Bibliography
- ECHEVERRI CJ, PERRIMON N: High-throughput RNAi screening in cultured cells: a user's guide. Nat. Rev. Genet. (2006) 7:373-384.
- HANNON GJ: RNAi: A Guide to Gene Silencing. (1st Edition). Cold Spring Harbor Press: Cold Spring Harbor, NY, USA (2003):436.
- MOFF5AT J, SABATINI DM: Building mammalian signalling pathways with RNAi screens. Nat. Rev. Mol. Cell Biol. (2006) 7:177-187.
- SACHSE C, ECHEVERRI CJ: Oncology studies using siRNA libraries: the dawn of RNAi-based genomics. Oncogene (2004) 23:8384-8391.
- HANEY SA: RNAi in the drug discovery process. In: RNA Interference Technology Basic Science to Drug Development. Appasani K (Ed.), Cambridge University Press, Cambridge, UK (2005):331-346.
- BERNARDS R, BRUMMELKAMP TR, BEIJERSBERGEN RL: shRNA libraries and their use in cancer genetics. Nat. Methods (2006) 3:701-706.
- LI CX, PARKER A, MENOCAL E, XIANG S, BORODYANSKY L, FRUEHAUF J: Delivery of RNAi interference. Cell Cycle (2006) 5:2103-2109.
- HANEY S: Increasing the robustness and validity of RNAi screening data. Pharmacogenomics (2007) 8:1037-1049.
- SAIJO N: What are the reasons for negative Phase III trials of molecular-target-based drugs? Cancer Sci. (2004) 95:772-776.
- HANEY SA: Anticancer drug development incorporating RNAi and high content screening: synergistic approaches to improve target identification and validation. Expert Opin. Drug Discov. (2006) 1:19-29.
- HANEY SA, LAPAN P, PAN J, ZHANG J: High content screening moves to the front of the line. Drug Discov. Today (2006) 11:889-894.
- GIULIANO KA, CHEN YT, TAYLOR DL: High-content screening with siRNA optimizes a cell biological approach to drug discovery: defining the role of P53 activation in the cellular response to anticancer drugs. J. Biomol. Screen. (2004) 9:557-568.
- PERLMAN ZE, MITCHISON TJ, MAYER TU: High-content screening and profiling of drug activity in an automated centrosome-duplication assay. Chembiochem (2005) 6:145-151.
- GIULIANO KA: High-content profiling of drug–drug interactions: cellular targets involved in the modulation of microtubule drug action by the antifungal ketoconazole. J. Biomol. Screen. (2003) 8(2):125-135.
- TAYLOR DL, GIULIANO KA: Multiplexed high content screening assays create a systems cell biology approach to drug discovery. Drug Discov. Today (2005) 2(2):149-154.
- BOUTROS M, BRAS LP, HUBER W: Analysis of cell-based RNAi screens. Genome Biol. (2006) 7:R66.
- CHATTERJEE-KISHORE M: From genome to phenome – RNAi library screening and hit characterization using signaling pathway analysis. Curr. Opin. Drug Discov. Dev. (2006) 9:231-239.
- ECHEVERRI CJ, BEACHY PA, BAUM B et al.: Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat. Methods (2006) 3:777-779.
- HUPPI K, MARTIN SE, CAPLEN NJ: Defining and assaying RNAi in mammalian cells. Mol. Cell (2005) 17:1-10.
- CHU E, DEVITA VT: Principles of Cancer Management: Chemotherapy, in cancer principles and practice. DeVita VT, Hellman S, Rosenberg SA (Eds), Lippincott, Williams and Wilkins: Philadelphia, USA (2001):289-306.
- MENDELSOHN J: The Molecular Basis of Cancer (2nd Edition), Saunders WB Co., Philiadelphia, PA, USA (2001):691.
- SUGGITT M, BIBBY MC: 50 years of preclinical anticancer drug screening: empirical to target-driven approaches. Clin. Cancer Res. (2005) 11:971-981.
- JAIN RK, DUDA DG, CLARK JW, LOEFFLER JS: Lessons from Phase III clinical trials on anti-VEGF therapy for cancer. Nat. Clin. Pract. Oncol. (2006) 3:24-40.
- LIPINSKI CA: Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods (2000) 44:235-249.
- GIULIANO K, DIBIASIO RL, DUNLAY RT et al.: High-content screening: a new approach to easing key bottlenecks in the drug discovery process. J. Biomol. Screen. (1997) 2:249-259.
- TENCZA SB, SIPE MA: Detection and classification of threat agents via high-content assays of mammalian cells. J. Appl. Toxicol. (2004) 24:371-377.
- BERTELSEN M, SANFRIDSON A: Inflammatory pathway analysis using a high content screening platform. Assay Drug Dev. Technol. (2005) 3:261-271.
- GURWITZ D, HARING R: Ligand-selective signaling and high-content screening for GPCR drugs. Drug Discov. Today (2003) 8:1108-1109.
- EVANS JG, MATSUDAIRA P: Linking microscopy and high content screening in large-scale biomedical research. Methods Mol. Biol. (2007) 356:33-38.
- PERLMAN ZE, SLACK MD, FENG Y et al.: Multidimensional drug profiling by automated microscopy. Science (2004) 306(5699):1194-1198.
- MOFFAT J, GRUENEBERG D, YANG X et al.: A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 124:1283-1298.
- ROOT DE, HACOHEN N, HAHN WC, LANDER ES, SBATINI ES: Genome-scale loss-of-function screening with a lentiviral RNAi library. Nat. Methods (2006) 3:715-719.
- WILLINGHAM AT, DEVERAUX QL, HAMPTON GM, AZA-BLANC P: RNAi and HTS: exploring cancer by systematic loss-of-function. Oncogene (2004) 23:8392-8400.
- BAKAL C et al.: Quantitative morphological signatures define local signaling networks regulating cell morphology. Science (2007) 316:1753-1756.
- KAMB A, WEE S, LENGAUER C: Why is cancer drug discovery so difficult? Nat. Rev. Drug Discov. (2007) 6:115-120.
- CAPDEVILA J, MENDEZ G, MACARULLA T et al.: New approaches in systemic treatment of advanced colorectal cancer: the molecular targets era. Expert Rev. Anticancer Ther. (2007) 7:1027-1041.
- GRALLA RJ, GRIESINGER F: Interpreting clinical trials in lung cancer: impact of methodology and endpoints. J. Thoracic Oncol. (2007) 2:S51-S58.
- HOERING A, CROWLEY J: Clinical trial designs for multiple myeloma. Clin. Adv. Hematol. Oncol. (2007) 5:309-316.
- MILLAR AW, LYNCH KP: Rethinking clinical trials for cytostatic drugs. Nat. Rev. Cancer (2003) 3:540-545.
- KELLOFF GJ, SIGMAN CC: New science-based endpoints to accelerate oncology drug development. Eur. J. Cancer (2005) 41:491-501.
- KUMMAR S, GUTIERREZ M, DOROSHOW JH, MURGO AJ: Drug development in oncology: classical cytotoxics and molecularly targeted agents. Br. J. Clin. Pharmacol. (2006) 62:15-26.
- PEREZ EA, RODEHEFFER R: Clinical cardiac tolerability of trastuzumab. J. Clin. Oncol. (2004) 22:322-329.
- KERKELA R, GRAZETTE L, YACOBI R et al.: Cardiotoxicity of the cancer therapeutic agent imatinib mesylate. Nat. Med. (2006) 12:908-916.
- FORCE T, KRAUSE DS, VAN ETTEN RA: Molecular mechanisms of cardiotoxicity of tyrosine kinase inhibition. Nat. Rev. Cancer (2007) 7:332-344.
- BRUMMELKAMP TR, NIJMAN SM, DIRAC AM, BERNARDS R: Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-κB. Nature (2003) 424:797-801.
- LAKHANI SR: Putting the brakes on cylindromatosis? N. Engl. J. Med. (2004) 350:187-188.
- AZA-BLANC P, COOPER CL, WAGNER K, BATALOV S, DEVERAUX QL, COOKE MP: Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell (2003) 12:627-637.
- BERNS K, HIJMANS EM, MULLENDERS J et al.: A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature (2004) 428:431-437.
- PADDISON PJ, SILVA JM, CONKLIN DS et al.: A resource for large-scale RNA-interference-based screens in mammals. Nature (2004) 428:427-431.
- KITTLER R, PUTZ G, PELLETIER L et al.: An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature (2004) 432:1036-1040.
- MACKEIGAN JP, MURPHY LO, BLENIS J: Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance. Nat. Cell Biol. (2005) 7:591-600.
- BERNARDS R: A functional approach to questions about life, death and phosphorylation. Cancer Cell (2005) 7:503-504.
- LANG P, YEOW K, NICHOLS A, SCHEER A: Cellular imaging in drug discovery. Nat. Rev. Drug Discov. (2006) 5:343-356.
- HOFFMAN AF, GARIPPA RJ: A pharmaceutical company user's perspective on the potential of high content screening in drug discovery. Methods Mol. Biol. (2006) 356:19-31.
- KAU TR, SCHROEDER F, RAMASWAMY S et al.: A chemical genetic screen identifies inhibitors of regulated nuclear export of a Forkhead transcription factor in PTEN-deficient tumor cells. Cancer Cell (2003) 4:463-476.
- BRUMMELKAMP TR, FABIUS AWM, MULLENDERS J et al.: An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors. Nat. Chem. Biol. (2006) 2:202-206.
- BARTZ SR, ZHANG Z, BURCHARD J et al.: Small interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Mol. Cell. Biol. (2006) 26:9377-9386.
- WHITEHURST AW, BODEMANN BO, CARDENAS J et al.: Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature (2007) 446:815-819.
- VASSILEV LT, VU BT, GRAVES B et al.: In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science (2004) 303:844-848.
- SIMON MA, BOWTELL DD, DODSON GS, LAVERTY TR, RUBIN GM: Ras1 and a putative guanine nucleotide exchange factor perform crucial steps in signaling by the sevenless protein tyrosine kinase. Cell (1991) 67:701-716.
- HORVITZ HR, STERNBERG PW: Multiple intercellular signalling systems control the development of the Caenorhabditis elegans vulva. Nature (1991) 351:535-541.
- CARPENTER AE, SABATINI DM: Systematic genome-wide screens of gene function. Nat. Rev. Genet. (2004) 5:11-22.
- DASGUPTA R, PERRIMON N: Using RNAi to catch Drosophila genes in a web of interactions: insights into cancer research. Oncogene (2004) 23:8359-8365.
- BOUTROS M, KIGER AA, ARMKNECHT S et al.: Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science (2004) 303:832-835.
- BAEG GH, ZHOU R, PERRIMON N: Genome-wide RNAi analysis of the JAK/STAT signaling components. Genes Dev. (2005) 19:1861-1870.
- MÜLLER P, KUTTENKEULER D, GESELLCHEN V, ZEIDLER MP, BOUTROS M: Identification of JAK/STAT signaling components by genome-wide RNA interference. Nature (2005) 436:871-875.
- DASGUPTA R, KAYKAS A, MOON RT et al.: Functional genomic analysis of the Wnt-Wingless signaling pathway. Science (2005) 308:826-833.
- LUM L, YAO S, MOZER B et al.: Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science (2003) 299:2039-2045.
- NYBAKKEN K, VOKES SA, LIN TY MCMAHON AP, PERRIMON N: A genome-wide RNAi interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nat. Genet. (2005) 37:1323-1332.
- GOSHIMA G, WOLLMAN R, GOODWIN SS et al.: Genes required for the mitotic spindle assembly in Drosophila S2 cells. Science (2007) 316:417-421.
- EGGERT US, KIGER AA, RICHTER C et al.: Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol. (2004) 2:E379.
- VAN HAAFTEN G, ROMEIJN R, POTHOF J et al.: Identification of conserved pathways of DNA-damage response and radiation protection by genome-wide RNAi. Curr. Biol. (2006) 16:1344-1350.
- TANG R, CHANGCHIEN CR, WU MC et al.: Colorectal cancer without high microsatellite instability and chromosomal instability – an alternative genetic pathway to human colorectal cancer. Carcinogenesis (2004) 25:841-846.
- DE CASTRO IP, DE CARCER G, MALUMBRES M: A census of mitotic cancer genes: new insights into tumor biology and cancer therapy. Carcinogenesis (2007) 28:899-912.
- DRAVIAM VM, XIE S, SORGER PK: Chromosome segregation and genomic instability. Curr. Opin. Genet. Dev. (2004) 14:120-125.
- WALSH T, CASADEI S, COATS KH et al.: Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer. J. Am. Med. Assoc. (2006) 295:1379-1388.
- WEINSTEIN IB, BEGEMANN M, ZHOU P et al.: Disorders in cell circuitry associated with multistage carcinogenesis: exploitable targets for cancer prevention and therapy. Clin. Cancer Res. (1997) 3:2696-2702.
- WEINSTEIN IB, JOE AK: Mechanisms of disease: oncogene addiction – a rationale for molecular targeting in cancer therapy. Nat. Clin. Pract. Oncol. (2006) 3:448-457.
- GREENMAN C et al.: Patterns of somatic mutation in human cancer genomes. Nature (2007) 446:153-158.
- SHARMA SV, GAJOWNICZEK P, WAY IP et al.: A common signaling cascade may underlie “addiction” to the Src, BCR-ABL, and EGF receptor oncogenes. Cancer Cell (2006) 10:425-.
- LOBO NA, SHIMONO Y, QIAN D, CLARKE MF: The biology of cancer stem cells. Annu. Rev. Cell Dev. Biol. (2007) (In Press).
- LI C, HEIDT DG, DALERBA P et al.: Identification of pancreatic cancer stem cells. Cancer Res. (2007) 67:1030-1037.
- HERRMANN PC, HUBER SL, HERRIER T et al.: Distinct populations of cancer stem cells determine tumor growth and metastatic activity in human pancreatic cancer. Cell Stem Cell (2007) 1:313-323.
- STINGL J, CALDAS C: Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis. Nat. Rev. Cancer (2007) 7:791-799.
- LAWSON DA, WITTE ON: Stem cells in prostate cancer initiation and progression. J. Clin. Investig. (2007) 117:2044-2050.
- GARRAWAY LA, SELLERS WR: Lineage dependency and lineage-survival oncogenes in human cancer. Nat. Rev. Cancer (2006) 6:593-602.
- THIERY JP, SLEEMAN JP: Complex networks orchestrate epithelial–mesenchymal transitions. Nat. Rev. Mol. Cell. Biol. (2006) 7:131-142.
- Tarin D: The fallacy of epithelial mesenchymal transition in neoplasia. Cancer Res. (2005) 65:5996-6001.
- THOMPSON EW, NEWGREEN DF: Carcinoma invastion and metastasis: a role for epithelial-mesenchymal transition? Cancer Res. (2005) 65:5991-5994.
- YANG J, MANI SA, WEINBERG RA: Exploring a new twist on tumor metastasis. Cancer Res. (2006) 66:4549-4552.
- BOLOS V, GREGO-BESSA J, DE LA POMPA JL: Notch signaling in development and cancer. Endocr. Rev. (2007) 28:339-363.
- ZHOU X, CAO X, PERLMAN Z, WONG STC: A computerized cellular imaging system for high content analysis in Monastrol suppressor screens. J. Biomed. Inform. (2006) 39:115-125.
- CARPENTER AE: CellProfiler: open-source, versatile software for high throughput cell image analysis. Genome Biol. (2006) 7:R100.
- ADAMS CL: Compound classification using image-based cellular phenotypes. In: Methods in Enzymology: Measuring Biological Responses with Automated Microscopy. Inglese J (Ed.), Academic Press (2006):440-468.
- LOO LH, WU LF, ALTSCHULER SJ: Image-based multivariate profiling of drug responses from single cells. Nat. Methods (2007) 4:445-453.
- CONDEELIS J, POLLARD JW: Macrophages: obligate partners for tumor cell migration, invasion, and metastasis. Cell (2006) 124:263-266.
- BHOWMICK NA, NEILSON EG, MOSES HL: Stromal fibroblasts in cancer initiation and progression. Nature (2004) 432:332-337.
- JUNG YD, AHMAD SA, LIU W et al.: The role of the microenvironment and intercellular cross-talk in tumor angiogenesis. Semin. Cancer Biol. (2002) 12:105-112.
- HAMMOND SL, HAM RG, STAMPFER MR: Serum-free growth of human mammary epithelial cells: rapid clonal growth in defined medium and extended serial passage with pituitary extract. Proc. Natl. Acad. Sci. USA (1984) 81:5435-5439.
- ROMANOV SR, KOZAKIEWICZ BK, HOLST CR, STAMPFER MR, HAUPT LM, TLSTY TD: Normal human mammary epithelial cells spontaneously escape senescence and aquire genomic changes. Nature (2001) 409:633-637.
- STAMPFER MR, BARTLEY JC: Induction of transformation and continuous cell lines from normal human mammary epithelial cells after exposure to benzo(a)pyrene. Proc. Natl. Acad. Sci. USA (1985) 82:2394-2398.
- INCE TA, RICHARDSON AL, BELL GW et al.: Transformation of different human breast epithelial cell types leads to distinct tumor phenotypes. Cancer Cell (2007) 12:160-170.
- WESTBROOK TF, MARTIN ES, SCHLABACH MR et al.: A genetic screen for candidate tumor suppressors identifies REST. Cell (2005) 121:837-848.
- KOLFSCHOTEN IG, VAN LEEUWEN B, BERNS K et al.: A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell (2005) 121:849-858.
- NIJMAN SM, HUANG T, DIRAC A et al.: The deubiquitinating enzyme USP1 regulates the Fanconi anemia pathway. Mol. Cell (2005) 17:331-339.
- SILVA JM, LI MZ, CHANG K et al.: Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet. (2005) 37:1281-1288.
- NICKE B, BASTIEN J, KHANNA S et al.: Involvement of MINK, a Ste20 family kinase, in Ras oncogene-induced growth arrest in human ovarian surface epithelial cells. Mol. Cell (2005) 20:673-685.
- NGO VN, DAVIS RE, LAMY L et al.: A loss-of-function RNA interference screen for molecular targets in cancer. Nature (2006) 441:106-110.
- LLANOS S, EFEYAN A, MONSECH J, DOMINGUEZ O, SERRANO M: A high-throughput loss-of-function screening identifies novel p53 regulators. Cell Cycle (2006) 5:1880-1885.
- MORGAN-LAPPE SE, TUCKER LA, HUANG X et al.: Identification of Ras-related nuclear protein, targeting protein for xenopus kinesin-like protein 2, and stearoyl-CoA desaturase 1 as promising cancer targets from an RNAi-based screen. Cancer Res. (2006) 67:4390-4398.
Websites
- www.rnaiglobal.org RNAi Global (2007).
- www.miare.org MIARE: Minimum Information about an RNAi Experiment (2007).