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 2020

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1. MAUDE: inferring expression changes in sorting-based CRISPR screens. de Boer CG, Ray JP, Hacohen N, Regev A. Genome Biol. pubmed:32493396;  doi:10.1186/s13059-020-02046-8

2. Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator. Shemesh OA, Linghu C, Piatkevich KD, Goodwin D, Celiker OT, Gritton HJ, Romano MF, Gao R, Yu CJ, Tseng HA, Bensussen S, Narayan S, Yang CT, Freifeld L, Siciliano CA, Gupta I, Wang J, Pak N, Yoon YG, Ullmann JFP, Guner-Ataman B, Noamany H, Sheinkopf ZR, Park WM, Asano S, Keating AE, Trimmer JS, Reimer J, Tolias AS, Bear MF, Tye KM, Han X, Ahrens MB, Boyden ES. Neuron. pubmed:32592656;  doi:10.1016/j.neuron.2020.05.029

3. A single-cell landscape of high-grade serous ovarian cancer. Izar B, Tirosh I, Stover EH, Wakiro I, Cuoco MS, Alter I, Rodman C, Leeson R, Su MJ, Shah P, Iwanicki M, Walker SR, Kanodia A, Melms JC, Mei S, Lin JR, Porter CBM, Slyper M, Waldman J, Jerby-Arnon L, Ashenberg O, Brinker TJ, Mills C, Rogava M, Vigneau S, Sorger PK, Garraway LA, Konstantinopoulos PA, Liu JF, Matulonis U, Johnson BE, Rozenblatt-Rosen O, Rotem A, Regev A. Nat Med. pubmed:32572264;  doi:10.1038/s41591-020-0926-0

4. Cell Atlas of The Human Fovea and Peripheral Retina. Yan W, Peng YR, van Zyl T, Regev A, Shekhar K, Juric D, Sanes JR. Sci Rep. pubmed:32555229;  doi:10.1038/s41598-020-66092-9

5. Partitioning of cancer therapeutics in nuclear condensates. Klein IA, Boija A, Afeyan LK, Hawken SW, Fan M, Dall'Agnese A, Oksuz O, Henninger JE, Shrinivas K, Sabari BR, Sagi I, Clark VE, Platt JM, Kar M, McCall PM, Zamudio AV, Manteiga JC, Coffey EL, Li CH, Hannett NM, Guo YE, Decker TM, Lee TI, Zhang T, Weng JK, Taatjes DJ, Chakraborty A, Sharp PA, Chang YT, Hyman AA, Gray NS, Young RA. Science. pubmed:32554597;  doi:10.1126/science.aaz4427

6. H3.3 Nucleosome Assembly Mutants Display a Late-Onset Maternal Effect. Burkhart KB, Sando SR, Corrionero A, Horvitz HR. Curr Biol. pubmed:32470364;  doi:10.1016/j.cub.2020.04.046

7. Functional analysis of CX3CR1 in human induced pluripotent stem (iPS) cell-derived microglia-like cells. Murai N, Mitalipova M, Jaenisch R. Eur J Neurosci. pubmed:32579729;  doi:10.1111/ejn.14879

8. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects. Mereu E, Lafzi A, Moutinho C, Ziegenhain C, McCarthy DJ, Alvarez-Varela A, Batlle E, Sagar, Grun D, Lau JK, Boutet SC, Sanada C, Ooi A, Jones RC, Kaihara K, Brampton C, Talaga Y, Sasagawa Y, Tanaka K, Hayashi T, Braeuning C, Fischer C, Sauer S, Trefzer T, Conrad C, Adiconis X, Nguyen LT, Regev A, Levin JZ, Parekh S, Janjic A, Wange LE, Bagnoli JW, Enard W, Gut M, Sandberg R, Nikaido I, Gut I, Stegle O, Heyn H. Nat Biotechnol. pubmed:32518403;  doi:10.1038/s41587-020-0469-4

9. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Ding J, Adiconis X, Simmons SK, Kowalczyk MS, Hession CC, Marjanovic ND, Hughes TK, Wadsworth MH, Burks T, Nguyen LT, Kwon JYH, Barak B, Ge W, Kedaigle AJ, Carroll S, Li S, Hacohen N, Rozenblatt-Rosen O, Shalek AK, Villani AC, Regev A, Levin JZ. Nat Biotechnol. pubmed:32341560;  doi:10.1038/s41587-020-0465-8

10. YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Re-entry into Systemic Circulation. Benjamin DC, Kang JH, Hamza B, King EM, Lamar JM, Manalis SR, Hynes RO. Cancer Res. pubmed:32591412;  doi:10.1158/0008-5472.CAN-20-0212

11. Phosphocholine accumulation and PHOSPHO1 depletion promote adipose tissue thermogenesis. Jiang M, Chavarria TE, Yuan B, Lodish HF, Huang NJ. Proc Natl Acad Sci U S A. pubmed:32554489;  doi:10.1073/pnas.1916550117

12. Disease-associated astrocytes in Alzheimer's disease and aging. Habib N, McCabe C, Medina S, Varshavsky M, Kitsberg D, Dvir-Szternfeld R, Green G, Dionne D, Nguyen L, Marshall JL, Chen F, Zhang F, Kaplan T, Regev A, Schwartz M. Nat Neurosci. pubmed:32341542;  doi:10.1038/s41593-020-0624-8

13. Guidelines and definitions for research on epithelial-mesenchymal transition. Yang J, Antin P, Berx G, Blanpain C, Brabletz T, Bronner M, Campbell K, Cano A, Casanova J, Christofori G, Dedhar S, Derynck R, Ford HL, Fuxe J, Garcia de Herreros A, Goodall GJ, Hadjantonakis AK, Huang RJY, Kalcheim C, Kalluri R, Kang Y, Khew-Goodall Y, Levine H, Liu J, Longmore GD, Mani SA, Massague J, Mayor R, McClay D, Mostov KE, Newgreen DF, Nieto MA, Puisieux A, Runyan R, Savagner P, Stanger B, Stemmler MP, Takahashi Y, Takeichi M, Theveneau E, Thiery JP, Thompson EW, Weinberg RA, Williams ED, Xing J, Zhou BP, Sheng G. Nat Rev Mol Cell Biol. pubmed:32300252;  doi:10.1038/s41580-020-0237-9

14. Increased lysosomal biomass is responsible for the resistance of triple-negative breast cancers to CDK4/6 inhibition. Fassl A, Brain C, Abu-Remaileh M, Stukan I, Butter D, Stepien P, Feit AS, Bergholz J, Michowski W, Otto T, Sheng Q, Loo A, Michael W, Tiedt R, DeAngelis C, Schiff R, Jiang B, Jovanovic B, Nowak K, Ericsson M, Cameron M, Gray N, Dillon D, Zhao JJ, Sabatini DM, Jeselsohn R, Brown M, Polyak K, Sicinski P. Sci Adv. pubmed:32704543;  doi:10.1126/sciadv.abb2210

15. Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition. Ngo B, Kim E, Osorio-Vasquez V, Doll S, Bustraan S, Liang RJ, Luengo A, Davidson SM, Ali A, Ferraro GB, Fischer GM, Eskandari R, Kang DS, Ni J, Plasger A, Rajasekhar VK, Kastenhuber ER, Bacha S, Sriram RK, Stein BD, Bakhoum SF, Snuderl M, Cotzia P, Healey JH, Mainolfi N, Suri V, Friedman A, Manfredi M, Sabatini DM, Jones DR, Yu M, Zhao JJ, Jain RK, Keshari KR, Davies MA, Vander Heiden MG, Hernando E, Mann M, Cantley LC, Pacold ME. Cancer Discov. pubmed:32571778;  doi:10.1158/2159-8290.CD-19-1228

16. A stapled POL kappa peptide targets REV1 to inhibit mutagenic translesion synthesis. Chatterjee N, D'Souza S, Shabab M, Harris CA, Hilinski GJ, Verdine GL, Walker GC. Environ Mol Mutagen. pubmed:32573829;  doi:10.1002/em.22395

17. Tenofovir prodrugs potently inhibit Epstein-Barr virus lytic DNA replication by targeting the viral DNA polymerase. Drosu NC, Edelman ER, Housman DE. Proc Natl Acad Sci U S A. pubmed:32409608;  doi:10.1073/pnas.2002392117

18. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Lavaert M, Liang KL, Vandamme N, Park JE, Roels J, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Vandekerckhove B, Leclercq G, Regev A, Van Vlierberghe P, Guilliams M, Teichmann SA, Saeys Y, Taghon T. Immunity. pubmed:32304633;  doi:10.1016/j.immuni.2020.03.019

19. Targeting Cancer Gene Dependencies with Anthrax-Mediated Delivery of Peptide Nucleic Acids. Lu Z, Paolella BR, Truex NL, Loftis AR, Liao X, Rabideau AE, Brown MS, Busanovich J, Beroukhim R, Pentelute BL. ACS Chem Biol. pubmed:32348107;  doi:10.1021/acschembio.9b01027

20. Ultra-large chemical libraries for the discovery of high-affinity peptide binders. Quartararo AJ, Gates ZP, Somsen BA, Hartrampf N, Ye X, Shimada A, Kajihara Y, Ottmann C, Pentelute BL. Nat Commun. pubmed:32576815;  doi:10.1038/s41467-020-16920-3

21. Novel Technology to Capture Objective Data from Patients' Recovery from Laparoscopic Endometriosis Surgery. Loring M, Kabelac Z, Munir U, Yue S, Ephraim HY, Rahul H, Isaacson KB, Griffith LG, Katabi D. J Minim Invasive Gynecol. pubmed:32615330;  doi:10.1016/j.jmig.2020.06.011

22. Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition. Stopfer LE, Mesfin JM, Joughin BA, Lauffenburger DA, White FM. Nat Commun. pubmed:32488085;  doi:10.1038/s41467-020-16588-9

23. Engineering PEG-based hydrogels to foster efficient endothelial network formation in free-swelling and confined microenvironments. Brown A, He H, Trumper E, Valdez J, Hammond P, Griffith LG. Biomaterials. pubmed:32172030;  doi:10.1016/j.biomaterials.2020.119921

24. "Menstruation: Science and Society". Critchley HOD, Babayev E, Bulun SE, Clark S, Garcia-Grau I, Gregersen PK, Kilcoyne A, Kim JJ, Lavender M, Marsh EE, Matteson KA, Maybin JA, Metz C, Moreno I, Silk K, Sommer M, Simon C, Tariyal R, Taylor HS, Wagner GP, Griffith LG. Am J Obstet Gynecol. pubmed:32707266;  doi:10.1016/j.ajog.2020.06.004

25. Computationally Guided Intracerebral Drug Delivery via Chronically Implanted Microdevices. Ramadi KB, Bashyam A, Frangieh CJ, Rousseau EB, Cotler MJ, Langer R, Graybiel AM, Cima MJ. Cell Rep. pubmed:32521259;  doi:10.1016/j.celrep.2020.107734

26. Self-assembled cGAMP-STINGDeltaTM signaling complex as a bioinspired platform for cGAMP delivery. He Y, Hong C, Yan EZ, Fletcher SJ, Zhu G, Yang M, Li Y, Sun X, Irvine DJ, Li J, Hammond PT. Sci Adv. pubmed:32582856;  doi:10.1126/sciadv.aba7589

27. Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines. Mehta NK, Pradhan RV, Soleimany AP, Moynihan KD, Rothschilds AM, Momin N, Rakhra K, Mata-Fink J, Bhatia SN, Wittrup KD, Irvine DJ. Nat Biomed Eng. pubmed:32483299;  doi:10.1038/s41551-020-0563-4

28. A Nanoprimer To Improve the Systemic Delivery of siRNA and mRNA. Saunders NRM, Paolini MS, Fenton OS, Poul L, Devalliere J, Mpambani F, Darmon A, Bergere M, Jibault O, Germain M, Langer R. Nano Lett. pubmed:32357299;  doi:10.1021/acs.nanolett.0c00752

29. Biohybrid systems: Borrowing from nature to make better machines. Menciassi A, Takeuchi S, Kamm RD. APL Bioeng. pubmed:32596624;  doi:10.1063/5.0014918

30. Development of a long-acting direct-acting antiviral system for hepatitis C virus treatment in swine. Verma M, Chu JN, Salama JAF, Faiz MT, Eweje F, Gwynne D, Lopes A, Hess K, Soares V, Steiger C, McManus R, Koeppen R, Hua T, Hayward A, Collins J, Tamang SM, Ishida K, Miller JB, Katz S, Slocum AH, Sulkowski MS, Thomas DL, Langer R, Traverso G. Proc Natl Acad Sci U S A. pubmed:32424082;  doi:10.1073/pnas.2004746117

31. Mortality and Paclitaxel-Coated Devices: An Individual Patient Data Meta-Analysis. Rocha-Singh KJ, Duval S, Jaff MR, Schneider PA, Ansel GM, Lyden SP, Mullin CM, Ioannidis JPA, Misra S, Tzafriri AR, Edelman ER, Granada JF, White CJ, Beckman JA. Circulation. pubmed:32370548;  doi:10.1161/CIRCULATIONAHA.119.044697

32. A comparison of microfluidic methods for high-throughput cell deformability measurements. Urbanska M, Munoz HE, Shaw Bagnall J, Otto O, Manalis SR, Di Carlo D, Guck J. Nat Methods. pubmed:32341544;  doi:10.1038/s41592-020-0818-8

33. From micro to nano: evolution and impact of drug delivery in treating disease. Hrkach J, Langer R. Drug Deliv Transl Res. pubmed:32385828;  doi:10.1007/s13346-020-00769-6

34. Controlling timing and location in vaccines. Irvine DJ, Aung A, Silva M. Adv Drug Deliv Rev. pubmed:32598970;  doi:10.1016/j.addr.2020.06.019

35. Expansion Microscopy for Beginners: Visualizing Microtubules in Expanded Cultured HeLa Cells. Zhang C, Kang JS, Asano SM, Gao R, Boyden ES. Curr Protoc Neurosci. pubmed:32497404;  doi:10.1002/cpns.96

36. Role of nanoscale antigen organization on B-cell activation probed using DNA origami. Veneziano R, Moyer TJ, Stone MB, Wamhoff EC, Read BJ, Mukherjee S, Shepherd TR, Das J, Schief WR, Irvine DJ, Bathe M. Nat Nanotechnol. pubmed:32601450;  doi:10.1038/s41565-020-0719-0

37. Parallel evolution of polymer chemistry and immunology: Integrating mechanistic biology with materials design. Sadtler K, Collins J, Byrne JD, Langer R. Adv Drug Deliv Rev. pubmed:32589903;  doi:10.1016/j.addr.2020.06.021

38. Nanoparticle delivery of immunostimulatory oligonucleotides enhances response to checkpoint inhibitor therapeutics. Buss CG, Bhatia SN. Proc Natl Acad Sci U S A. pubmed:32493746;  doi:10.1073/pnas.2001569117

39. Massively multiplexed nucleic acid detection with Cas13. Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen TF, Kehe J, Nguyen TG, Carter A, Kulesa A, Barnes JR, Dugan VG, Hung DT, Blainey PC, Sabeti PC. Nature. pubmed:32349121;  doi:10.1038/s41586-020-2279-8

40. A rapidly deployable individualized system for augmenting ventilator capacity. Srinivasan SS, Ramadi KB, Vicario F, Gwynne D, Hayward A, Lagier D, Langer R, Frassica JJ, Baron RM, Traverso G. Sci Transl Med. pubmed:32424018;  doi:10.1126/scitranslmed.abb9401