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: December 2018

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1. CDK12 regulates DNA repair genes by suppressing intronic polyadenylation. Dubbury SJ, Boutz PL, Sharp PA. Nature. pubmed:30487607;  doi:10.1038/s41586-018-0758-y

2. Neurohormonal signaling via a sulfotransferase antagonizes insulin-like signaling to regulate a Caenorhabditis elegans stress response. Burton NO, Dwivedi VK, Burkhart KB, Kaplan REW, Baugh LR, Horvitz HR. Nat Commun. pubmed:30514845;  doi:10.1038/s41467-018-07640-w

3. Transcriptome alterations in myotonic dystrophy skeletal muscle and heart. Wang ET, Treacy D, Eichinger K, Struck A, Estabrook J, Olafson H, Wang TT, Bhatt K, Westbrook T, Sedehizadeh S, Ward A, Day J, Brook D, Berglund JA, Cooper T, Housman D, Thornton C, Burge C. Hum Mol Genet. pubmed:30561649;  doi:10.1093/hmg/ddy432

4. Transcriptional repression of CDC6 and SLD2 during meiosis is associated with production of short heterogeneous RNA isoforms. Phizicky DV, Bell SP. Chromosoma. pubmed:30276463;  doi:10.1007/s00412-018-0681-x

5. SRC tyrosine kinase activates the YAP/TAZ axis and thereby drives tumor growth and metastasis. Lamar JM, Xiao Y, Norton E, Jiang ZG, Gerhard GM, Kooner S, Warren JSA, Hynes RO. J Biol Chem. pubmed:30559289;  doi:10.1074/jbc.RA118.004364

6. Activating Embryonic Development in Drosophila. Aviles-Pagan EE, Orr-Weaver TL. Semin Cell Dev Biol. pubmed:29448071;  doi:10.1016/j.semcdb.2018.02.019

7. Lack of evidence for substrate channeling or flux between wildtype and mutant isocitrate dehydrogenase to produce the oncometabolite 2-hydroxyglutarate. Dexter JP, Ward PS, Dasgupta T, Hosios AM, Gunawardena J, Vander Heiden MG. J Biol Chem. pubmed:30381394;  doi:10.1074/jbc.RA118.004278

8. Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age. Mann M, Mehta A, de Boer CG, Kowalczyk MS, Lee K, Haldeman P, Rogel N, Knecht AR, Farouq D, Regev A, Baltimore D. Cell Rep. pubmed:30540934;  doi:10.1016/j.celrep.2018.11.056

9. Acquired HER2 mutations in ER(+) metastatic breast cancer confer resistance to estrogen receptor-directed therapies. Nayar U, Cohen O, Kapstad C, Cuoco MS, Waks AG, Wander SA, Painter C, Freeman S, Persky NS, Marini L, Helvie K, Oliver N, Rozenblatt-Rosen O, Ma CX, Regev A, Winer EP, Lin NU, Wagle N. Nat Genet. pubmed:30531871;  doi:10.1038/s41588-018-0287-5

10. Author Correction: Comprehensive comparative analysis of 5'-end RNA-sequencing methods. Adiconis X, Haber AL, Simmons SK, Moonshine AL, Ji Z, Busby MA, Shi X, Jacques J, Lancaster MA, Pan JQ, Regev A, Levin JZ. Nat Methods. pubmed:30459407;  doi:10.1038/s41592-018-0237-2

11. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL, Regev A, Behrens T, Hacohen N. Genome Res. pubmed:30446528;  doi:10.1101/gr.240390.118

12. Lipidomic Analysis of alpha-Synuclein Neurotoxicity Identifies Stearoyl CoA Desaturase as a Target for Parkinson Treatment. Fanning S, Haque A, Imberdis T, Baru V, Barrasa MI, Nuber S, Termine D, Ramalingam N, Ho GPH, Noble T, Sandoe J, Lou Y, Landgraf D, Freyzon Y, Newby G, Soldner F, Terry-Kantor E, Kim TE, Hofbauer HF, Becuwe M, Jaenisch R, Pincus D, Clish CB, Walther TC, Farese RVJr, Srinivasan S, Welte MA, Kohlwein SD, Dettmer U, Lindquist S, Selkoe D. Mol Cell. pubmed:30527540;  doi:10.1016/j.molcel.2018.11.028

13. SIRT1 deacetylase in aging-induced neuromuscular degeneration and amyotrophic lateral sclerosis. Herskovits AZ, Hunter TA, Maxwell N, Pereira K, Whittaker CA, Valdez G, Guarente LP. Aging Cell. pubmed:30295421;  doi:10.1111/acel.12839

14. Non-overlapping Control of Transcriptome by Promoter- and Super-Enhancer-Associated Dependencies in Multiple Myeloma. Fulciniti M, Lin CY, Samur MK, Lopez MA, Singh I, Lawlor MA, Szalat RE, Ott CJ, Avet-Loiseau H, Anderson KC, Young RA, Bradner JE, Munshi NC. Cell Rep. pubmed:30590042;  doi:10.1016/j.celrep.2018.12.016

15. Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains. Boija A, Klein IA, Sabari BR, Dall'Agnese A, Coffey EL, Zamudio AV, Li CH, Shrinivas K, Manteiga JC, Hannett NM, Abraham BJ, Afeyan LK, Guo YE, Rimel JK, Fant CB, Schuijers J, Lee TI, Taatjes DJ, Young RA. Cell. pubmed:30449618;  doi:10.1016/j.cell.2018.10.042

16. CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L. Nat Methods. pubmed:30504875;  doi:10.1038/s41592-018-0225-6

17. The Genetic Landscape of Diamond-Blackfan Anemia. Ulirsch JC, Verboon JM, Kazerounian S, Guo MH, Yuan D, Ludwig LS, Handsaker RE, Abdulhay NJ, Fiorini C, Genovese G, Lim ET, Cheng A, Cummings BB, Chao KR, Beggs AH, Genetti CA, Sieff CA, Newburger PE, Niewiadomska E, Matysiak M, Vlachos A, Lipton JM, Atsidaftos E, Glader B, Narla A, Gleizes PE, O'Donohue MF, Montel-Lehry N, Amor DJ, McCarroll SA, O'Donnell-Luria AH, Gupta N, Gabriel SB, MacArthur DG, Lander ES, Lek M, Da Costa L, Nathan DG, Korostelev AA, Do R, Sankaran VG, Gazda HT. Am J Hum Genet. pubmed:30503522;  doi:10.1016/j.ajhg.2018.10.027

18. FAM210B is an erythropoietin target and regulates erythroid heme synthesis by controlling mitochondrial iron import and ferrochelatase activity. Yien YY, Shi J, Chen C, Cheung JT, Grillo AS, Shrestha R, Li L, Zhang X, Kafina MD, Kingsley PD, King MJ, Ablain J, Li H, Zon L, Palis J, Burke MD, Bauer DE, Orkin SH, Koehler CM, Phillips JD, Kaplan J, Ward DM, Lodish HF, Paw BH. J Biol Chem. pubmed:30366982;  doi:10.1074/jbc.RA118.002742

19. Affinity-based capture and identification of protein effectors of the growth regulator ppGpp. Wang B, Dai P, Ding D, Del Rosario A, Grant RA, Pentelute BL, Laub MT. Nat Chem Biol. pubmed:30559427;  doi:10.1038/s41589-018-0183-4

20. Blood-brain-barrier organoids for investigating the permeability of CNS therapeutics. Bergmann S, Lawler SE, Qu Y, Fadzen CM, Wolfe JM, Regan MS, Pentelute BL, Agar NYR, Cho CF. Nat Protoc. pubmed:30382243;  doi:10.1038/s41596-018-0066-x

21. Biofilm-Inspired Encapsulation of Probiotics for the Treatment of Complex Infections. Li Z, Behrens AM, Ginat N, Tzeng SY, Lu X, Sivan S, Langer R, Jaklenec A. Adv Mater. pubmed:30328144;  doi:10.1002/adma.201803925

22. B-Aminoacrylate Synthetic Hydrogels: Easily Accessible and Operationally Simple Biomaterials Networks. Fenton O, Andresen J, Paolini M, Langer R. Angew Chem Int Ed Engl. pubmed:30209869;  doi:10.1002/anie.201808452

23. Quantification of somatic mutation flow across individual cell division events by lineage sequencing. Brody Y, Kimmerling RJ, Maruvka YE, Benjamin D, Elacqua JJ, Haradhvala NJ, Kim J, Mouw KW, Frangaj K, Koren A, Getz G, Manalis SR, Blainey PC. Genome Res. pubmed:30459213;  doi:10.1101/gr.238543.118

24. Subendothelial matrix components influence endothelial cell apoptosis in vitro. Saemisch M, Balcells M, Riesinger L, Nickmann M, Bhaloo SI, Edelman ER, Methe H. Am J Physiol Cell Physiol. pubmed:30566394;  doi:10.1152/ajpcell.00005.2018

25. A 3D microvascular network model to study the impact of hypoxia on the extravasation potential of breast cell lines. Song J, Miermont A, Lim CT, Kamm RD. Sci Rep. pubmed:30560881;  doi:10.1038/s41598-018-36381-5

26. A Computationally Designed Peptide Derived from Escherichia coli as a Potential Drug Template for Antibacterial and Antibiofilm Therapies. Cardoso MH, Candido ES, Chan LY, Der Torossian Torres M, Oshiro KGN, Rezende SB, Porto WF, Lu TK, de la Fuente-Nunez C, Craik DJ, Franco OL. ACS Infect Dis. pubmed:30346140;  doi:10.1021/acsinfecdis.8b00219

27. Designable 3D Microshapes Fabricated at the Intersection of Structured Flow and Optical Fields. Yuan R, Nagarajan MB, Lee J, Voldman J, Doyle PS, Fink Y. Small. pubmed:30369043;  doi:10.1002/smll.201803585

28. Innate immune recognition of glycans targets HIV nanoparticle immunogens to germinal centers. Tokatlian T, Read BJ, Jones CA, Kulp DW, Menis S, Chang JYH, Steichen JM, Kumari S, Allen JD, Dane EL, Liguori A, Sangesland M, Lingwood D, Crispin M, Schief WR, Irvine DJ. Science. pubmed:30573546;  doi:10.1126/science.aat9120

29. Altered Binding of Tumor Antigenic Peptides to MHC Class I Affects CD8(+) T Cell-Effector Responses. Clancy-Thompson E, Devlin CA, Tyler PM, Servos MM, Ali LR, Ventre KS, Bhuiyan MA, Bruck PT, Birnbaum ME, Dougan SK. Cancer Immunol Res. pubmed:30352798;  doi:10.1158/2326-6066.CIR-18-0348

30. Effect of working environment and procedural strategies on mechanical performance of bioresorbable vascular scaffolds. Wang PJ, Rikhtegar Nezami F, Gorji MB, Berti F, Petrini L, Wierzbicki T, Migliavacca F, Edelman ER. Acta Biomater. pubmed:30342288;  doi:10.1016/j.actbio.2018.10.020

31. Targeting small molecule drugs to T cells with antibody-directed cell-penetrating gold nanoparticles. Yang YS, Moynihan KD, Bekdemir A, Dichwalkar TM, Noh MM, Watson N, Melo M, Ingram J, Suh H, Ploegh H, Stellacci FR, Irvine DJ. Biomater Sci. pubmed:30444251;  doi:10.1039/c8bm01208c

32. Reply to Slogrove, et al. Goetghebuer T, Smolen KK, Adler C, Das J, McBride T, Smits G, Lecomte S, Haelterman E, Barlow P, Piedra PA, van der Klis F, Kollmann TR, Lauffenburger DA, Alter G, Levy J, Marchant A. Clin Infect Dis. pubmed:30535371;  doi:10.1093/cid/ciy1058

33. Protease activity sensors noninvasively classify bacterial infections and antibiotic responses. Buss CG, Dudani JS, Akana RTK, Fleming HE, Bhatia SN. EBioMedicine. pubmed:30503861;  doi:10.1016/j.ebiom.2018.11.031

34. 3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds. Oran D, Rodriques SG, Gao R, Asano S, Skylar-Scott MA, Chen F, Tillberg PW, Marblestone AH, Boyden ES. Science. pubmed:30545883;  doi:10.1126/science.aau5119

35. Highly adjustable 3D nano-architectures and chemistries via assembled 1D biological templates. Ohmura JF, Burpo FJ, Lescott CJ, Ransil A, Yoon Y, Records WC, Belcher AM. Nanoscale. pubmed:30574649;  doi:10.1039/c8nr04864a

36. Quantitative Label-Free Imaging of 3D Vascular Networks Self-Assembled in Synthetic Hydrogels. Kaushik G, Gil DA, Torr E, Berge ES, Soref C, Uhl P, Fontana G, Antosiewicz-Bourget J, Edington C, Schwartz MP, Griffith LG, Thomson JA, Skala MC, Daly WT, Murphy WL. Adv Healthc Mater. pubmed:30565891;  doi:10.1002/adhm.201801186

37. Biodegradable wafers releasing Temozolomide and Carmustine for the treatment of brain cancer. Shapira-Furman T, Serra R, Gorelick N, Doglioli M, Tagliaferri V, Cecia A, Peters M, Kumar A, Rottenberg Y, Langer R, Brem H, Tyler B, Domb AJ. J Control Release. pubmed:30605703;  doi:10.1016/j.jconrel.2018.12.048