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: July 2018

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1. JDP2: An oncogenic bZIP transcription factor in T cell acute lymphoblastic leukemia. Mansour MR, He S, Li Z, Lobbardi R, Abraham BJ, Hug C, Rahman S, Leon TE, Kuang YY, Zimmerman MW, Blonquist T, Gjini E, Gutierrez A, Tang Q, Garcia-Perez L, Pike-Overzet K, Anders L, Berezovskaya A, Zhou Y, Zon LI, Neuberg D, Fielding AK, Staal FJT, Langenau DM, Sanda T, Young RA, Look AT. J Exp Med. pubmed:29941549;  doi:10.1084/jem.20170484

2. High MITF Expression is Associated with Super-enhancers and Suppressed by CDK7 Inhibition in Melanoma. Eliades P, Abraham BJ, Ji Z, Miller DM, Christensen CL, Kwiatkowski N, Kumar R, Njauw CN, Taylor M, Miao B, Zhang T, Wong KK, Gray NS, Young RA, Tsao H. J Invest Dermatol. pubmed:29408204;  doi:10.1016/j.jid.2017.09.056

3. Hypoxia-inducible factor cell non-autonomously regulates C elegans stress responses and behavior via a nuclear receptor. Pender CL, Horvitz HR. Elife. pubmed:30010540;  doi:10.7554/eLife.36828

4. Histidine catabolism is a major determinant of methotrexate sensitivity. Kanarek N, Keys HR, Cantor JR, Lewis CA, Chan SH, Kunchok T, Abu-Remaileh M, Freinkman E, Schweitzer LD, Sabatini DM. Nature. pubmed:29995852;  doi:10.1038/s41586-018-0316-7

5. Deptor modulates activation responses in CD4(+) T cells and enhances immunoregulation following transplantation. Wedel J, Bruneau S, Liu K, Kong SW, Sage PT, Sabatini DM, Laplante M, Briscoe DM. Am J Transplant. pubmed:29969188;  doi:10.1111/ajt.14995

6. Aspartate is an endogenous metabolic limitation for tumour growth. Sullivan LB, Luengo A, Danai LV, Bush LN, Diehl FF, Hosios AM, Lau AN, Elmiligy S, Malstrom S, Lewis CA, Vander Heiden MG. Nat Cell Biol. pubmed:29941931;  doi:10.1038/s41556-018-0125-0

7. An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC. Elife. pubmed:30059005;  doi:10.7554/eLife.37184

8. Important late stage symbiotic role of the Sinorhizobium meliloti exopolysaccharide succinoglycan. Arnold MFF, Penterman J, Shabab M, Chen EJ, Walker GC. J Bacteriol. pubmed:29632097;  doi:10.1128/JB.00665-17

9. Modeling chemotherapy-induced stress to identify rational combination therapies in the DNA damage response pathway. Alkan O, Schoeberl B, Shah M, Koshkaryev A, Heinemann T, Drummond DC, Yaffe MB, Raue A. Sci Signal. pubmed:30042127;  doi:10.1126/scisignal.aat0229

10. GeNets: a unified web platform for network-based genomic analyses. Li T, Kim A, Rosenbluh J, Horn H, Greenfeld L, An D, Zimmer A, Liberzon A, Bistline J, Natoli T, Li Y, Tsherniak A, Narayan R, Subramanian A, Liefeld T, Wong B, Thompson D, Calvo S, Carr S, Boehm J, Jaffe J, Mesirov J, Hacohen N, Regev A, Lage K. Nat Methods. pubmed:29915188;  doi:10.1038/s41592-018-0039-6

11. Comprehensive comparative analysis of 5'-end RNA-sequencing methods. Adiconis X, Haber AL, Simmons SK, Levy Moonshine A, Ji Z, Busby MA, Shi X, Jacques J, Lancaster MA, Pan JQ, Regev A, Levin JZ. Nat Methods. pubmed:29867192;  doi:10.1038/s41592-018-0014-2

12. A Tumor Cell-Intrinsic Yin-Yang Determining Immune Evasion. Horton B, Spranger S. Immunity. pubmed:30021140;  doi:10.1016/j.immuni.2018.07.001

13. A team effort: natural killer cells on the first leg of the tumor immunity relay race. Fessenden TB, Duong E, Spranger S. J Immunother Cancer. pubmed:29986768;  doi:10.1186/s40425-018-0380-4

14. Epithelial-Mesenchymal Transition Induces Podocalyxin to Promote Extravasation via Ezrin Signaling. Frose J, Chen MB, Hebron KE, Reinhardt F, Hajal C, Zijlstra A, Kamm RD, Weinberg RA. Cell Rep. pubmed:30044991;  doi:10.1016/j.celrep.2018.06.092

15. BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization. de Boer CG, Regev A. BMC Bioinformatics. pubmed:29970004;  doi:10.1186/s12859-018-2255-6

16. Human induced pluripotent stem cell-derived glial cells and neural progenitors display divergent responses to Zika and dengue infections. Muffat J, Li Y, Omer A, Durbin A, Bosch I, Bakiasi G, Richards E, Meyer A, Gehrke L, Jaenisch R. Proc Natl Acad Sci U S A. pubmed:29915057;  doi:10.1073/pnas.1719266115

17. Inflamed neutrophils sequestered at entrapped tumor cells via chemotactic confinement promote tumor cell extravasation. Chen MB, Hajal C, Benjamin DC, Yu C, Azizgolshani H, Hynes RO, Kamm RD. Proc Natl Acad Sci U S A. pubmed:29915060;  doi:10.1073/pnas.1715932115

18. Coactivator condensation at super-enhancers links phase separation and gene control. Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, Li CH, Guo YE, Day DS, Schuijers J, Vasile E, Malik S, Hnisz D, Lee TI, Cisse II, Roeder RG, Sharp PA, Chakraborty AK, Young RA. Science. pubmed:29930091;  doi:10.1126/science.aar3958

19. Molecular mechanisms of the preventable causes of cancer in the United States. Golemis EA, Scheet P, Beck TN, Scolnick E, Hunter DJ, Hawk E, Hopkins N. Genes Dev. pubmed:29945886;  doi:10.1101/gad.314849.118

20. Positional specificity of different transcription factor classes within enhancers. Grossman SR, Engreitz J, Ray JP, Nguyen TH, Hacohen N, Lander ES. Proc Natl Acad Sci U S A. pubmed:29987030;  doi:10.1073/pnas.1804663115

21. Failed Progenitor Specification Underlies the Cardiopharyngeal Phenotypes in a Zebrafish Model of 22q11.2 Deletion Syndrome. Guner-Ataman B, Gonzalez-Rosa JM, Shah HN, Butty VL, Jeffrey S, Abrial M, Boyer LA, Burns CG, Burns CE. Cell Rep. pubmed:30067987;  doi:10.1016/j.celrep.2018.06.117

22. Building Capacity for a Global Genome Editing Observatory: Conceptual Challenges. Hurlbut JB, Jasanoff S, Saha K, Ahmed A, Appiah A, Bartholet E, Baylis F, Bennett G, Church G, Cohen IG, Daley G, Finneran K, Hurlbut W, Jaenisch R, Lwoff L, Kimes JP, Mills P, Moses J, Park BS, Parens E, Salzman R, Saxena A, Simmet H, Simoncelli T, Snead OC, Rajan KS, Truog RD, Williams P, Woopen C. Trends Biotechnol. pubmed:29871776;  doi:10.1016/j.tibtech.2018.04.009

23. Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyoty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ. Cell Host Microbe. pubmed:30001517;  doi:10.1016/j.chom.2018.06.007

24. Templated Self-assembly of a PS-branch-PDMS Bottlebrush Copolymer. Cheng LC, Gadelrab KR, Kawamoto K, Yager KG, Johnson JA, Alexander-Katz A, Ross CA. Nano Lett. pubmed:29877712;  doi:10.1021/acs.nanolett.8b01389

25. Janus Graft Block Copolymers: Design of Polymer Architecture for Independently Tuned Nanostructures and Polymer Properties. Guo ZH, Le AN, Feng X, Choo Y, Liu B, Wang D, Wan Z, Gu Y, Zhao J, Li V, Osuji C, Johnson JA, Zhong M. Angew Chem Int Ed Engl. pubmed:29697893;  doi:10.1002/anie.201802844

26. Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription. Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE. Nucleic Acids Res. pubmed:29961805;  doi:10.1093/nar/gky529

27. Engineering circular RNA for potent and stable translation in eukaryotic cells. Wesselhoeft RA, Kowalski PS, Anderson DG. Nat Commun. pubmed:29980667;  doi:10.1038/s41467-018-05096-6

28. Poly(beta-amino ester)-co-poly(caprolactone) Terpolymers as Nonviral Vectors for mRNA Delivery In Vitro and In Vivo. Capasso Palmiero U, Kaczmarek JC, Fenton OS, Anderson DG. Adv Healthc Mater. pubmed:29761648;  doi:10.1002/adhm.201800249

29. Hepatic connexin 32 associates with nonalcoholic fatty liver disease severity. Luther J, Gala MK, Borren N, Masia R, Goodman RP, Moeller IH, DiGiacomo E, Ehrlich A, Warren A, Yarmush ML, Ananthakrishnan A, Corey K, Kaplan LM, Bhatia S, Chung RT, Patel SJ. Hepatol Commun. pubmed:30202815;  doi:10.1002/hep4.1179

30. Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer. Viswanathan SR, Nogueira MF, Buss CG, Krill-Burger JM, Wawer MJ, Malolepsza E, Berger AC, Choi PS, Shih J, Taylor AM, Tanenbaum B, Pedamallu CS, Cherniack AD, Tamayo P, Strathdee CA, Lage K, Carr SA, Schenone M, Bhatia SN, Vazquez F, Tsherniak A, Hahn WC, Meyerson M. Nat Genet. pubmed:29955178;  doi:10.1038/s41588-018-0155-3

31. Design and experimental validation of Unilateral Linear Halbach magnet arrays for single-sided magnetic resonance. Bashyam A, Li M, Cima MJ. J Magn Reson. pubmed:29763794;  doi:10.1016/j.jmr.2018.05.004

32. Chondroitin Sulphate Attenuates Atherosclerosis in ApoE Knockout Mice Involving Cellular Regulation of the Inflammatory Response. Melgar-Lesmes P, Sanchez-Herrero A, Lozano-Juan F, Hernandez JMT, Montell E, Jimenez W, Edelman ER, Balcells M. Thromb Haemost. pubmed:29874688;  doi:10.1055/s-0038-1657753

33. Evaporative Cooling Hydrogel Packaging for Storing Biologics Outside of the Cold Chain. Ferber S, Behrens AM, McHugh KJ, Rosenberg EM, Linehan AR, Sugarman JL, Jayawardena HSN, Langer R, Jaklenec A. Adv Healthc Mater. pubmed:29732715;  doi:10.1002/adhm.201800220

34. Chemoproteomics of matrix metalloproteases in a model of cartilage degeneration suggests functional biomarkers associated with posttraumatic osteoarthritis. Ravindra KC, Ahrens CC, Wang Y, Ramseier JY, Wishnok JS, Griffith LG, Grodzinsky AJ, Tannenbaum SR. J Biol Chem. pubmed:29794029;  doi:10.1074/jbc.M117.818542

35. Rationally Designed Polycationic Carriers for Potent Polymeric siRNA-Mediated Gene Silencing. Wu C, Li J, Wang W, Hammond PT. ACS Nano. pubmed:29944833;  doi:10.1021/acsnano.7b08777

36. Peptide-Programmable Nanoparticle Superstructures with Tailored Electrocatalytic Activity. Kang ES, Kim YT, Ko YS, Kim NH, Cho G, Huh YH, Kim JH, Nam J, Thach TT, Youn D, Kim YD, Yun WS, DeGrado WF, Kim SY, Hammond PT, Lee J, Kwon YU, Ha DH, Kim YH. ACS Nano. pubmed:29842775;  doi:10.1021/acsnano.8b01146

37. Nanofibrillar Patches of Commensal Skin Bacteria. Glinel K, Behrens A, Langer RS, Jaklenec A, Jonas AM. Biomacromolecules. pubmed:29979873;  doi:10.1021/acs.biomac.8b00735

38. Ionizable Amino-Polyesters Synthesized via Ring Opening Polymerization of Tertiary Amino-Alcohols for Tissue Selective mRNA Delivery. Kowalski PS, Capasso Palmiero U, Huang Y, Rudra A, Langer R, Anderson DG. Adv Mater. pubmed:29975801;  doi:10.1002/adma.201801151

39. Caffeine-catalyzed gels. DiCiccio AM, Lee YL, Glettig DL, Walton ESE, de la Serna EL, Montgomery VA, Grant TM, Langer R, Traverso G. Biomaterials. pubmed:29660635;  doi:10.1016/j.biomaterials.2018.04.010

40. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D, Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M. Cell. pubmed:29909985;  doi:10.1016/j.cell.2018.05.036

41. Thermal processing of thermogelling nanoemulsions as a route to tune material properties. Cheng LC, Godfrin PD, Swan JW, Doyle PS. Soft Matter. pubmed:29923590;  doi:10.1039/c8sm00814k

42. A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality. Daigle TL, Madisen L, Hage TA, Valley MT, Knoblich U, Larsen RS, Takeno MM, Huang L, Gu H, Larsen R, Mills M, Bosma-Moody A, Siverts LA, Walker M, Graybuck LT, Yao Z, Fong O, Nguyen TN, Garren E, Lenz GH, Chavarha M, Pendergraft J, Harrington J, Hirokawa KE, Harris JA, Nicovich PR, McGraw MJ, Ollerenshaw DR, Smith KA, Baker CA, Ting JT, Sunkin SM, Lecoq J, Lin MZ, Boyden ES, Murphy GJ, da Costa NM, Waters J, Li L, Tasic B, Zeng H. Cell. pubmed:30007418;  doi:10.1016/j.cell.2018.06.035

43. High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ. Nucleic Acids Res. pubmed:29718339;  doi:10.1093/nar/gky296

44. In vitro models of molecular and nano-particle transport across the blood-brain barrier. Hajal C, Campisi M, Mattu C, Chiono V, Kamm RD. Biomicrofluidics. pubmed:29887937;  doi:10.1063/1.5027118

45. Contact guidance and collective migration in the advancing epithelial monolayer. Lee G, Atia L, Lan B, Sharma Y, Nissim L, Wu MR, Pery E, Lu TK, Park CY, Butler JP, Fredberg JJ. Connect Tissue Res. pubmed:28945485;  doi:10.1080/03008207.2017.1384471

46. Focal, remote-controlled, chronic chemical modulation of brain microstructures. Ramadi KB, Dagdeviren C, Spencer KC, Joe P, Cotler M, Rousseau E, Nunez-Lopez C, Graybiel AM, Langer R, Cima MJ. Proc Natl Acad Sci U S A. pubmed:29941557;  doi:10.1073/pnas.1804372115

47. Folding artificial mucosa with cell-laden hydrogels guided by mechanics models. Chan HF, Zhao R, Parada GA, Meng H, Leong KW, Griffith LG, Zhao X. Proc Natl Acad Sci U S A. pubmed:29967135;  doi:10.1073/pnas.1802361115

48. Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro. Gee MH, Sibener LV, Birnbaum ME, Jude KM, Yang X, Fernandes RA, Mendoza JL, Glassman CR, Garcia KC. Proc Natl Acad Sci U S A. pubmed:30021852;  doi:10.1073/pnas.1802746115

49. Optimized Computer-Aided Segmentation and Three-Dimensional Reconstruction Using Intracoronary Optical Coherence Tomography. Athanasiou L, Nezami FR, Galon MZ, Lopes AC, Lemos PA, de la Torre Hernandez JM, Ben-Assa E, Edelman ER. IEEE J Biomed Health Inform. pubmed:29969405;  doi:10.1109/JBHI.2017.2762520

50. Influence of protein corona and caveolae-mediated endocytosis on nanoparticle uptake and transcytosis. Ho YT, Kamm RD, Kah JCY. Nanoscale. pubmed:29926047;  doi:10.1039/c8nr02393j

51. Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding. Sibener LV, Fernandes RA, Kolawole EM, Carbone CB, Liu F, McAffee D, Birnbaum ME, Yang X, Su LF, Yu W, Dong S, Gee MH, Jude KM, Davis MM, Groves JT, Goddard WA3rd, Heath JR, Evavold BD, Vale RD, Garcia KC. Cell. pubmed:30053426;  doi:10.1016/j.cell.2018.06.017

52. Automated in vivo patch clamp evaluation of extracellular multielectrode array spike recording capability. Allen BD, Moore-Kochlacs C, Bernstein JG, Kinney J, Scholvin J, Seoane L, Chronopoulos C, Lamantia C, Kodandaramaiah SB, Tegmark M, Boyden ES. J Neurophysiol. pubmed:29995597;  doi:10.1152/jn.00650.2017