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: January 2020

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1. CRISPR-mediated modeling and functional validation of candidate tumor suppressor genes in small cell lung cancer. Ng SR, Rideout WM3rd, Akama-Garren EH, Bhutkar A, Mercer KL, Schenkel JM, Bronson RT, Jacks T. Proc Natl Acad Sci U S A. pubmed:31871154;  doi:10.1073/pnas.1821893117

2. Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing. Babu VMP, Sankari S, Budnick JA, Caswell CC, Walker GC. Nucleic Acids Res. pubmed:31777930;  doi:10.1093/nar/gkz1095

3. Aneuploidy and a deregulated DNA damage response suggest haploinsufficiency in breast tissues of BRCA2 mutation carriers. Karaayvaz-Yildirim M, Silberman RE, Langenbucher A, Saladi SV, Ross KN, Zarcaro E, Desmond A, Yildirim M, Vivekanandan V, Ravichandran H, Mylavagnanam R, Specht MC, Ramaswamy S, Lawrence M, Amon A, Ellisen LW. Sci Adv. pubmed:32064343;  doi:10.1126/sciadv.aay2611

4. The Taste Receptor TAS1R3 Regulates Small Intestinal Tuft Cell Homeostasis. Howitt MR, Cao YG, Gologorsky MB, Li JA, Haber AL, Biton M, Lang J, Michaud M, Regev A, Garrett WS. Immunohorizons. pubmed:31980480;  doi:10.4049/immunohorizons.1900099

5. Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells. Zhang B, Ma S, Rachmin I, He M, Baral P, Choi S, Goncalves WA, Shwartz Y, Fast EM, Su Y, Zon LI, Regev A, Buenrostro JD, Cunha TM, Chiu IM, Fisher DE, Hsu YC. Nature. pubmed:31969699;  doi:10.1038/s41586-020-1935-3

6. A human ciliopathy reveals essential functions for NEK10 in airway mucociliary clearance. Chivukula RR, Montoro DT, Leung HM, Yang J, Shamseldin HE, Taylor MS, Dougherty GW, Zariwala MA, Carson J, Daniels MLA, Sears PR, Black KE, Hariri LP, Almogarri I, Frenkel EM, Vinarsky V, Omran H, Knowles MR, Tearney GJ, Alkuraya FS, Sabatini DM. Nat Med. pubmed:31959991;  doi:10.1038/s41591-019-0730-x

7. Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation. Basak A, Munschauer M, Lareau CA, Montbleau KE, Ulirsch JC, Hartigan CR, Schenone M, Lian J, Wang Y, Huang Y, Wu X, Gehrke L, Rice CM, An X, Christou HA, Mohandas N, Carr SA, Chen JJ, Orkin SH, Lander ES, Sankaran VG. Nat Genet. pubmed:31959994;  doi:10.1038/s41588-019-0568-7

8. mTOR at the nexus of nutrition, growth, ageing and disease. Liu GY, Sabatini DM. Nat Rev Mol Cell Biol. pubmed:31937935;  doi:10.1038/s41580-019-0199-y

9. A novel histological index for evaluation of environmental enteric dysfunction identifies geographic-specific features of enteropathy among children with suboptimal growth. Liu TC, VanBuskirk K, Ali SA, Kelly MP, Holtz LR, Yilmaz OH, Sadiq K, Iqbal N, Amadi B, Syed S, Ahmed T, Moore S, Ndao IM, Isaacs MH, Pfeifer JD, Atlas H, Tarr PI, Denno DM, Moskaluk CA. PLoS Negl Trop Dis. pubmed:31929525;  doi:10.1371/journal.pntd.0007975

10. Dynamic and regulated TAF gene expression during mouse embryonic germ cell development. Gura MA, Mikedis MM, Seymour KA, de Rooij DG, Page DC, Freiman RN. PLoS Genet. pubmed:31914128;  doi:10.1371/journal.pgen.1008515

11. GCNA Interacts with Spartan and Topoisomerase II to Regulate Genome Stability. Dokshin GA, Davis GM, Sawle AD, Eldridge MD, Nicholls PK, Gourley TE, Romer KA, Molesworth LW, Tatnell HR, Ozturk AR, de Rooij DG, Hannon GJ, Page DC, Mello CC, Carmell MA. Dev Cell. pubmed:31839538;  doi:10.1016/j.devcel.2019.11.006

12. Modulation of the immune microenvironment by tumor-intrinsic oncogenic signaling. Nguyen KB, Spranger S. J Cell Biol. pubmed:31816057;  doi:10.1083/jcb.201908224

13. Deciphering eukaryotic gene-regulatory logic with 100 million random promoters. de Boer CG, Vaishnav ED, Sadeh R, Abeyta EL, Friedman N, Regev A. Nat Biotechnol. pubmed:31792407;  doi:10.1038/s41587-019-0315-8

14. Identification of a Master Regulator of Differentiation in Toxoplasma. Waldman BS, Schwarz D, Wadsworth MH2nd, Saeij JP, Shalek AK, Lourido S. Cell. pubmed:31955846;  doi:10.1016/j.cell.2019.12.013

15. Automated Flow Synthesis of Tumor Neoantigen Peptides for Personalized Immunotherapy. Truex NL, Holden RL, Wang BY, Chen PG, Hanna S, Hu Z, Shetty K, Olive O, Neuberg D, Hacohen N, Keskin DB, Ott PA, Wu CJ, Pentelute BL. Sci Rep. pubmed:31959774;  doi:10.1038/s41598-019-56943-5

16. Prevention of tuberculosis in macaques after intravenous BCG immunization. Darrah PA, Zeppa JJ, Maiello P, Hackney JA, Wadsworth MH2nd, Hughes TK, Pokkali S, Swanson PA2nd, Grant NL, Rodgers MA, Kamath M, Causgrove CM, Laddy DJ, Bonavia A, Casimiro D, Lin PL, Klein E, White AG, Scanga CA, Shalek AK, Roederer M, Flynn JL, Seder RA. Nature. pubmed:31894150;  doi:10.1038/s41586-019-1817-8

17. Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies. Martin-Gayo E, Gao C, Chen HR, Ouyang Z, Kim D, Kolb KE, Shalek AK, Walker BD, Lichterfeld M, Yu XG. Cell Rep. pubmed:31995767;  doi:10.1016/j.celrep.2019.12.087

18. Cytoskeletal tension actively sustains the migratory T-cell synaptic contact. Kumari S, Mak M, Poh YC, Tohme M, Watson N, Melo M, Janssen E, Dustin M, Geha R, Irvine DJ. EMBO J. pubmed:31894880;  doi:10.15252/embj.2019102783

19. DOCK2 Sets the Threshold for Entry into the Virtual Memory CD8(+) T Cell Compartment by Negatively Regulating Tonic TCR Triggering. Mahajan VS, Demissie E, Alsufyani F, Kumari S, Yuen GJ, Viswanadham V, Huang A, Tran JQ, Moon JJ, Irvine DJ, Pillai S. J Immunol. pubmed:31740487;  doi:10.4049/jimmunol.1900440

20. Adenine base editing in an adult mouse model of tyrosinaemia. Song CQ, Jiang T, Richter M, Rhym LH, Koblan LW, Zafra MP, Schatoff EM, Doman JL, Cao Y, Dow LE, Zhu LJ, Anderson DG, Liu DR, Yin H, Xue W. Nat Biomed Eng. pubmed:31740768;  doi:10.1038/s41551-019-0357-8

21. Analysis: Intravascular Devices with a Higher Risk of Polymer Emboli: The Need for Particulate Generation Testing. Chopra AM, Rapkiewicz A, Daggubati R, Sequeira A, Hu YC, Bhatt DL, Sharma SK, Cruz JP, Tzafriri AR, Edelman ER. Biomed Instrum Technol. pubmed:31961742;  doi:10.2345/0899-8205-54.1.37

22. Models for Monocytic Cells in the Tumor Microenvironment. Lee SWL, Adriani G, Kamm RD, Gillrie MR. Adv Exp Med Biol. pubmed:32036607;  doi:10.1007/978-3-030-35723-8_7

23. Enhancing cancer immunotherapy with nanomedicine. Irvine DJ, Dane EL. Nat Rev Immunol. pubmed:32005979;  doi:10.1038/s41577-019-0269-6

24. Light-degradable hydrogels as dynamic triggers for gastrointestinal applications. Raman R, Hua T, Gwynne D, Collins J, Tamang S, Zhou J, Esfandiary T, Soares V, Pajovic S, Hayward A, Langer R, Traverso G. Sci Adv. pubmed:32010768;  doi:10.1126/sciadv.aay0065

25. The Use of Microfluidic Platforms to Probe the Mechanism of Cancer Cell Extravasation. Coughlin MF, Kamm RD. Adv Healthc Mater. pubmed:31994845;  doi:10.1002/adhm.201901410

26. Application of a gut-immune co-culture system for the study of N-glycan-dependent host-pathogen interactions of Campylobacter jejuni. Zamora CY, Ward EM, Kester JC, Chen WLK, Velazquez JG, Griffith LG, Imperiali B. Glycobiology. pubmed:31965157;  doi:10.1093/glycob/cwz105

27. Development and Challenges of Antimicrobial Peptides for Therapeutic Applications. Chen CH, Lu TK. Antibiotics (Basel). pubmed:31941022;  doi:10.3390/antibiotics9010024

28. Reduction of the therapeutic dose of silencing RNA by packaging it in extracellular vesicles via a pre-microRNA backbone. Reshke R, Taylor JA, Savard A, Guo H, Rhym LH, Kowalski PS, Trung MT, Campbell C, Little W, Anderson DG, Gibbings D. Nat Biomed Eng. pubmed:31937944;  doi:10.1038/s41551-019-0502-4

29. On-chip 3D neuromuscular model for drug screening and precision medicine in neuromuscular disease. Osaki T, Uzel SGM, Kamm RD. Nat Protoc. pubmed:31932771;  doi:10.1038/s41596-019-0248-1

30. Genetic encoding of targeted MRI contrast agents for tumor imaging. Schuerle S, Furubayashi M, Soleimany A, Gwisai T, Huang W, Voigt CA, Bhatia SN. ACS Synth Biol. pubmed:31922737;  doi:10.1021/acssynbio.9b00416

31. Expansion, in vivo-ex vivo cycling, and genetic manipulation of primary human hepatocytes. Michailidis E, Vercauteren K, Mancio-Silva L, Andrus L, Jahan C, Ricardo-Lax I, Zou C, Kabbani M, Park P, Quirk C, Pyrgaki C, Razooky B, Verhoye L, Zoluthkin I, Lu WY, Forbes SJ, Chiriboga L, Theise ND, Herzog RW, Suemizu H, Schneider WM, Shlomai A, Meuleman P, Bhatia SN, Rice CM, de Jong YP. Proc Natl Acad Sci U S A. pubmed:31915293;  doi:10.1073/pnas.1919035117

32. Engineering Helical Modular Polypeptide-Based Hydrogels as Synthetic Extracellular Matrices for Cell Culture. He H, Sofman M, Wang AJ, Ahrens CC, Wang W, Griffith LG, Hammond PT. Biomacromolecules. pubmed:31846304;  doi:10.1021/acs.biomac.9b01297

33. Host-Informed Expression of CRISPR Guide RNA for Genomic Engineering in Komagataella phaffii. Dalvie NC, Leal J, Whittaker CA, Yang Y, Brady JR, Love KR, Love JC. ACS Synth Biol. pubmed:31825599;  doi:10.1021/acssynbio.9b00372

34. Identification and local delivery of vasodilators for the reduction of ureteral contractions. Lee CX, Cheah JH, Soule CK, Ding H, Whittaker CA, Karhohs K, Burds AA, Subramanyam KS, Carpenter AE, Eisner BH, Cima MJ. Nat Biomed Eng. pubmed:31792422;  doi:10.1038/s41551-019-0482-4

35. Equilibrium structure and deformation response of 2D kinetoplast sheets. Klotz AR, Soh BW, Doyle PS. Proc Natl Acad Sci U S A. pubmed:31811027;  doi:10.1073/pnas.1911088116

36. Pharmacometrics and Systems Pharmacology 2030. Mentre F, Friberg LE, Duffull S, French J, Lauffenburger DA, Li L, Mager DE, Sinha V, Sobie E, Zhao P. Clin Pharmacol Ther. pubmed:31758700;  doi:10.1002/cpt.1683

37. From Molecule to Patient: A Biotech Perspective. Langer R, Jaklenec A, Traverso G, Hartman D. Clin Pharmacol Ther. pubmed:31749166;  doi:10.1002/cpt.1676

38. Chiral Supraparticles for Controllable Nanomedicine. Yeom J, Guimaraes PPG, Ahn HM, Jung BK, Hu Q, McHugh K, Mitchell MJ, Yun CO, Langer R, Jaklenec A. Adv Mater. pubmed:31686433;  doi:10.1002/adma.201903878

39. A special issue dedicated to Dr Bruce N Ames: Introduction. Walker GC. Mutat Res. pubmed:32087846;  doi:10.1016/j.mrgentox.2019.503115