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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: October 2019

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1. Tissue Site and the Cancer Immunity Cycle. Horton BL, Fessenden TB, Spranger S. Trends Cancer. pubmed:31706507;  doi:10.1016/j.trecan.2019.07.006

2. Gain-of-Function Claims for Type-2-Diabetes-Associated Coding Variants in SLC16A11 Are Not Supported by the Experimental Data. Hoch E, Florez JC, Lander ES, Jacobs SBR. Cell Rep. pubmed:31618643;  doi:10.1016/j.celrep.2019.09.021

3. Combinatorial prediction of marker panels from single-cell transcriptomic data. Delaney C, Schnell A, Cammarata LV, Yao-Smith A, Regev A, Kuchroo VK, Singer M. Mol Syst Biol. pubmed:31657111;  doi:10.15252/msb.20199005

4. Cancer-associated mutations in human pyruvate kinase M2 impair enzyme activity. Liu VM, Howell AJ, Hosios AM, Li Z, Israelsen WJ, Vander Heiden MG. FEBS Lett. pubmed:31642061;  doi:10.1002/1873-3468.13648

5. Cotargeting among microRNAs in the brain. Cherone JM, Jorgji V, Burge CB. Genome Res. pubmed:31649056;  doi:10.1101/gr.249201.119

6. Nutrient mTORC1 signaling underpins regulatory T cell control of immune tolerance. Do MH, Wang X, Zhang X, Chou C, Nixon BG, Capistrano KJ, Peng M, Efeyan A, Sabatini DM, Li MO. J Exp Med. pubmed:31649036;  doi:10.1084/jem.20190848

7. MHC-II neoantigens shape tumour immunity and response to immunotherapy. Alspach E, Lussier DM, Miceli AP, Kizhvatov I, DuPage M, Luoma AM, Meng W, Lichti CF, Esaulova E, Vomund AN, Runci D, Ward JP, Gubin MM, Medrano RFV, Arthur CD, White JM, Sheehan KCF, Chen A, Wucherpfennig KW, Jacks T, Unanue ER, Artyomov MN, Schreiber RD. Nature. pubmed:31645760;  doi:10.1038/s41586-019-1671-8

8. The microbiota regulate neuronal function and fear extinction learning. Chu C, Murdock MH, Jing D, Won TH, Chung H, Kressel AM, Tsaava T, Addorisio ME, Putzel GG, Zhou L, Bessman NJ, Yang R, Moriyama S, Parkhurst CN, Li A, Meyer HC, Teng F, Chavan SS, Tracey KJ, Regev A, Schroeder FC, Lee FS, Liston C, Artis D. Nature. pubmed:31645720;  doi:10.1038/s41586-019-1644-y

9. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Genome Biol. pubmed:31639029;  doi:10.1186/s13059-019-1842-9

10. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide alpha-CGRP Modulates Group 2 Innate Lymphoid Cell Responses. Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ. Immunity. pubmed:31618654;  doi:10.1016/j.immuni.2019.09.004

11. Substrate-based kinase activity inference identifies MK2 as driver of colitis. Strasser SD, Ghazi PC, Starchenko A, Boukhali M, Edwards A, Suarez-Lopez L, Lyons J, Changelian PS, Monahan JB, Jacobsen J, Brubaker DK, Joughin BA, Yaffe MB, Haas W, Lauffenburger DA, Haigis KM. Integr Biol (Camb). pubmed:31617572;  doi:10.1093/intbio/zyz025

12. Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses. Wallrapp A, Burkett PR, Riesenfeld SJ, Kim SJ, Christian E, Abdulnour RE, Thakore PI, Schnell A, Lambden C, Herbst RH, Khan P, Tsujikawa K, Xavier RJ, Chiu IM, Levy BD, Regev A, Kuchroo VK. Immunity. pubmed:31604686;  doi:10.1016/j.immuni.2019.09.005

13. Architecture of human Rag GTPase heterodimers and their complex with mTORC1. Anandapadamanaban M, Masson GR, Perisic O, Berndt A, Kaufman J, Johnson CM, Santhanam B, Rogala KB, Sabatini DM, Williams RL. Science. pubmed:31601764;  doi:10.1126/science.aax3939

14. Structural basis for the docking of mTORC1 on the lysosomal surface. Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils AP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM. Science. pubmed:31601708;  doi:10.1126/science.aay0166

15. High-definition spatial transcriptomics for in situ tissue profiling. Vickovic S, Eraslan G, Salmen F, Klughammer J, Stenbeck L, Schapiro D, Aijo T, Bonneau R, Bergenstrahle L, Navarro JF, Gould J, Griffin GK, Borg A, Ronaghi M, Frisen J, Lundeberg J, Regev A, Stahl PL. Nat Methods. pubmed:31501547;  doi:10.1038/s41592-019-0548-y

16. Single-cell transcriptomic profiling of the aging mouse brain. Ximerakis M, Lipnick SL, Innes BT, Simmons SK, Adiconis X, Dionne D, Mayweather BA, Nguyen L, Niziolek Z, Ozek C, Butty VL, Isserlin R, Buchanan SM, Levine SS, Regev A, Bader GD, Levin JZ, Rubin LL. Nat Neurosci. pubmed:31551601;  doi:10.1038/s41593-019-0491-3

17. Decoding human fetal liver haematopoiesis. Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chedotal A, Roberts I, Gottgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M. Nature. pubmed:31597962;  doi:10.1038/s41586-019-1652-y

18. Mechanosensing during directed cell migration requires dynamic actin polymerization at focal adhesions. Puleo JI, Parker SS, Roman MR, Watson AW, Eliato KR, Peng L, Saboda K, Roe DJ, Ros R, Gertler FB, Mouneimne G. J Cell Biol. pubmed:31594807;  doi:10.1083/jcb.201902101

19. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Menon M, Mohammadi S, Davila-Velderrain J, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP. Nat Commun. pubmed:31653841;  doi:10.1038/s41467-019-12780-8

20. Antibody-targeting of ultra-small nanoparticles enhances imaging sensitivity and enables longitudinal tracking of multiple myeloma. Detappe A, Reidy M, Yu Y, Mathieu C, Nguyen HV, Coroller TP, Lam F, Jarolim P, Harvey P, Protti A, Nguyen QD, Johnson JA, Cremillieux Y, Tillement O, Ghobrial IM, Ghoroghchian PP. Nanoscale. pubmed:31650133;  doi:10.1039/c9nr06512a

21. Induction of metabolic quiescence defines the transitional to follicular B cell switch. Farmer JR, Allard-Chamard H, Sun N, Ahmad M, Bertocchi A, Mahajan VS, Aicher T, Arnold J, Benson MD, Morningstar J, Barmettler S, Yuen G, Murphy SJH, Walter JE, Ghebremichael M, Shalek AK, Batista F, Gerszten R, Pillai S. Sci Signal. pubmed:31641080;  doi:10.1126/scisignal.aaw5573

22. Modular Polymer Antigens to Optimize Immunity. Bennett NR, Jarvis CM, Alam MM, Zwick DB, Olson JM, Nguyen HV, Johnson JA, Cook ME, Kiessling LL. Biomacromolecules. pubmed:31609600;  doi:10.1021/acs.biomac.9b01049

23. Revisiting Airway Epithelial Remodeling in Type 2 Immunity: Beyond Goblet Cell Metaplasia. Barrett NA, Shalek AK. J Allergy Clin Immunol. pubmed:31600548;  doi:10.1016/j.jaci.2019.09.017

24. Germline-Encoded Affinity for Cognate Antigen Enables Vaccine Amplification of a Human Broadly Neutralizing Response against Influenza Virus. Sangesland M, Ronsard L, Kazer SW, Bals J, Boyoglu-Barnum S, Yousif AS, Barnes R, Feldman J, Quirindongo-Crespo M, McTamney PM, Rohrer D, Lonberg N, Chackerian B, Graham BS, Kanekiyo M, Shalek AK, Lingwood D. Immunity. pubmed:31563464;  doi:10.1016/j.immuni.2019.09.001

25. Voices in methods development. Anikeeva P, Boyden E, Brangwynne C, Cisse II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EWJr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X. Nat Methods. pubmed:31562479;  doi:10.1038/s41592-019-0585-6

26. A Novel, Safe, Fast, Efficient Treatment for Her2-positive and Negative Bladder Cancer Utilizing an EGF-Anthrax Toxin Chimera. Jack S, Madhivanan K, Ramadesikan S, Subramanian S, Edwards DF2nd, Elzey BD, Dhawan D, McCluskey A, Kischuk EM, Loftis AR, Truex N, Santos M, Lu M, Rabideau A, Pentelute B, Collier J, Kaimakliotis H, Koch M, Ratliff TL, Knapp DW, Aguilar RC. Int J Cancer. pubmed:31584195;  doi:10.1002/ijc.32719

27. Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain. Brady JR, Whittaker CA, Tan MC, Kristensen DL2nd, Ma D, Dalvie NC, Love KR, Love JC. Biotechnol Bioeng. pubmed:31654411;  doi:10.1002/bit.27209

28. Expansion of the CD4(+) effector T cell repertoire characterizes peanut-allergic patients with heightened clinical sensitivity. Ruiter B, Smith NP, Monian B, Tu AA, Fleming E, Virkud YV, Patil SU, Whittaker CA, Love JC, Shreffler WG. J Allergy Clin Immunol. pubmed:31654649;  doi:10.1016/j.jaci.2019.09.033

29. A multilamellar nanoliposome stabilized by interlayer hydrogen bonds increases antimalarial drug efficacy. Fotoran WL, Muntefering T, Kleiber N, Miranda BNM, Liebau E, Irvine DJ, Wunderlich G. Nanomedicine. pubmed:31648039;  doi:10.1016/j.nano.2019.102099

30. Not All T Cell Synapses Are Built the Same Way. Kumari S, Colin-York H, Irvine DJ, Fritzsche M. Trends Immunol. pubmed:31645298;  doi:10.1016/j.it.2019.09.009

31. Enantiomeric glycosylated cationic block co-beta-peptides eradicate Staphylococcus aureus biofilms and antibiotic-tolerant persisters. Zhang K, Du Y, Si Z, Liu Y, Turvey ME, Raju C, Keogh D, Ruan L, Jothy SL, Reghu S, Marimuthu K, De PP, Ng OT, Mediavilla JR, Kreiswirth BN, Chi YR, Ren J, Tam KC, Liu XW, Duan H, Zhu Y, Mu Y, Hammond PT, Bazan GC, Pethe K, Chan-Park MB. Nat Commun. pubmed:31636263;  doi:10.1038/s41467-019-12702-8

32. Blood-Brain Barrier Dysfunction in a 3D In Vitro Model of Alzheimer's Disease. Shin Y, Choi SH, Kim E, Bylykbashi E, Kim JA, Chung S, Kim DY, Kamm RD, Tanzi RE. Adv Sci (Weinh). pubmed:31637161;  doi:10.1002/advs.201900962

33. Optical Pooled Screens in Human Cells. Feldman D, Singh A, Schmid-Burgk JL, Carlson RJ, Mezger A, Garrity AJ, Zhang F, Blainey PC. Cell. pubmed:31626775;  doi:10.1016/j.cell.2019.09.016

34. Dehydration assessment via portable, single sided magnetic resonance sensor. Bashyam A, Frangieh CJ, Li M, Cima MJ. Magn Reson Med. pubmed:31631380;  doi:10.1002/mrm.28004

35. MicroRNA delivery through nanoparticles. Lee SWL, Paoletti C, Campisi M, Osaki T, Adriani G, Kamm RD, Mattu C, Chiono V. J Control Release. pubmed:31622695;  doi:10.1016/j.jconrel.2019.10.007

36. Emerging Frontiers in Microbiome Engineering. Inda ME, Broset E, Lu TK, de la Fuente-Nunez C. Trends Immunol. pubmed:31601521;  doi:10.1016/j.it.2019.08.007

37. Virus-Templated Nickel Phosphide Nanofoams as Additive-Free, Thin-Film Li-Ion Microbattery Anodes. Records WC, Wei S, Belcher AM. Small. pubmed:31513358;  doi:10.1002/smll.201903166

38. Complex DNA knots detected with a nanopore sensor. Kumar Sharma R, Agrawal I, Dai L, Doyle PS, Garaj S. Nat Commun. pubmed:31578328;  doi:10.1038/s41467-019-12358-4

39. Can Fish and Cell Phones Teach Us about Our Health?. Lee MA, Duarte CM, Eguiluz VM, Heller DA, Langer R, Meekan MG, Sikes HD, Srivastava M, Strano MS, Wilson RP. ACS Sens. pubmed:31576740;  doi:10.1021/acssensors.9b00947

40. Twenty-Four-Hour Ex Vivo Perfusion with Acellular Solution Enables Successful Replantation of Porcine Forelimbs. Krezdorn N, Macleod F, Tasigiorgos S, Turk M, Wo L, Kiwanuka H, Lopdrup B I DR, Kollar B, Edelman ER, Pomahac B. Plast Reconstr Surg. pubmed:31568296;  doi:10.1097/PRS.0000000000006084

41. Stereotactic Radiotherapy for Renal Denervation: To Beam, or Not to Beam?. Mahfoud F, Edelman E, Bhatt N. J Am Coll Cardiol. pubmed:31558255;  doi:10.1016/j.jacc.2019.07.054

42. Population imaging of neural activity in awake behaving mice. Piatkevich KD, Bensussen S, Tseng HA, Shroff SN, Lopez-Huerta VG, Park D, Jung EE, Shemesh OA, Straub C, Gritton HJ, Romano MF, Costa E, Sabatini BL, Fu Z, Boyden ES, Han X. Nature. pubmed:31597963;  doi:10.1038/s41586-019-1641-1

43. Endoscopically Injectable Shear-Thinning Hydrogels Facilitating Polyp Removal. Pang Y, Liu J, Moussa ZL, Collins JE, McDonnell S, Hayward AM, Jajoo K, Langer R, Traverso G. Adv Sci (Weinh). pubmed:31592420;  doi:10.1002/advs.201901041

44. A luminal unfolding microneedle injector for oral delivery of macromolecules. Abramson A, Caffarel-Salvador E, Soares V, Minahan D, Tian RY, Lu X, Dellal D, Gao Y, Kim S, Wainer J, Collins J, Tamang S, Hayward A, Yoshitake T, Lee HC, Fujimoto J, Fels J, Frederiksen MR, Rahbek U, Roxhed N, Langer R, Traverso G. Nat Med. pubmed:31591601;  doi:10.1038/s41591-019-0598-9

45. A crosslinked polymer skin barrier film for moderate to severe atopic dermatitis: A pilot study in adults. Bouthillette M, Beccati D, Akthakul A, Ramadurai N, Nashat A, Langer R, Anderson RR, Sakamoto FH. J Am Acad Dermatol. pubmed:31589946;  doi:10.1016/j.jaad.2019.09.073

46. Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis. Yehl K, Lemire S, Yang AC, Ando H, Mimee M, Torres MT, de la Fuente-Nunez C, Lu TK. Cell. pubmed:31585083;  doi:10.1016/j.cell.2019.09.015