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: June 2019

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1. DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction. Weinstein JA, Regev A, Zhang F. Cell. pubmed:31230717;  doi:10.1016/j.cell.2019.05.019

2. Clot activators do not expedite the time to predict massive transfusion in trauma patients analyzed with tissue plasminogen activator thrombelastography. Walker CB, Moore EE, Kam A, Dexter-Meldrum J, Nydam TL, Chapman MP, Chandler J, Sauaia A, Barrett CD, Yaffe MB, Moore HB. Surgery. pubmed:31230841;  doi:10.1016/j.surg.2019.05.011

3. Large-scale chemical-genetics yields new M tuberculosis inhibitor classes. Johnson EO, LaVerriere E, Office E, Stanley M, Meyer E, Kawate T, Gomez JE, Audette RE, Bandyopadhyay N, Betancourt N, Delano K, Da Silva I, Davis J, Gallo C, Gardner M, Golas AJ, Guinn KM, Kennedy S, Korn R, McConnell JA, Moss CE, Murphy KC, Nietupski RM, Papavinasasundaram KG, Pinkham JT, Pino PA, Proulx MK, Ruecker N, Song N, Thompson M, Trujillo C, Wakabayashi S, Wallach JB, Watson C, Ioerger TR, Lander ES, Hubbard BK, Serrano-Wu MH, Ehrt S, Fitzgerald M, Rubin EJ, Sassetti CM, Schnappinger D, Hung DT. Nature. pubmed:31217586;  doi:10.1038/s41586-019-1315-z

4. Gut Organoids: Mini-Tissues in Culture to Study Intestinal Physiology and Disease. Almeqdadi M, Mana MD, Roper J, Yilmaz OH. Am J Physiol Cell Physiol. pubmed:31216420;  doi:10.1152/ajpcell.00300.2017

5. Phenotypic selection with an intrabody library reveals an anti-apoptotic function of PKM2 requiring Mitofusin-1. Liu T, Kuwana T, Zhang H, Vander Heiden MG, Lerner RA, Newmeyer DD. PLoS Biol. pubmed:31181072;  doi:10.1371/journal.pbio.2004413

6. Breakthrough Moments: Genome Editing and Organoids. Roper J, Yilmaz OH. Cell Stem Cell. pubmed:31173713;  doi:10.1016/j.stem.2019.05.008

7. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. Nat Commun. pubmed:31160565;  doi:10.1038/s41467-019-10307-9

8. Why haploinsufficiency persists. Morrill SA, Amon A. Proc Natl Acad Sci U S A. pubmed:31142641;  doi:10.1073/pnas.1900437116

9. Rate of brain aging and APOE epsilon4 are synergistic risk factors for Alzheimer's disease. Glorioso CA, Pfenning AR, Lee SS, Bennett DA, Sibille EL, Kellis M, Guarente LP. Life Sci Alliance. pubmed:31133613;  doi:10.26508/lsa.201900303

10. A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia. Baryawno N, Przybylski D, Kowalczyk MS, Kfoury Y, Severe N, Gustafsson K, Kokkaliaris KD, Mercier F, Tabaka M, Hofree M, Dionne D, Papazian A, Lee D, Ashenberg O, Subramanian A, Vaishnav ED, Rozenblatt-Rosen O, Regev A, Scadden DT. Cell. pubmed:31130381;  doi:10.1016/j.cell.2019.04.040

11. A Small Molecule Targeting Mutagenic Translesion Synthesis Improves Chemotherapy. Wojtaszek JL, Chatterjee N, Najeeb J, Ramos A, Lee M, Bian K, Xue JY, Fenton BA, Park H, Li D, Hemann MT, Hong J, Walker GC, Zhou P. Cell. pubmed:31178121;  doi:10.1016/j.cell.2019.05.028

12. Protein aggregation mediates stoichiometry of protein complexes in aneuploid cells. Brennan CM, Vaites LP, Wells JN, Santaguida S, Paulo JA, Storchova Z, Harper JW, Marsh JA, Amon A. Genes Dev. pubmed:31196865;  doi:10.1101/gad.327494.119

13. Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis. Ludwig LS, Lareau CA, Bao EL, Nandakumar SK, Muus C, Ulirsch JC, Chowdhary K, Buenrostro JD, Mohandas N, An X, Aryee MJ, Regev A, Sankaran VG. Cell Rep. pubmed:31189107;  doi:10.1016/j.celrep.2019.05.046

14. Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Velasco S, Kedaigle AJ, Simmons SK, Nash A, Rocha M, Quadrato G, Paulsen B, Nguyen L, Adiconis X, Regev A, Levin JZ, Arlotta P. Nature. pubmed:31168097;  doi:10.1038/s41586-019-1289-x

15. Determinants of nutrient limitation in cancer. Sullivan MR, Vander Heiden MG. Crit Rev Biochem Mol Biol. pubmed:31162937;  doi:10.1080/10409238.2019.1611733

16. Aneuploidy drives lethal progression in prostate cancer. Stopsack KH, Whittaker CA, Gerke TA, Loda M, Kantoff PW, Mucci LA, Amon A. Proc Natl Acad Sci U S A. pubmed:31085648;  doi:10.1073/pnas.1902645116

17. Rebalancing protein homeostasis enhances tumor antigen presentation. Jaeger AM, Stopfer L, Lee S, Gaglia G, Sandel D, Santagata S, Lin NU, Trepel JB, White FM, Jacks T, Lindquist S, Whitesell L. Clin Cancer Res. pubmed:31213460;  doi:10.1158/1078-0432.CCR-19-0596

18. Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair Deficient Colorectal Cancer. Gurjao C, Liu D, Hofree M, AlDubayan SH, Wakiro I, Su MJ, Felt K, Gjini E, Brais LK, Rotem A, Rosenthal MH, Rozenblatt-Rosen O, Rodig S, Ng K, Van Allen EM, Corsello SM, Ogino S, Regev A, Nowak JA, Giannakis M. Cancer Immunol Res. pubmed:31217164;  doi:10.1158/2326-6066.CIR-18-0683

19. Anchoring of intratumorally administered cytokines to collagen safely potentiates systemic cancer immunotherapy. Momin N, Mehta NK, Bennett NR, Ma L, Palmeri JR, Chinn MM, Lutz EA, Kang B, Irvine DJ, Spranger S, Wittrup KD. Sci Transl Med. pubmed:31243150;  doi:10.1126/scitranslmed.aaw2614

20. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Xiao R, Chen JY, Liang Z, Luo D, Chen G, Lu ZJ, Chen Y, Zhou B, Li H, Du X, Yang Y, San M, Wei X, Liu W, Lecuyer E, Graveley BR, Yeo GW, Burge CB, Zhang MQ, Zhou Y, Fu XD. Cell. pubmed:31251911;  doi:10.1016/j.cell.2019.06.001

21. Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis. Ardain A, Domingo-Gonzalez R, Das S, Kazer SW, Howard NC, Singh A, Ahmed M, Nhamoyebonde S, Rangel-Moreno J, Ogongo P, Lu L, Ramsuran D, de la Luz Garcia-Hernandez M, K Ulland T, Darby M, Park E, Karim F, Melocchi L, Madansein R, Dullabh KJ, Dunlap M, Marin-Agudelo N, Ebihara T, Ndung'u T, Kaushal D, Pym AS, Kolls JK, Steyn A, Zuniga J, Horsnell W, Yokoyama WM, Shalek AK, Kloverpris HN, Colonna M, Leslie A, Khader SA. Nature. pubmed:31168092;  doi:10.1038/s41586-019-1276-2

22. Mutations in pmrB confer cross-resistance between the LptD inhibitor POL7080 and colistin in Pseudomonas aeruginosa. Romano KP, Warrier T, Poulsen BE, Nguyen PH, Loftis AR, Saebi A, Pentelute BL, Hung DT. Antimicrob Agents Chemother. pubmed:31235628;  doi:10.1128/AAC.00511-19

23. Thermoresponsive nanoemulsion-based gel synthesized through a low-energy process. Hashemnejad SM, Badruddoza AZM, Zarket B, Ricardo Castaneda C, Doyle PS. Nat Commun. pubmed:31227703;  doi:10.1038/s41467-019-10749-1

24. Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors. Chu ND, Bi HS, Emerson RO, Sherwood AM, Birnbaum ME, Robins HS, Alm EJ. BMC Immunol. pubmed:31226930;  doi:10.1186/s12865-019-0300-5

25. Aorticorenal Ganglia Pacing: A Step Forward in Unblinding Renal Denervation Procedures?. Mahfoud F, Tschernig T, Edelman ER. JACC Cardiovasc Interv. pubmed:31221302;  doi:10.1016/j.jcin.2019.05.020

26. Fc Glycan-Mediated Regulation of Placental Antibody Transfer. Jennewein MF, Goldfarb I, Dolatshahi S, Cosgrove C, Noelette FJ, Krykbaeva M, Das J, Sarkar A, Gorman MJ, Fischinger S, Boudreau CM, Brown J, Cooperrider JH, Aneja J, Suscovich TJ, Graham BS, Lauer GM, Goetghebuer T, Marchant A, Lauffenburger D, Kim AY, Riley LE, Alter G. Cell. pubmed:31204102;  doi:10.1016/j.cell.2019.05.044

27. Massively parallel screening of synthetic microbial communities. Kehe J, Kulesa A, Ortiz A, Ackerman CM, Thakku SG, Sellers D, Kuehn S, Gore J, Friedman J, Blainey PC. Proc Natl Acad Sci U S A. pubmed:31186361;  doi:10.1073/pnas.1900102116

28. Hemodynamic consequences of a multilayer flow modulator in aortic dissection. Athanasiou LS, Nezami FR, Edelman ER. Med Biol Eng Comput. pubmed:31209712;  doi:10.1007/s11517-019-01997-w

29. Steerable Microinvasive Probes for Localized Drug Delivery to Deep Tissue. Cotler MJ, Rousseau EB, Ramadi KB, Fang J, Graybiel AM, Langer R, Cima MJ. Small. pubmed:31183933;  doi:10.1002/smll.201901459

30. IFN-gamma-independent immune markers of Mycobacterium tuberculosis exposure. Lu LL, Smith MT, Yu KKQ, Luedemann C, Suscovich TJ, Grace PS, Cain A, Yu WH, McKitrick TR, Lauffenburger D, Cummings RD, Mayanja-Kizza H, Hawn TR, Boom WH, Stein CM, Fortune SM, Seshadri C, Alter G. Nat Med. pubmed:31110348;  doi:10.1038/s41591-019-0441-3

31. Gamma Entrainment Binds Higher-Order Brain Regions and Offers Neuroprotection. Adaikkan C, Middleton SJ, Marco A, Pao PC, Mathys H, Kim DN, Gao F, Young JZ, Suk HJ, Boyden ES, McHugh TJ, Tsai LH. Neuron. pubmed:31076275;  doi:10.1016/j.neuron.2019.04.011

32. Outlooks on Three-Dimensional Printing for Ocular Biomaterials Research. Fenton OS, Paolini M, Andresen JL, Muller FJ, Langer R. J Ocul Pharmacol Ther. pubmed:31211652;  doi:10.1089/jop.2018.0142

33. Microfluidic assessment of metastatic potential. Wan Z, Kamm RD. Nat Biomed Eng. pubmed:31175331;  doi:10.1038/s41551-019-0412-5

34. Analysis of an Integrated Human Multi-organ Microphysiological System for Combined Tolcapone Metabolism and Brain Metabolomics. Wang X, Cirit M, Wishnok JS, Griffith LG, Tannenbaum SR. Anal Chem. pubmed:31181164;  doi:10.1021/acs.analchem.9b02224

35. A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS). Wu MR, Nissim L, Stupp D, Pery E, Binder-Nissim A, Weisinger K, Enghuus C, Palacios SR, Humphrey M, Zhang Z, Maria Novoa E, Kellis M, Weiss R, Rabkin SD, Tabach Y, Lu TK. Nat Commun. pubmed:31253799;  doi:10.1038/s41467-019-10912-8

36. Creating fluorescent quantum defects in carbon nanotubes using hypochlorite and light. Lin CW, Bachilo SM, Zheng Y, Tsedev U, Huang S, Weisman RB, Belcher AM. Nat Commun. pubmed:31253811;  doi:10.1038/s41467-019-10917-3

37. Long-term implant fibrosis prevention in rodents and non-human primates using crystallized drug formulations. Farah S, Doloff JC, Muller P, Sadraei A, Han HJ, Olafson K, Vyas K, Tam HH, Hollister-Lock J, Kowalski PS, Griffin M, Meng A, McAvoy M, Graham AC, McGarrigle J, Oberholzer J, Weir GC, Greiner DL, Langer R, Anderson DG. Nat Mater. pubmed:31235902;  doi:10.1038/s41563-019-0377-5