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: February 2013

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Publications Citing Koch Institute Faculty Members

1. Aberrant splicing of HTT generates the pathogenic exon 1 protein in Huntington disease. Sathasivam K, Neueder A, Gipson TA, Landles C, Benjamin AC, Bondulich MK, Smith DL, Faull RL, Roos RA, Howland D, Detloff PJ, Housman DE, Bates GP. Proc Natl Acad Sci U S A. pubmed:23341618;  doi:10.1073/pnas.1221891110

2. Exogenous delivery of chaperonin subunit fragment ApiCCT1 modulates mutant Huntingtin cellular phenotypes. Sontag EM, Joachimiak LA, Tan Z, Tomlinson A, Housman DE, Glabe CG, Potkin SG, Frydman J, Thompson LM. Proc Natl Acad Sci U S A. pubmed:23365139;  doi:10.1073/pnas.1222663110

3. Widespread regulation of translation by elongation pausing in heat shock. Shalgi R, Hurt JA, Krykbaeva I, Taipale M, Lindquist S, Burge CB. Mol Cell. pubmed:23290915;  doi:10.1016/j.molcel.2012.11.028

4. Rapid generation of human B-cell lymphomas via combined expression of Myc and Bcl2 and their use as a preclinical model for biological therapies. Leskov I, Pallasch CP, Drake A, Iliopoulou BP, Souza A, Shen CH, Schweighofer CD, Abruzzo L, Frenzel LP, Wendtner CM, Hemann MT, Chen J. Oncogene. pubmed:22484426;  doi:10.1038/onc.2012.117

5. Extensive changes in DNA methylation are associated with expression of mutant huntingtin. Ng CW, Yildirim F, Yap YS, Dalin S, Matthews BJ, Velez PJ, Labadorf A, Housman DE, Fraenkel E. Proc Natl Acad Sci U S A. pubmed:23341638;  doi:10.1073/pnas.1221292110

6. Directional cell migration in an extracellular pH gradient: a model study with an engineered cell line and primary microvascular endothelial cells. Paradise RK, Whitfield MJ, Lauffenburger DA, Van Vliet KJ. Exp Cell Res. pubmed:23153553;  doi:10.1016/j.yexcr.2012.11.006

7. Control of substrate access to the active site in methane monooxygenase. Lee SJ, McCormick MS, Lippard SJ, Cho US. Nature. pubmed:23395959;  doi:10.1038/nature11880

8. Long noncoding RNAs regulate adipogenesis. Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL. Proc Natl Acad Sci U S A. pubmed:23401553;  doi:10.1073/pnas.1222643110

9. Single-cell analysis of ribonucleotide reductase transcriptional and translational response to DNA damage. Mazumder A, Tummler K, Bathe M, Samson LD. Mol Cell Biol. pubmed:23184665;  doi:10.1128/MCB.01020-12

10. Allosteric regulation of PKM2 allows cellular adaptation to different physiological states. Gui DY, Lewis CA, Vander Heiden MG. Sci Signal. pubmed:23423437;  doi:10.1126/scisignal.2003925

11. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Jacob AI, Kohrer C, Davies BW, RajBhandary UL, Walker GC. Mol Cell. pubmed:23273979;  doi:10.1016/j.molcel.2012.11.025

12. Understanding metabolic regulation and its influence on cell physiology. Metallo CM, Vander Heiden MG. Mol Cell. pubmed:23395269;  doi:10.1016/j.molcel.2013.01.018

13. Multiplexed protease activity assay for low-volume clinical samples using droplet-based microfluidics and its application to endometriosis. Chen CH, Miller MA, Sarkar A, Beste MT, Isaacson KB, Lauffenburger DA, Griffith LG, Han J. J Am Chem Soc. pubmed:23157326;  doi:10.1021/ja307866z

14. Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development. Dawlaty MM, Breiling A, Le T, Raddatz G, Barrasa MI, Cheng AW, Gao Q, Powell BE, Li Z, Xu M, Faull KF, Lyko F, Jaenisch R. Dev Cell. pubmed:23352810;  doi:10.1016/j.devcel.2012.12.015

15. Matrix Remodeling Maintains ESC Self-Renewal by Activating Stat3. Przybyla LM, Theunissen TW, Jaenisch R, Voldman J. Stem Cells. pubmed:23404867;  doi:10.1002/stem.1360

16. Targeted anti-inflammatory systemic therapy for restenosis: the Biorest Liposomal Alendronate with Stenting sTudy (BLAST)-a double blind, randomized clinical trial. Banai S, Finkelstein A, Almagor Y, Assali A, Hasin Y, Rosenschein U, Apruzzese P, Lansky AJ, Kume T, Edelman ER. Am Heart J. pubmed:23351827;  doi:10.1016/j.ahj.2012.10.023

17. Importance of Receptor-Targeted Systems In The Battle Against Atherosclerosis. Rosas E, Sobenin I, Orekhov A, Edelman ER, Balcells M. Curr Pharm Des. pubmed:23438961;  

18. Tunable localized surface plasmon-enabled broadband light-harvesting enhancement for high-efficiency panchromatic dye-sensitized solar cells. Dang X, Qi J, Klug MT, Chen PY, Yun DS, Fang NX, Hammond PT, Belcher AM. Nano Lett. pubmed:23339821;  doi:10.1021/nl3043823

19. A vector-free microfluidic platform for intracellular delivery. Sharei A, Zoldan J, Adamo A, Sim WY, Cho N, Jackson E, Mao S, Schneider S, Han MJ, Lytton-Jean A, Basto PA, Jhunjhunwala S, Lee J, Heller DA, Kang JW, Hartoularos GC, Kim KS, Anderson DG, Langer R, Jensen KF. Proc Natl Acad Sci U S A. pubmed:23341631;  doi:10.1073/pnas.1218705110

20. A highly tunable biocompatible and multifunctional biodegradable elastomer. Pereira MJ, Ouyang B, Sundback CA, Lang N, Friehs I, Mureli S, Pomerantseva I, McFadden J, Mochel MC, Mwizerwa O, Del Nido P, Sarkar D, Masiakos PT, Langer R, Ferreira LS, Karp JM. Adv Mater. pubmed:23239051;  doi:10.1002/adma.201203824

21. The dynamic lives of T cells: new approaches and themes. Yamanaka YJ, Gierahn TM, Love JC. Trends Immunol. pubmed:23200626;  doi:10.1016/

22. Systematic identification of signal-activated stochastic gene regulation. Neuert G, Munsky B, Tan RZ, Teytelman L, Khammash M, van Oudenaarden A. Science. pubmed:23372015;  doi:10.1126/science.1231456

23. A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Bienko M, Crosetto N, Teytelman L, Klemm S, Itzkovitz S, van Oudenaarden A. Nat Methods. pubmed:23263692;  doi:10.1038/nmeth.2306

24. Catch-and-release probes applied to semi-intact cells reveal ubiquitin-specific protease expression in Chlamydia trachomatis infection. Claessen JH, Witte MD, Yoder NC, Zhu AY, Spooner E, Ploegh HL. Chembiochem. pubmed:23335262;  doi:10.1002/cbic.201200701

25. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Sigova AA, Mullen AC, Molinie B, Gupta S, Orlando DA, Guenther MG, Almada AE, Lin C, Sharp PA, Giallourakis CC, Young RA. Proc Natl Acad Sci U S A. pubmed:23382218;  doi:10.1073/pnas.1221904110

26. Peptide targeting and imaging of damaged lung tissue in influenza-infected mice. Li N, Yin L, Thevenin D, Yamada Y, Limmon G, Chen J, Chow VT, Engelman DM, Engelward BP. Future Microbiol. pubmed:23374130;  doi:10.2217/fmb.12.134

27. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, Sougnez C, Stewart C, Sivachenko A, Wang L, Wan Y, Zhang W, Shukla SA, Vartanov A, Fernandes SM, Saksena G, Cibulskis K, Tesar B, Gabriel S, Hacohen N, Meyerson M, Lander ES, Neuberg D, Brown JR, Getz G, Wu CJ. Cell. pubmed:23415222;  doi:10.1016/j.cell.2013.01.019

28. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Drier Y, Lawrence MS, Carter SL, Stewart C, Gabriel SB, Lander ES, Meyerson M, Beroukhim R, Getz G. Genome Res. pubmed:23124520;  doi:10.1101/gr.141382.112

29. Human Fetal Hepatic Progenitor Cells Are Distinct from, but Closely Related to, Hematopoietic Stem/Progenitor Cells. Chen Q, Khoury M, Limmon G, Choolani M, Chan JK, Chen J. Stem Cells. pubmed:23404852;  doi:10.1002/stem.1359

30. Identifying recent adaptations in large-scale genomic data. Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL, Lander ES, Schaffner SF, Sabeti PC. Cell. pubmed:23415221;  doi:10.1016/j.cell.2013.01.035

31. A catalytically inactive mutant of the deubiquitylase YOD-1 enhances antigen cross-presentation. Sehrawat S, Koenig PA, Kirak O, Schlieker C, Fankhauser M, Ploegh HL. Blood. pubmed:23243279;  doi:10.1182/blood-2012-08-447409