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 2019

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1. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, Bonnemann CG, Mandl KD, White PS. Dev Cell. pubmed:30930166;  doi:10.1016/j.devcel.2019.03.001

2. Induction and Therapeutic Targeting of Human NPM1c(+) Myeloid Leukemia in the Presence of Autologous Immune System in Mice. Kaur M, Drake AC, Hu G, Rudnick S, Chen Q, Phennicie R, Attar R, Nemeth J, Gaudet F, Chen J. J Immunol. pubmed:30710044;  doi:10.4049/jimmunol.1800366

3. A strategic research alliance: Turner syndrome and sex differences. San Roman AK, Page DC. Am J Med Genet C Semin Med Genet. pubmed:30790449;  doi:10.1002/ajmg.c.31677

4. Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers. Ji Z, He L, Regev A, Struhl K. Proc Natl Acad Sci U S A. pubmed:30910960;  doi:10.1073/pnas.1821068116

5. Widespread PERK-dependent repression of ER targets in response to ER stress. Gonen N, Sabath N, Burge CB, Shalgi R. Sci Rep. pubmed:30867432;  doi:10.1038/s41598-019-38705-5

6. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Yang EW, Bahn JH, Hsiao EY, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X. Nat Commun. pubmed:30902979;  doi:10.1038/s41467-019-09292-w

7. 2018 William Allan Award: Discovering the Genes for Common Disease: From Families to Populations. Lander ES. Am J Hum Genet. pubmed:30849323;  doi:10.1016/j.ajhg.2019.01.016

8. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus C, Li LH, Pelka K, Ge W, Oren Y, Brack A, Law T, Rodman C, Chen JH, Boland GM, Hacohen N, Rozenblatt-Rosen O, Aryee MJ, Buenrostro JD, Regev A, Sankaran VG. Cell. pubmed:30827679;  doi:10.1016/j.cell.2019.01.022

9. NAD(+) supplementation rejuvenates aged gut adult stem cells. Igarashi M, Miura M, Williams E, Jaksch F, Kadowaki T, Yamauchi T, Guarente L. Aging Cell. pubmed:30917412;  doi:10.1111/acel.12935

10. Increased Serine Synthesis Provides an Advantage for Tumors Arising in Tissues Where Serine Levels Are Limiting. Sullivan MR, Mattaini KR, Dennstedt EA, Nguyen AA, Sivanand S, Reilly MF, Meeth K, Muir A, Darnell AM, Bosenberg MW, Lewis CA, Vander Heiden MG. Cell Metab. pubmed:30905671;  doi:10.1016/j.cmet.2019.02.015

11. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output. Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE. PLoS Biol. pubmed:30897078;  doi:10.1371/journal.pbio.2006540

12. Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells. Kroger C, Afeyan A, Mraz J, Eaton EN, Reinhardt F, Khodor YL, Thiru P, Bierie B, Ye X, Burge CB, Weinberg RA. Proc Natl Acad Sci U S A. pubmed:30910979;  doi:10.1073/pnas.1812876116

13. Pan-TAM tyrosine kinase inhibitor BMS-777607 enhances anti-PD-1 mAb efficacy in a murine model of triple-negative breast cancer. Kasikara C, Davra V, Calianese D, Geng K, Spires TE, Quigley M, Wichroski M, Sriram G, Suarez-Lopez L, Yaffe MB, Kotenko SV, De Lorenzo MS, Birge RB. Cancer Res. pubmed:30877108;  doi:10.1158/0008-5472.CAN-18-2614

14. Locating and Characterizing a Transgene Integration Site by Nanopore Sequencing. Nicholls PK, Bellott DW, Cho TJ, Pyntikova T, Page DC. G3 (Bethesda). pubmed:30837263;  doi:10.1534/g3.119.300582

15. Conformational Stabilization and Rapid Labeling of a 29-Residue Peptide by a Small Molecule Reaction Partner. Evans ED, Gates ZP, Sun ZJ, Mijalis AJ, Pentelute BL. Biochemistry. pubmed:30724554;  doi:10.1021/acs.biochem.8b00940

16. Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. van Galen P, Hovestadt V, Wadsworth Ii MH, Hughes TK, Griffin GK, Battaglia S, Verga JA, Stephansky J, Pastika TJ, Lombardi Story J, Pinkus GS, Pozdnyakova O, Galinsky I, Stone RM, Graubert TA, Shalek AK, Aster JC, Lane AA, Bernstein BE. Cell. pubmed:30827681;  doi:10.1016/j.cell.2019.01.031

17. RNA Circularization Diminishes Immunogenicity and Can Extend Translation Duration In Vivo. Wesselhoeft RA, Kowalski PS, Parker-Hale FC, Huang Y, Bisaria N, Anderson DG. Mol Cell. pubmed:30902547;  doi:10.1016/j.molcel.2019.02.015

18. Stabilization of the Max Homodimer with a Small Molecule Attenuates Myc-Driven Transcription. Struntz NB, Chen A, Deutzmann A, Wilson RM, Stefan E, Evans HL, Ramirez MA, Liang T, Caballero F, Wildschut MHE, Neel DV, Freeman DB, Pop MS, McConkey M, Muller S, Curtin BH, Tseng H, Frombach KR, Butty VL, Levine SS, Feau C, Elmiligy S, Hong JA, Lewis TA, Vetere A, Clemons PA, Malstrom SE, Ebert BL, Lin CY, Felsher DW, Koehler AN. Cell Chem Biol. pubmed:30880155;  doi:10.1016/j.chembiol.2019.02.009

19. Simultaneous spatiotemporal tracking and oxygen sensing of transient implants in vivo using hot-spot MRI and machine learning. Spanoudaki V, Doloff JC, Huang W, Norcross SR, Farah S, Langer R, Anderson DG. Proc Natl Acad Sci U S A. pubmed:30808810;  doi:10.1073/pnas.1815909116

20. Deep-tissue optical imaging of near cellular-sized features. Dang X, Bardhan NM, Qi J, Gu L, Eze NA, Lin CW, Kataria S, Hammond PT, Belcher AM. Sci Rep. pubmed:30846704;  doi:10.1038/s41598-019-39502-w

21. Improving Drug Discovery by Nucleic Acid Delivery in Engineered Human Microlivers. Mancio-Silva L, Fleming HE, Miller AB, Milstein S, Liebow A, Haslett P, Sepp-Lorenzino L, Bhatia SN. Cell Metab. pubmed:30840913;  doi:10.1016/j.cmet.2019.02.003

22. Endothelial miR-30c suppresses tumor growth via inhibition of TGF-beta-induced Serpine1. McCann JV, Xiao L, Kim DJ, Khan OF, Kowalski PS, Anderson DG, Pecot CV, Azam SH, Parker JS, Tsai YS, Wolberg AS, Turner SD, Tatsumi K, Mackman N, Dudley AC. J Clin Invest. pubmed:30855280;  doi:10.1172/JCI123106

23. A gastric resident drug delivery system for prolonged gram-level dosing of tuberculosis treatment. Verma M, Vishwanath K, Eweje F, Roxhed N, Grant T, Castaneda M, Steiger C, Mazdiyasni H, Bensel T, Minahan D, Soares V, Salama JAF, Lopes A, Hess K, Cleveland C, Fulop DJ, Hayward A, Collins J, Tamang SM, Hua T, Ikeanyi C, Zeidman G, Mule E, Boominathan S, Popova E, Miller JB, Bellinger AM, Collins D, Leibowitz D, Batra S, Ahuja S, Bajiya M, Batra S, Sarin R, Agarwal U, Khaparde SD, Gupta NK, Gupta D, Bhatnagar AK, Chopra KK, Sharma N, Khanna A, Chowdhury J, Stoner R, Slocum AH, Cima MJ, Furin J, Langer R, Traverso G. Sci Transl Med. pubmed:30867322;  doi:10.1126/scitranslmed.aau6267

24. Selective antibacterial activity of the cationic peptide PaDBS1R6 against Gram-negative bacteria. Fensterseifer ICM, Felicio MR, Alves ESF, Cardoso MH, Torres MDT, Matos CO, Silva ON, Lu TK, Freire MV, Neves NC, Goncalves S, Liao LM, Santos NC, Porto WF, de la Fuente-Nunez C, Franco OL. Biochim Biophys Acta Biomembr. pubmed:30926365;  doi:10.1016/j.bbamem.2019.03.016

25. Directing curli polymerization with DNA origami nucleators. Mao X, Li K, Liu M, Wang X, Zhao T, An B, Cui M, Li Y, Pu J, Li J, Wang L, Lu TK, Fan C, Zhong C. Nat Commun. pubmed:30918257;  doi:10.1038/s41467-019-09369-6

26. An Artificial Tissue Homeostasis Circuit Designed via Analog Circuit Techniques. Teo JJY, Weiss R, Sarpeshkar R. IEEE Trans Biomed Circuits Syst. pubmed:30908238;  doi:10.1109/TBCAS.2019.2907074

27. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Berghuis BA, Yu FB, Schulz F, Blainey PC, Woyke T, Quake SR. Proc Natl Acad Sci U S A. pubmed:30814220;  doi:10.1073/pnas.1815631116