL. Science. pubmed:31395785;  doi:10.1126/science.aax3649

17. Cyclophosphamide Enhances Cancer Antibody Immunotherapy in the Resistant Bone Marrow Niche by Modulating Macrophage FcgammaR Expression. Roghanian A, Hu G, Fraser C, Singh M, Foxall RB, Meyer MJ, Lees E, Huet H, Glennie MJ, Beers SA, Lim SH, Ashton-Key M, Thirdborough SM, Cragg M, Chen J. Cancer Immunol Res. pubmed:31451483;  doi:10.1158/2326-6066.CIR-18-0835

18. A conserved Mcm4 motif is required for Mcm2-7 double-hexamer formation and origin DNA unwinding. Champasa K, Blank C, Friedman LJ, Gelles J, Bell SP. Elife. pubmed:31385807;  doi:10.7554/eLife.45538

19. Chimeras of Cell-Penetrating Peptides Demonstrate Synergistic Improvement in Antisense Efficacy. Fadzen CM, Holden R, Wolfe JM, Choo ZN, Schissel CK, Yao M, Hanson GJ, Pentelute BL. Biochemistry. pubmed:31450889;  doi:10.1021/acs.biochem.9b00413

20. A Deep Learning Model to Triage Screening Mammograms: A Simulation Study. Yala A, Schuster T, Miles R, Barzilay R, Lehman C. Radiology. pubmed:31385754;  doi:10.1148/radiol.2019182908

21. Hydrogel-Coated Microneedle Arrays for Minimally Invasive Sampling and Sensing of Specific Circulating Nucleic Acids from Skin Interstitial Fluid. Al Sulaiman D, Chang JYH, Bennett NR, Topouzi H, Higgins CA, Irvine DJ, Ladame S. ACS Nano. pubmed:31411871;  doi:10.1021/acsnano.9b04783

22. In vivo and in vitro evaluation of a biodegradable magnesium vascular stent designed by shape optimization strategy. Chen C, Chen J, Wu W, Shi Y, Jin L, Petrini L, Shen L, Yuan G, Ding W, Ge J, Edelman ER, Migliavacca F. Biomaterials. pubmed:31419654;  doi:10.1016/j.biomaterials.2019.119414

23. OrgaQuant: Human Intestinal Organoid Localization and Quantification Using Deep Convolutional Neural Networks. Kassis T, Hernandez-Gordillo V, Langer R, Griffith LG. Sci Rep. pubmed:31462669;  doi:10.1038/s41598-019-48874-y

24. Taking paclitaxel coated balloons to a higher level: Predicting coating dissolution kinetics, tissue retention and dosing dynamics. Tzafriri AR, Parikh SA, Edelman ER. J Control Release. pubmed:31430500;  doi:10.1016/j.jconrel.2019.08.019

25. Immunogenicity of RNA Replicons Encoding HIV Env Immunogens Designed for Self-Assembly into Nanoparticles. Melo M, Porter E, Zhang Y, Silva M, Li N, Dobosh B, Liguori A, Skog P, Landais E, Menis S, Sok D, Nemazee D, Schief WR, Weiss R, Irvine DJ. Mol Ther. pubmed:31515132;  doi:10.1016/j.ymthe.2019.08.007

26. Rapid and high-precision sizing of single particles using parallel suspended microchannel resonator arrays and deconvolution. Stockslager MA, Olcum S, Knudsen SM, Kimmerling RJ, Cermak N, Payer KR, Agache V, Manalis SR. Rev Sci Instrum. pubmed:31472632;  doi:10.1063/1.5100861

27. A 'poly-transfection' method for rapid, one-pot characterization and optimization of genetic systems. Gam JJ, DiAndreth B, Jones RD, Huh J, Weiss R. Nucleic Acids Res. pubmed:31372658;  doi:10.1093/nar/gkz623

28. An on-chip model of protein paracellular and transcellular permeability in the microcirculation. Offeddu GS, Haase K, Gillrie MR, Li R, Morozova O, Hickman D, Knutson CG, Kamm RD. Biomaterials. pubmed:31112823;  doi:10.1016/j.biomaterials.2019.05.022

29. Studying nucleic envelope and plasma membrane mechanics of eukaryotic cells using confocal reflectance interferometric microscopy. Singh VR, Yang YA, Yu H, Kamm RD, Yaqoob Z, So PTC. Nat Commun. pubmed:31409824;  doi:10.1038/s41467-019-11645-4

30. Validation of a Semiautomated Natural Language Processing-Based Procedure for Meta-Analysis of Cancer Susceptibility Gene Penetrance. Deng Z, Yin K, Bao Y, Armengol VD, Wang C, Tiwari A, Barzilay R, Parmigiani G, Braun D, Hughes KS. JCO Clin Cancer Inform. pubmed:31419182;  doi:10.1200/CCI.19.00043

31. Using Large Datasets to Understand Nanotechnology. Paunovska K, Loughrey D, Sago CD, Langer R, Dahlman JE. Adv Mater. pubmed:31429126;  doi:10.1002/adma.201902798

32. Single-Nucleotide-Resolution Computing and Memory in Living Cells. Farzadfard F, Gharaei N, Higashikuni Y, Jung G, Cao J, Lu TK. Mol Cell. pubmed:31442423;  doi:10.1016/j.molcel.2019.07.011

33. Synthetic Genetic Circuits for Self-Actuated Cellular Nanomaterial Fabrication Devices. Olmez TT, Sahin Kehribar E, Isilak ME, Lu TK, Seker UOS. ACS Synth Biol. pubmed:31419103;  doi:10.1021/acssynbio.9b00235

34. Computer-aided design of mastoparan-like peptides enables the generation of non-toxic variants with extended antibacterial properties. Oshiro KGN, Candido ES, Chan LY, Torres MT, Monges BED, Rodrigues SG, Porto WF, Ribeiro SM, Troeira Henriques S, Lu TK, de la Fuente-Nunez C, Craik DJ, Franco OL, Cardoso MH. J Med Chem. pubmed:31411881;  doi:10.1021/acs.jmedchem.9b00915