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: March 2020

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1. Is There a Role for Tissue Plasminogen Activator (tPA) as a Novel Treatment for Refractory COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS)?. Moore HB, Barrett CD, Moore EE, McIntyre RC, Moore PK, Talmor DS, Moore FA, Yaffe MB. J Trauma Acute Care Surg. pubmed:32281766;  doi:10.1097/TA.0000000000002694

2. Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells. Michowski W, Chick JM, Chu C, Kolodziejczyk A, Wang Y, Suski JM, Abraham B, Anders L, Day D, Dunkl LM, Li Cheong Man M, Zhang T, Laphanuwat P, Bacon NA, Liu L, Fassl A, Sharma S, Otto T, Jecrois E, Han R, Sweeney KE, Marro S, Wernig M, Geng Y, Moses A, Li C, Gygi SP, Young RA, Sicinski P. Mol Cell. pubmed:32240602;  doi:10.1016/j.molcel.2020.03.010

3. Dietary modifications for enhanced cancer therapy. Kanarek N, Petrova B, Sabatini DM. Nature. pubmed:32214253;  doi:10.1038/s41586-020-2124-0

4. Gut-Liver Physiomimetics Reveal Paradoxical Modulation of IBD-Related Inflammation by Short-Chain Fatty Acids. Trapecar M, Communal C, Velazquez J, Maass CA, Huang YJ, Schneider K, Wright CW, Butty V, Eng G, Yilmaz O, Trumper D, Griffith LG. Cell Syst. pubmed:32191873;  doi:10.1016/j.cels.2020.02.008

5. Drosophila enabled promotes synapse morphogenesis and regulates active zone form and function. McNeill EM, Thompson C, Berke B, Chou VT, Rusch J, Duckworth A, DeProto J, Taylor A, Gates J, Gertler F, Keshishian H, Van Vactor D. Neural Dev. pubmed:32183907;  doi:10.1186/s13064-020-00141-x

6. Circulating Factors in Trauma Plasma Activate Specific Human Immune Cell Subsets. Cahill LA, Guo F, Nguyen J, Zhang F, Seshadri A, Keegan J, Hauser CJ, Otterbein LE, Robson S, Shaefi S, Yaffe MB, Lederer JA. Injury. pubmed:32171537;  doi:10.1016/j.injury.2020.03.009

7. A Metabolomics Analysis of Adiposity and Advanced Prostate Cancer Risk in the Health Professionals Follow-Up Study. Dickerman BA, Ebot EM, Healy BC, Wilson KM, Eliassen AH, Ascherio A, Pernar CH, Zeleznik OA, Vander Heiden MG, Clish CB, Giovannucci E, Mucci LA. Metabolites. pubmed:32164144;  doi:10.3390/metabo10030099

8. Influence of Tranexamic Acid on Inflammatory Signaling in Trauma. Barrett CD, Kong YW, Yaffe MB. Semin Thromb Hemost. pubmed:32160643;  doi:10.1055/s-0040-1702169

9. Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features. Ray JP, de Boer CG, Fulco CP, Lareau CA, Kanai M, Ulirsch JC, Tewhey R, Ludwig LS, Reilly SK, Bergman DT, Engreitz JM, Issner R, Finucane HK, Lander ES, Regev A, Hacohen N. Nat Commun. pubmed:32144282;  doi:10.1038/s41467-020-15022-4

10. MicroRNAs organize intrinsic variation into stem cell states. Chakraborty M, Hu S, Visness E, Del Giudice M, De Martino A, Bosia C, Sharp PA, Garg S. Proc Natl Acad Sci U S A. pubmed:32139605;  doi:10.1073/pnas.1920695117

11. A Synthesis Concerning Conservation and Divergence of Cell Types across Epithelia. Montoro DT, Haber AL, Rood JE, Regev A, Rajagopal J. Cold Spring Harb Perspect Biol. pubmed:32122885;  doi:10.1101/cshperspect.a035733

12. DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis. Shao Z, Flynn RA, Crowe JL, Zhu Y, Liang J, Jiang W, Aryan F, Aoude P, Bertozzi CR, Estes VM, Lee BJ, Bhagat G, Zha S, Calo E. Nature. pubmed:32103174;  doi:10.1038/s41586-020-2041-2

13. CD36 - the Achilles' heel of Treg cells. Horton BL, Spranger S. Nat Immunol. pubmed:32066948;  doi:10.1038/s41590-020-0601-0

14. A framework for advancing our understanding of cancer-associated fibroblasts. Sahai E, Astsaturov I, Cukierman E, DeNardo DG, Egeblad M, Evans RM, Fearon D, Greten FR, Hingorani SR, Hunter T, Hynes RO, Jain RK, Janowitz T, Jorgensen C, Kimmelman AC, Kolonin MG, Maki RG, Powers RS, Pure E, Ramirez DC, Scherz-Shouval R, Sherman MH, Stewart S, Tlsty TD, Tuveson DA, Watt FM, Weaver V, Weeraratna AT, Werb Z. Nat Rev Cancer. pubmed:31980749;  doi:10.1038/s41568-019-0238-1

15. Relevance and Regulation of Cell Density. Neurohr GE, Amon A. Trends Cell Biol. pubmed:31980346;  doi:10.1016/j.tcb.2019.12.006

16. Secondary Amino Alcohols: Traceless Cleavable Linkers for Use in Affinity Capture and Release. Pomplun S, Shugrue C, Schmitt AM, Schissel CK, Farquhar CE, Pentelute B. Angew Chem Int Ed Engl. pubmed:32227406;  doi:10.1002/anie.202003478

17. Introduction: Peptide Chemistry. Loas A, Pentelute BL. Chem Rev. pubmed:32208601;  doi:10.1021/acs.chemrev.0c00136

18. IL-5Ralpha marks nasal polyp IgG4 and IgE-expressing cells in aspirin-exacerbated respiratory disease. Buchheit KM, Dwyer DF, Ordovas-Montanes J, Katz HR, Lewis E, Vukovic M, Lai J, Bankova L, Bhattacharyya N, Shalek AK, Barrett NA, Boyce JA, Laidlaw TM. J Allergy Clin Immunol. pubmed:32199912;  doi:10.1016/j.jaci.2020.02.035

19. Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Taketani M, Zhang J, Zhang S, Triassi AJ, Huang YJ, Griffith LG, Voigt CA. Nat Biotechnol. pubmed:32231334;  doi:10.1038/s41587-020-0468-5

20. A retrievable implant for the long-term encapsulation and survival of therapeutic xenogeneic cells. Bose S, Volpatti LR, Thiono D, Yesilyurt V, McGladrigan C, Tang Y, Facklam A, Wang A, Jhunjhunwala S, Veiseh O, Hollister-Lock J, Bhattacharya C, Weir GC, Greiner DL, Langer R, Anderson DG. Nat Biomed Eng. pubmed:32231313;  doi:10.1038/s41551-020-0538-5

21. Shaping humoral immunity to vaccines through antigen-displaying nanoparticles. Irvine DJ, Read BJ. Curr Opin Immunol. pubmed:32200132;  doi:10.1016/j.coi.2020.01.007

22. Impact of concomitant vasoactive treatment and mechanical left ventricular unloading in a porcine model of profound cardiogenic shock. Udesen NLJ, Helgestad OKL, Banke ABS, Frederiksen PH, Josiassen J, Jensen LO, Schmidt H, Edelman ER, Chang BY, Ravn HB, Moller JE. Crit Care. pubmed:32188462;  doi:10.1186/s13054-020-2816-8

23. Machine Learning Uncovers Food- and Excipient-Drug Interactions. Reker D, Shi Y, Kirtane AR, Hess K, Zhong GJ, Crane E, Lin CH, Langer R, Traverso G. Cell Rep. pubmed:32187543;  doi:10.1016/j.celrep.2020.02.094

24. Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer. Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner GJ, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes ME, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg DS, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop I, Love JC, Makrigiorgos GM, Partridge AH, Mayer EL, Golub TR, Adalsteinsson VA. Clin Cancer Res. pubmed:32170028;  doi:10.1158/1078-0432.CCR-19-3005

25. Microfluidic platform for three-dimensional cell culture under spatiotemporal heterogeneity of oxygen tension. Koens R, Tabata Y, Serrano JC, Aratake S, Yoshino D, Kamm RD, Funamoto K. APL Bioeng. pubmed:32161836;  doi:10.1063/1.5127069

26. Magnetic Retrieval of Encapsulated Beta Cell Transplants from Diabetic Mice Using Dual-Function MRI Visible and Retrievable Microcapsules. Delcassian D, Luzhansky I, Spanoudaki V, Bochenek M, McGladrigan C, Nguyen A, Norcross S, Zhu Y, Shan CS, Hausser R, Shakesheff KM, Langer R, Anderson DG. Adv Mater. pubmed:32134138;  doi:10.1002/adma.201904502

27. Embedded droplet printing in yield-stress fluids. Nelson AZ, Kundukad B, Wong WK, Khan SA, Doyle PS. Proc Natl Acad Sci U S A. pubmed:32127482;  doi:10.1073/pnas.1919363117

28. Mixed Valvular Disease Following Transcatheter Aortic Valve Replacement: Quantification and Systematic Differentiation Using Clinical Measurements and Image-Based Patient-Specific In Silico Modeling. Keshavarz-Motamed Z, Khodaei S, Rikhtegar Nezami F, Amrute JM, Lee SJ, Brown J, Ben-Assa E, Garcia Camarero T, Ruano Calvo J, Sellers S, Blanke P, Leipsic J, de la Torre Hernandez JM, Edelman ER. J Am Heart Assoc. pubmed:32106747;  doi:10.1161/JAHA.119.015063

29. Engineered immunogen binding to alum adjuvant enhances humoral immunity. Moyer TJ, Kato Y, Abraham W, Chang JYH, Kulp DW, Watson N, Turner HL, Menis S, Abbott RK, Bhiman JN, Melo MB, Simon HA, Herrera-De la Mata S, Liang S, Seumois G, Agarwal Y, Li N, Burton DR, Ward AB, Schief WR, Crotty S, Irvine DJ. Nat Med. pubmed:32066977;  doi:10.1038/s41591-020-0753-3

30. An immune-cell signature of bacterial sepsis. Reyes M, Filbin MR, Bhattacharyya RP, Billman K, Eisenhaure T, Hung DT, Levy BD, Baron RM, Blainey PC, Goldberg MB, Hacohen N. Nat Med. pubmed:32066974;  doi:10.1038/s41591-020-0752-4

31. Endometrioma, the follicular fluid inflammatory network and its association with oocyte and embryo characteristics. Yland J, Carvalho LFP, Beste M, Bailey A, Thomas C, Abrao MS, Racowsky C, Griffith L, Missmer SA. Reprod Biomed Online. pubmed:32057676;  doi:10.1016/j.rbmo.2019.12.005

32. Clostridioides difficile-Associated Antibiotics Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms. Kester JC, Brubaker DK, Velazquez J, Wright C, Lauffenburger DA, Griffith LG. Antimicrob Agents Chemother. pubmed:31988098;  doi:10.1128/AAC.01404-19

33. Trends in Therapeutic Conjugates: Bench to Clinic. Rudra A, Li J, Shakur R, Bhagchandani S, Langer R. Bioconjug Chem. pubmed:31990184;  doi:10.1021/acs.bioconjchem.9b00828