Workshop Report 32


Adams BD, Wali VB, Cheng CJ, Inukai S, Booth CJ, Agarwal S, Rimm DL, Győrffy B, Santarpia L, Pusztai L, Saltzman WM, Slack FJ. 2016. miR-34a silences c-SRC to attenuate tumor growth in triple-negative breast cancer. Cancer Res 76:927-939.

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Ankley GT, Bennett RS, Erickson RJ, Hoff DJ, Hornung MW, Johnson RD, Mount DR, Nichols JW, Russom CL, Schmieder PK, Serrrano JA, Tietge JE, Villeneuve DL. 2010. Adverse outcome pathways: A conceptual framework to support ecotoxicology research and risk assessment. Env Toxicol Chem 29:730–741.

Arrigo P, Pulliero A. 2015. Effect of environmental chemical stress on nuclear noncoding RNA Involved in epigenetic control. Biomed Res Int 2015:761703.

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Baier SR, Nguyen C, Xie F, Wood JR, Zempleni J. 2014. MicroRNAs are absorbed in biologically meaningful amounts from nutritionally relevant doses of cow milk and affect gene expression in peripheral blood mononuclear cells, HEK-293 kidney cell cultures, and mouse livers. J Nutr 144(10):1495-1500.

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Bauer T, Trump S, Ishaque N, Thürmann L, Gu L, Bauer M, Bieg M, Gu Z, Weichenhan D, Mallm JP, Röder S, Herberth G, Takada E, Mücke O, Winter M, Junge KM, Grützmann K, Rolle-Kampczyk U, Wang Q, Lawerenz C, Borte M, Polte T, Schlesner M, Schanne M, Wiemann S, Geörg C, Stunnenberg HG, Plass C, Rippe K, Mizuguchi J, Herrmann C, Eils R, Lehmann I. 2016. Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children. Mol Syst Biol 12(3):861.

Bhan A, Hussain I, Ansari KI, Bobzean SA, Perrotti LI, Mandal SS. 2014. Bisphenol-A and diethylstilbestrol exposure induces the expression of breast cancer associated long noncoding RNA HOTAIR in vitro and in vivo. J Steroid Biochem Mol Biol 141:160-170.

Boll K, Reiche K, Kasack K, Mörbt N, Kretzschmar AK, Tomm JM, Verhaegh G, Schalken J, von Bergen M, Horn F, Hackermüller J. 2013. MiR-130a, miR-203 and miR-205 jointly repress key oncogenic pathways and are downregulated in prostate carcinoma. Oncogene 32:277-285.

Brocke-Heidrich K, Kretzschmar AK, Pfeifer G, Henze C, Löffler D, Koczan D, Thiesen HJ, Burger R, Gramatzki M, Horn F. 2004. Interleukin-6-dependent gene expression profiles in multiple myeloma INA-6 cells reveal a Bcl-2 family-independent survival pathway closely associated with Stat3 activation. Blood 103:242-251.

Calin GA, Croce CM. 2006. MicroRNA signatures in human cancers. Nat Rev Cancer 6(11):857-866.

Chen X, Ba Y, Ma L, Cai X, Yin Y, Wang K, Guo J, Zhang Y, Chen J, Guo X, Li Q, Li X, Wang W, Zhang Y, Wang J, Jiang X, Xiang Y, Xu C, Zheng P, Zhang J, Li R, Zhang H, Shang X, Gong T, Ning G, Wang J, Zen K, Zhang J, Zhang CY. 2008. Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18:997-1006.

Cheng CJ, Bahal R, Babar IA, Pincus Z, Barrera F, Liu C, Svoronos A, Braddock DT, Glazer PM, Engelman DM, Saltzman WM, Slack FJ. 2015. MicroRNA silencing for cancer therapy targeted to the tumour microenvironment. Nature 518:107-110.

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Chin LJ, Slack FJ. 2008. A truth serum for cancer - microRNAs have major potential as cancer biomarkers. Cell Res 18:983-984.

Croce CM. 2010. LINCing chromatin remodeling to metastasis. Nat Biotechnol 28:931-932.

Dai X, Tan C. 2015. Combination of microRNA therapeutics with small-molecule anticancer drugs: mechanism of action and co-delivery nanocarriers. Adv Drug Deliv Rev 81:184-197.

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Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775-1789.

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Hentze MW, Preiss T. 2013. Circular RNAs: splicing's enigma variations. EMBO J 32(7):923-925.

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Ivashuta SI, Petrick JS, Heisel SE, Zhang Y, Guo L, Reynolds TL, Rice JF, Allen E, Roberts JK. 2009. Endogenous small RNAs in grain: semi-quantification and sequence homology to human and animal genes. Food Chem Toxicol 47:353-360.

Jain K, Suryakumar G, Ganju L, Singh SB. 2014. Differential hypoxic tolerance is mediated by activation of heat shock response and nitric oxide pathway. Cell Stress Chaperones 19:801-812.

Jensen PD, Zhang Y, Wiggins BE, Petrick JS, Zhu J, Kerstetter RA, Heck GR, Ivashuta SI. 2013. Computational sequence analysis of predicted long dsRNA transcriptomes of major crops reveals sequence complementarity with human genes. GM Crops Food 4:90-97.

Johnson CD, Esquela-Kerscher A, Stefani G, Byrom M, Kelnar K, Ovcharenko D, Wilson M, Wang X, Shelton J, Shingara J, Chin L, Brown D, Slack FJ. 2007. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res 67:7713-7722.

Jonas S, Izaurralde E. 2015. Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet 16(7):421-433.

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Juliano R, Bauman J, Kang H, Ming X. 2009. Biological barriers to therapy with antisense and siRNA oligonucleotides. Mol Pharmaceut 6:686-695.

Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Sci 316(5830):1484-1488.

Kasinski AL, Slack FJ. 2011. MicroRNAs en route to the clinic: progress in validating and targeting microRNAs for cancer therapy. Nat Rev Cancer 11:849-864.

Kato M, Paranjape T, Müller RU, Nallur S, Gillespie E, Keane K, Esquela-Kerscher A, Weidhaas JB, Slack FJ. 2009. The mir-34 microRNA is required for the DNA damage response in vivo in C. elegans and in vitro in human breast cancer cells. Oncogene 28:2419-2424. Erratum in: Oncogene 28:3008, 2009.

Kim VN. 2005. MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6:376-385.

Klase Z, Kale P, Winograd R, Gupta MV, Heydarian M, Berro R, McCaffrey T, Kashanchi F. 2007. HIV-1 TAR element is processed by Dicer to yield a viral micro-RNA involved in chromatin remodeling of the viral LTR. BMC Mol Biol 8:63.

Koseki M, Goto K, Masuta C, Kanazawa A. 2005. The star-type color pattern in Petunia hybrida 'red Star' flowers is induced by sequence-specific degradation of chalcone synthase RNA. Plant Cell Physiol 46:1879-1883.

Koufaris C, Wright J, Currie RA, Gooderham NJ. 2012. Hepatic microRNA profiles offer predictive and mechanistic insights after exposure to genotoxic and epigenetic hepatocarcinogens. Toxicol Sci 128:532-543.

Koufaris C, Gooderham NJ. 2013. Are differences in microRNA regulation implicated in species-dependent response to toxicological exposures? Toxicol Sci 131:337-342.

Koufaris C, Wright J, Osborne M, Currie RA, Gooderham NJ. 2013. Time and dose-dependent effects of phenobarbital on the rat liver miRNAome. Toxicol 314:247-253.

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Laterza OF, Lim L, Garrett-Engele PW, Vlasakova K, Muniappa N, Tanaka WK, Johnson JM, Sina JF, Fare TL, Sistare FD, Glaab WE. 2009. Plasma MicroRNAs as sensitive and specific biomarkers of tissue injury. Clin Chem 55(11):1977-1983.

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