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: August 2018

Return to Progress index

1. Commensal microflora-induced T cell responses mediate progressive neurodegeneration in glaucoma. Chen H, Cho KS, Vu THK, Shen CH, Kaur M, Chen G, Mathew R, McHam ML, Fazelat A, Lashkari K, Au NPB, Tse JKY, Li Y, Yu H, Yang L, Stein-Streilein J, Ma CHE, Woolf CJ, Whary MT, Jager MJ, Fox JG, Chen J, Chen DF. Nat Commun. pubmed:30097565;  doi:10.1038/s41467-018-05681-9

2. JIP2 haploinsufficiency contributes to neurodevelopmental abnormalities in human pluripotent stem cell-derived neural progenitors and cortical neurons. Roessler R, Goldmann J, Shivalila C, Jaenisch R. Life Sci Alliance. pubmed:30456368;  doi:10.26508/lsa.201800094

3. Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. Teitz LS, Pyntikova T, Skaletsky H, Page DC. Am J Hum Genet. pubmed:30075113;  doi:10.1016/j.ajhg.2018.07.007

4. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Montoro DT, Haber AL, Biton M, Vinarsky V, Lin B, Birket SE, Yuan F, Chen S, Leung HM, Villoria J, Rogel N, Burgin G, Tsankov AM, Waghray A, Slyper M, Waldman J, Nguyen L, Dionne D, Rozenblatt-Rosen O, Tata PR, Mou H, Shivaraju M, Bihler H, Mense M, Tearney GJ, Rowe SM, Engelhardt JF, Regev A, Rajagopal J. Nature. pubmed:30069044;  doi:10.1038/s41586-018-0393-7

5. Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, De Jager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ, Regev A. Nat Genet. pubmed:29988122;  doi:10.1038/s41588-018-0156-2

6. Building Capacity for a Global Genome Editing Observatory: Institutional Design. Saha K, Hurlbut JB, Jasanoff S, 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:29891181;  doi:10.1016/j.tibtech.2018.04.008

7. DEPTOR Suppresses Lipogenesis and Ameliorates Hepatic Steatosis and Acute-on-Chronic Liver Injury in Alcoholic Liver Disease. Chen H, Shen F, Sherban A, Nocon A, Li Y, Wang H, Xu MJ, Rui X, Han J, Jiang B, Lee D, Li N, Keyhani-Nejad F, Fan JG, Liu F, Kamat A, Musi N, Guarente L, Pacher P, Gao B, Zang M. Hepatology. pubmed:29457836;  doi:10.1002/hep.29849

8. A Raf-competitive K-Ras binder can fail to functionally antagonize signaling. Kauke MJ, Tisdale AW, Kelly RL, Braun CJ, Hemann MT, Wittrup KD. Mol Cancer Ther. pubmed:29720559;  doi:10.1158/1535-7163.MCT-17-0645

9. Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Charbonnier C, Chung J, Crane PK, Cruchaga C, Cupples LA, Dartigues JF, Debette S, Deleuze JF, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, Ikram MA, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimaki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, Pericak-Vance MA, Perola M, Psaty BM, Quenez O, Rajabli F, Redon R, Reitz C, Remes AM, Salomaa V, Sarnowski C, Schmidt H, Schmidt M, Schmidt R, Soininen H, Thornton TA, Tosto G, Tzourio C, van der Lee SJ, van Duijn CM, Vardarajan B, Wang W, Wijsman E, Wilson RK, Witten D, Worley KC, Zhang X, Bellenguez C, Lambert JC, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, Destefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj AC, Fornage M, Farrer LA. Mol Psychiatry. pubmed:30108311;  doi:10.1038/s41380-018-0112-7

10. Androgen receptor polyglutamine expansion drives age-dependent quality control defects and muscle dysfunction. Nath SR, Yu Z, Gipson TA, Marsh GB, Yoshidome E, Robins DM, Todi SV, Housman DE, Lieberman AP. J Clin Invest. pubmed:29809168;  doi:10.1172/JCI99042

11. Critical Issues in Diamond-Blackfan Anemia and Prospects for Novel Treatment. Li H, Lodish HF, Sieff CA. Hematol Oncol Clin North Am. pubmed:30047421;  doi:10.1016/j.hoc.2018.04.005

12. Incomplete base excision repair contributes to cell death from antibiotics and other stresses. Gruber CC, Walker GC. DNA Repair (Amst). pubmed:30181041;  doi:10.1016/j.dnarep.2018.08.014

13. Dietary regulation of the origins of cancer. Yilmaz OH. Sci Transl Med. pubmed:30089636;  doi:10.1126/scitranslmed.aat8285

14. Nutritional Regulation of Intestinal Stem Cells. Alonso S, Yilmaz OH. Annu Rev Nutr. pubmed:29799767;  doi:10.1146/annurev-nutr-082117-051644

15. PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode. Frappier V, Duran M, Keating AE. Protein Sci. pubmed:30251349;  doi:10.1002/pro.3431

16. Deregulation of the G1/S-phase transition is the proximal cause of mortality in old yeast mother cells. Neurohr GE, Terry RL, Sandikci A, Zou K, Li H, Amon A. Genes Dev. pubmed:30042134;  doi:10.1101/gad.312140.118

17. Epithelial-to-mesenchymal transition in cancer: complexity and opportunities. Zhang Y, Weinberg RA. Front Med. pubmed:30043221;  doi:10.1007/s11684-018-0656-6

18. Dynamic redox balance directs the oocyte-to-embryo transition via developmentally controlled reactive cysteine changes. Petrova B, Liu K, Tian C, Kitaoka M, Freinkman E, Yang J, Orr-Weaver TL. Proc Natl Acad Sci U S A. pubmed:30082411;  doi:10.1073/pnas.1807918115

19. Microenvironmental regulation of cancer cell metabolism: implications for experimental design and translational studies. Muir A, Danai LV, Vander Heiden MG. Dis Model Mech. pubmed:30104199;  doi:10.1242/dmm.035758

20. Rev7 dimerization is important for assembly and function of the Rev1/Polzeta translesion synthesis complex. Rizzo AA, Vassel FM, Chatterjee N, D'Souza S, Li Y, Hao B, Hemann MT, Walker GC, Korzhnev DM. Proc Natl Acad Sci U S A. pubmed:30111544;  doi:10.1073/pnas.1801149115

21. Dynamic changes in ORC localization and replication fork progression during tissue differentiation. Hua BL, Bell GW, Kashevsky H, Von Stetina JR, Orr-Weaver TL. BMC Genomics. pubmed:30134926;  doi:10.1186/s12864-018-4992-3

22. Deep-coverage whole genome sequences and blood lipids among 16,324 individuals. Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S. Nat Commun. pubmed:30140000;  doi:10.1038/s41467-018-05747-8

23. Numerous recursive sites contribute to accuracy of splicing in long introns in flies. Pai AA, Paggi JM, Yan P, Adelman K, Burge CB. PLoS Genet. pubmed:30148878;  doi:10.1371/journal.pgen.1007588

24. Hot lithium-oxygen batteries charge ahead. Feng S, Lunger JR, Johnson JA, Shao-Horn Y. Science. pubmed:30139863;  doi:10.1126/science.aau4792

25. Photoswitching topology in polymer networks with metal-organic cages as crosslinks. Gu Y, Alt EA, Wang H, Li X, Willard AP, Johnson JA. Nature. pubmed:30022167;  doi:10.1038/s41586-018-0339-0

26. Studies on a landscape of perfluoroaromatic-reactive peptides. Evans ED, Pentelute BL. Org Biomol Chem. pubmed:30065992;  doi:10.1039/c8ob01678j

27. Polymers at the Interface with Biology. Deming TJ, Klok HA, Armes SP, Becker ML, Champion JA, Chen EY, Heilshorn SC, van Hest JCM, Irvine DJ, Johnson JA, Kiessling LL, Maynard HD, de la Cruz MO, Sullivan MO, Tirrell MV, Anseth KS, Lecommandoux S, Percec S, Zhong Z, Albertsson AC. Biomacromolecules. pubmed:30099879;  doi:10.1021/acs.biomac.8b01029

28. Analyzing Dynamic Protein Complexes Assembled On and Released From Biolayer Interferometry Biosensor Using Mass Spectrometry and Electron Microscopy. Machen AJ, O'Neil PT, Pentelute BL, Villar MT, Artigues A, Fisher MT. J Vis Exp. pubmed:30124667;  doi:10.3791/57902

29. Characterization of a novel piperidine-based inhibitor of cathepsin B-dependent bacterial toxins and viruses. Hartmann S, Lopez Cruz R, Alameh S, Ho CC, Rabideau AE, Pentelute BL, Bradley KA, Martchenko M. ACS Infect Dis. pubmed:29749721;  doi:10.1021/acsinfecdis.8b00053

30. Allergic inflammatory memory in human respiratory epithelial progenitor cells. Ordovas-Montanes J, Dwyer DF, Nyquist SK, Buchheit KM, Vukovic M, Deb C, Wadsworth MH2nd, Hughes TK, Kazer SW, Yoshimoto E, Cahill KN, Bhattacharyya N, Katz HR, Berger B, Laidlaw TM, Boyce JA, Barrett NA, Shalek AK. Nature. pubmed:30135581;  doi:10.1038/s41586-018-0449-8

31. Report of the Key Opinion Leaders Meeting on Stem Cell-Derived Beta Cells. Odorico J, Markmann J, Melton D, Greenstein J, Hwa A, Nostro C, Rezania A, Oberholzer J, Pipeleers D, Yang L, Cowan C, Huangfu D, Egli D, Ben-David U, Vallier L, Grey ST, Tang Q, Roep B, Ricordi C, Naji A, Orlando G, Anderson DG, Poznansky M, Ludwig B, Tomei A, Greiner DL, Graham M, Carpenter M, Migliaccio G, D'Amour K, Hering B, Piemonti L, Berney T, Rickels M, Kay T, Adams A. Transplantation. pubmed:29781950;  doi:10.1097/TP.0000000000002217

32. Hydrogel-incorporating unit in a well: 3D cell culture for high-throughput analysis. Yu YJ, Kim YH, Na K, Min SY, Hwang OK, Park DK, Kim DY, Choi SH, Kamm RD, Chung S, Kim JA. Lab Chip. pubmed:30043033;  doi:10.1039/c8lc00525g

33. Graphene-Dendrimer Nanostars for Targeted Macrophage Overexpression of Metalloproteinase 9 and Hepatic Fibrosis Precision Therapy. Melgar-Lesmes P, Luquero A, Parra-Robert M, Mora A, Ribera J, Edelman ER, Jimenez W. Nano Lett. pubmed:30096241;  doi:10.1021/acs.nanolett.8b02498

34. A Role for Fc Function in Therapeutic Monoclonal Antibody-Mediated Protection against Ebola Virus. Gunn BM, Yu WH, Karim MM, Brannan JM, Herbert AS, Wec AZ, Halfmann PJ, Fusco ML, Schendel SL, Gangavarapu K, Krause T, Qiu X, He S, Das J, Suscovich TJ, Lai J, Chandran K, Zeitlin L, Crowe JEJr, Lauffenburger D, Kawaoka Y, Kobinger GP, Andersen KG, Dye JM, Saphire EO, Alter G. Cell Host Microbe. pubmed:30092199;  doi:10.1016/j.chom.2018.07.009

35. Antigen-specific antibody Fc glycosylation enhances humoral immunity via the recruitment of complement. Lofano G, Gorman MJ, Yousif AS, Yu WH, Fox JM, Dugast AS, Ackerman ME, Suscovich TJ, Weiner J, Barouch D, Streeck H, Little S, Smith D, Richman D, Lauffenburger D, Walker BD, Diamond MS, Alter G. Sci Immunol. pubmed:30120121;  doi:10.1126/sciimmunol.aat7796

36. In vivo systems biology approaches to chronic immune/inflammatory pathophysiology. Starchenko A, Lauffenburger DA. Curr Opin Biotechnol. pubmed:29494996;  doi:10.1016/j.copbio.2018.02.006

37. Scalable, Modular Three-Dimensional Silicon Microelectrode Assembly via Electroless Plating. Scholvin J, Zorzos A, Kinney J, Bernstein J, Moore-Kochlacs C, Kopell N, Fonstad C, Boyden ES. Micromachines (Basel). pubmed:30424369;  doi:10.3390/mi9090436

38. Optogenetic induction of the schizophrenia-related endophenotype of ventral hippocampal hyperactivity causes rodent correlates of positive and cognitive symptoms. Wolff AR, Bygrave AM, Sanderson DJ, Boyden ES, Bannerman DM, Kullmann DM, Katzel D. Sci Rep. pubmed:30150758;  doi:10.1038/s41598-018-31163-5

39. DNA Origami and G-Quadruplex Hybrid Complexes Induce Size-Control of Single-Walled Carbon Nanotubes via Biological Activation. Atsumi H, Belcher AM. ACS Nano. pubmed:30011182;  doi:10.1021/acsnano.8b02720

40. Scalable Gastric Resident Systems for Veterinary Application. Hayward A, Bensel T, Mazdiyasni H, Rogner J, Kirtane AR, Lee YL, Hua T, Bajpayee A, Collins J, McDonnell S, Cleveland C, Lopes A, Wahane A, Langer R, Traverso G. Sci Rep. pubmed:30087406;  doi:10.1038/s41598-018-30212-3

41. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Stewart MP, Langer R, Jensen KF. Chem Rev. pubmed:30052023;  doi:10.1021/acs.chemrev.7b00678

42. An impurity characterization based approach for the rapid development of integrated downstream purification processes. Timmick SM, Vecchiarello N, Goodwine C, Crowell LE, Love KR, Love JC, Cramer SM. Biotechnol Bioeng. pubmed:29679482;  doi:10.1002/bit.26718

43. Interstitial Flow Promotes Macrophage Polarization toward an M2 Phenotype. Li R, Serrano JC, Xing H, Lee TA, Azizgolshani H, Zaman M, Kamm RD. Mol Biol Cell. pubmed:29995595;  doi:10.1091/mbc.E18-03-0164

44. Vascularized microfluidic organ-chips for drug screening, disease models and tissue engineering. Osaki T, Sivathanu V, Kamm RD. Curr Opin Biotechnol. pubmed:29656237;  doi:10.1016/j.copbio.2018.03.011

45. Quantitative and multiplex microRNA assays from unprocessed cells in isolated nanoliter well arrays. Tentori AM, Nagarajan MB, Kim JJ, Zhang WC, Slack FJ, Doyle PS. Lab Chip. pubmed:29998262;  doi:10.1039/c8lc00498f

46. Two Vaccines for Staphylococcus aureus Induce a B-Cell-Mediated Immune Response. Dupont CD, Scully IL, Zimnisky RM, Monian B, Rossitto CP, O'Connell EB, Jansen KU, Anderson AS, Love JC. mSphere. pubmed:30135219;  doi:10.1128/mSphere.00217-18

47. Emerging applications for DNA writers and molecular recorders. Farzadfard F, Lu TK. Science. pubmed:30166483;  doi:10.1126/science.aat9249