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: February 2020

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1. Emerging Roles for Branched-Chain Amino Acid Metabolism in Cancer. Sivanand S, Vander Heiden MG. Cancer Cell. pubmed:32049045;  doi:10.1016/j.ccell.2019.12.011

2. The Angiosarcoma Project: enabling genomic and clinical discoveries in a rare cancer through patient-partnered research. Painter CA, Jain E, Tomson BN, Dunphy M, Stoddard RE, Thomas BS, Damon AL, Shah S, Kim D, Gomez Tejeda Zanudo J, Hornick JL, Chen YL, Merriam P, Raut CP, Demetri GD, Van Tine BA, Lander ES, Golub TR, Wagle N. Nat Med. pubmed:32042194;  doi:10.1038/s41591-019-0749-z

3. The scaffold protein IQGAP1 is crucial for extravasation and metastasis. Hebert JD, Tian C, Lamar JM, Rickelt S, Abbruzzese G, Liu X, Hynes RO. Sci Rep. pubmed:32051509;  doi:10.1038/s41598-020-59438-w

4. The primary mechanism of cytotoxicity of the chemotherapeutic agent CX-5461 is topoisomerase II poisoning. Bruno PM, Lu M, Dennis KA, Inam H, Moore CJ, Sheehe J, Elledge SJ, Hemann MT, Pritchard JR. Proc Natl Acad Sci U S A. pubmed:32041867;  doi:10.1073/pnas.1921649117

5. Identification of cancer driver genes based on nucleotide context. Dietlein F, Weghorn D, Taylor-Weiner A, Richters A, Reardon B, Liu D, Lander ES, Van Allen EM, Sunyaev SR. Nat Genet. pubmed:32015527;  doi:10.1038/s41588-019-0572-y

6. Formyl Peptide Receptor-1 Blockade Prevents Receptor Regulation by Mitochondrial Danger-Associated Molecular Patterns and Preserves Neutrophil Function After Trauma. Itagaki K, Kaczmarek E, Kwon WY, Chen L, Vlkova B, Zhang Q, Rica I, Yaffe MB, Campbell Y, Marusich MF, Wang JM, Gong WH, Gao JL, Jung F, Douglas G, Otterbein LE, Hauser CJ. Crit Care Med. pubmed:31939811;  doi:10.1097/CCM.0000000000004094

7. Quantifying residue-specific conformational dynamics of a highly reactive 29-mer peptide. Lindemann WR, Evans ED, Mijalis AJ, Saouaf OM, Pentelute BL, Ortony JH. Sci Rep. pubmed:32054898;  doi:10.1038/s41598-020-59047-7

8. Atomic structures of closed and open influenza B M2 proton channel reveal the conduction mechanism. Mandala VS, Loftis AR, Shcherbakov AA, Pentelute BL, Hong M. Nat Struct Mol Biol. pubmed:32015551;  doi:10.1038/s41594-019-0371-2

9. Distribution and storage of inflammatory memory in barrier tissues. Ordovas-Montanes J, Beyaz S, Rakoff-Nahoum S, Shalek AK. Nat Rev Immunol. pubmed:32015472;  doi:10.1038/s41577-019-0263-z

10. Layer-by-Layer Biomaterials for Drug Delivery. Alkekhia D, Hammond PT, Shukla A. Annu Rev Biomed Eng. pubmed:32084319;  doi:10.1146/annurev-bioeng-060418-052350

11. External Validation of a Deep Learning Model for Predicting Mammographic Breast Density in Routine Clinical Practice. Dontchos BN, Yala A, Barzilay R, Xiang J, Lehman CD. Acad Radiol. pubmed:32089465;  doi:10.1016/j.acra.2019.12.012

12. Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV. Int J Mol Sci. pubmed:32121243;  doi:10.3390/ijms21051644

13. The bioprinting roadmap. Sun W, Starly B, Daly AC, Burdick JA, Groll J, Skeldon G, Shu W, Sakai Y, Shinohara M, Nishikawa M, Jang J, Cho DW, Nie M, Takeuchi S, Ostrovidov S, Khademhosseini A, Kamm RD, Mironov V, Moroni L, Ozbolat IT. Biofabrication. pubmed:32031083;  doi:10.1088/1758-5090/ab5158

14. Cyclodextrins in drug delivery: applications in gene and combination therapy. Haley RM, Gottardi R, Langer R, Mitchell MJ. Drug Deliv Transl Res. pubmed:32077052;  doi:10.1007/s13346-020-00724-5

15. A Deep Learning Approach to Antibiotic Discovery. Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackerman Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. Cell. pubmed:32084340;  doi:10.1016/j.cell.2020.01.021

16. A geometrically adaptable heart valve replacement. Hofferberth SC, Saeed MY, Tomholt L, Fernandes MC, Payne CJ, Price K, Marx GR, Esch JJ, Brown DW, Brown J, Hammer PE, Bianco RW, Weaver JC, Edelman ER, Del Nido PJ. Sci Transl Med. pubmed:32075944;  doi:10.1126/scitranslmed.aay4006

17. Translating preclinical models to humans. Brubaker DK, Lauffenburger DA. Science. pubmed:32054749;  doi:10.1126/science.aay8086

18. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Holland CH, Tanevski J, Perales-Paton J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Genome Biol. pubmed:32051003;  doi:10.1186/s13059-020-1949-z

19. Glucose-responsive insulin patch for the regulation of blood glucose in mice and minipigs. Yu J, Wang J, Zhang Y, Chen G, Mao W, Ye Y, Kahkoska AR, Buse JB, Langer R, Gu Z. Nat Biomed Eng. pubmed:32015407;  doi:10.1038/s41551-019-0508-y

20. All-Optical Electrophysiology Reveals the Role of Lateral Inhibition in Sensory Processing in Cortical Layer 1. Fan LZ, Kheifets S, Bohm UL, Wu H, Piatkevich KD, Xie ME, Parot V, Ha Y, Evans KE, Boyden ES, Takesian AE, Cohen AE. Cell. pubmed:31978320;  doi:10.1016/j.cell.2020.01.001

21. Tuning Nanoparticle Interactions with Ovarian Cancer through Layer-by-Layer Modification of Surface Chemistry. Correa S, Boehnke N, Barberio AE, Deiss-Yehiely E, Shi A, Oberlton B, Smith SG, Zervantonakis I, Dreaden EC, Hammond PT. ACS Nano. pubmed:31971772;  doi:10.1021/acsnano.9b09213

22. Theranostic Layer-by-Layer Nanoparticles for Simultaneous Tumor Detection and Gene Silencing. Boehnke N, Correa S, Hao L, Wang W, Straehla JP, Bhatia SN, Hammond PT. Angew Chem Int Ed Engl. pubmed:31747099;  doi:10.1002/anie.201911762

23. Biology-inspired microphysiological systems to advance patient benefit and animal welfare in drug development. Marx U, Akabane T, Andersson TB, Baker E, Beilmann M, Beken S, Brendler-Schwaab S, Cirit M, David R, Dehne EM, Durieux I, Ewart L, Fitzpatrick SC, Frey O, Fuchs F, Griffith LG, Hamilton GA, Hartung T, Hoeng J, Hogberg H, Hughes DJ, Ingber DE, Iskandar A, Kanamori T, Kojima H, Kuehnl J, Leist M, Li B, Loskill P, Mendrick DL, Neumann T, Pallocca G, Rusyn I, Smirnova L, Steger-Hartmann T, Tagle DA, Tonevitsky A, Tsyb S, Trapecar M, Van de Water B, Van den Eijnden-van Raaij J, Vulto P, Watanabe K, Wolf A, Zhou X, Roth A. ALTEX. pubmed:32113184;  doi:10.14573/altex.2001241