Design of a genome-wide siRNA library using an artificial neural network

Huesken, Dieter; Lange, Joerg; Mickanin, Craig; Weiler, Jan; Asselbergs, Fred A.M.; Warner, Justin; Meloon, Brian; Engel, Sharon; Rosenberg, Avi; Cohen, Dalia; Labow, Mark; Reinhardt, Mischa; Natt, François; Hall, Jonathan

doi:10.1038/nbt1118

Cited by 338 publications

(419 citation statements)

References 25 publications

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“…16 As many of the initial studies of mGluR7 have relied on information from mGluR7 knockout animals, 10,12,38,39 which are bred on a C57BL/6 background, we chose to conduct our siRNA studies on this background. Seventy-four male C57BL/6 mice (23-31 g; Charles River, France) were housed and surgeries performed as described previously, 15 40 ). Starting day 7 of intracerebroventricular infusions, mice were trained to drink water from 15 ml Falcon tubes (cut at the base for an outlet) for 30-min sessions per day, between 900 and 1000 (morning session), and between 1630 and 1730 (evening session).…”

Section: Cta Following Amn082mentioning

confidence: 99%

mGluR7 facilitates extinction of aversive memories and controls amygdala plasticity

et al. 2007

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Formation and extinction of aversive memories in the mammalian brain are insufficiently understood at the cellular and molecular levels. Using the novel metabotropic glutamate receptor 7 (mGluR7) agonist AMN082, we demonstrate that mGluR7 activation facilitates the extinction of aversive memories in two different amygdala-dependent tasks. Conversely, mGluR7 knockdown using short interfering RNA attenuated the extinction of learned aversion. mGluR7 activation also blocked the acquisition of Pavlovian fear learning and its electrophysiological correlate long-term potentiation in the amygdala. The finding that mGluR7 critically regulates extinction, in addition to acquisition of aversive memories, demonstrates that this receptor may be relevant for the manifestation and treatment of anxiety disorders.

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Section: Cta Following Amn082mentioning

confidence: 99%

mGluR7 facilitates extinction of aversive memories and controls amygdala plasticity

et al. 2007

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“…Individual shRNA constructs were generated as described previously. Targeting sequences were selected based on RNAi Codex algorithms (16) or BIOPREDsi design (42) and are available upon request.…”

Section: Methodsmentioning

confidence: 99%

Topoisomerase levels determine chemotherapy response in vitro and in vivo

Burgess

Doles²,

Zender

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

279

236

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Topoisomerase poisons are chemotherapeutic agents that are used extensively for treating human malignancies. These drugs can be highly effective, yet tumors are frequently refractory to treatment or become resistant upon tumor relapse. Using a pool-based RNAi screening approach and a well characterized mouse model of lymphoma, we explored the genetic basis for heterogeneous responses to topoisomerase poisons in vitro and in vivo. These experiments identified Top2A expression levels as major determinants of response to the topoisomerase 2 poison doxorubicin and showed that suppression of Top2A produces resistance to doxorubicin in vitro and in vivo. Analogously, using a targeted RNAi approach, we demonstrated that suppression of Top1 produces resistance to the topoisomerase 1 poison camptothecin yet hypersensitizes cancer cells to doxorubicin. Importantly, lymphomas relapsing after treatment display spontaneous changes in topoisomerase levels as predicted by in vitro gene knockdown studies. These results highlight the utility of pooled shRNA screens for identifying genetic determinants of chemotherapy response and suggest strategies for improving the effectiveness of topoisomerase poisons in the clinic.A myriad of genetic factors influence the efficacy of cancer chemotherapy, including both somatic changes in the tumor itself as well as genetic polymorphisms present in the patient. These factors include increased expression of detoxification pumps that prevent access of the drug to its target (1), point mutations that disrupt the drug-target interaction (2, 3), and mutations in stress response pathways [e.g., p53 loss (4)]. To tailor treatment successfully to the individual patient, a more complete understanding of the genetic determinants of therapy response is necessary.RNA interference (RNAi) exploits a mechanism of gene regulation whereby double-stranded RNAs are processed by a conserved cellular machinery to suppress the expression of genes containing homologous sequences (5). Importantly, libraries of DNA-based vectors encoding short hairpin RNAs (shRNAs) capable of targeting most genes in the human and mouse genomes have been produced and enable forward genetic screens to be performed in mammalian cells. Indeed, by using human tumor-derived cell lines treated in vitro, RNAi has been used to evaluate potential drug targets (6) or to investigate mechanisms of drug action and drug resistance by screening for new molecules that modulate the response of tumor-derived cell lines to a given chemotherapeutic agent (7-10).Here, we evaluate the suitability of combining mouse models and RNAi to identify genetic modifiers of drug action in tumors in their natural site. Initially, we chose to investigate resistance to doxorubicin in the E -Myc mouse lymphoma system. Doxorubicin (Adriamycin) is an anthracycline DNA-damaging agent that exerts its effects primarily by targeting of the topoisomerase 2 activity and DNA intercalation (11). Along with etoposide and the camptothecin derivatives, doxorubicin is one of several t...

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“…The algorithm uses a neuronal network approach to design the siRNAs (21) and discards those sequences with high similarity to regions of other genes. Areas of the target sequence with known single nucleotide polymorphisms were avoided.…”

Section: Methodsmentioning

confidence: 99%

Silencing the Activity and Proliferative Properties of the Human EagI Potassium Channel by RNA Interference

Weber

Queiroz

Downie

et al. 2006

Journal of Biological Chemistry

116

118

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EagI potassium channels are natively expressed in the mammalian brain as well as in many cancer cell lines and tumor tissues. The role of EagI in malignant transformation has been suggested by several experiments, but the lack of specific EagI inhibitors has made it difficult to examine the influence of the channel on oncogenesis and its potential as a therapeutic target. We have used short interfering RNA to test the effects of EagI reduction on the behavior of tumor cells in vitro. By generating and optimizing an EagI-specific short interfering RNA system, we were able to study the effects of EagI depletion on several cancer cell lines that endogenously express this protein. We show here that our short interfering RNA sequences act specifically on EagI, reproducibly induce a significant decrease in the proliferation of tumor cell lines, and do not trigger any observable nonspecific responses.

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Design of a genome-wide siRNA library using an artificial neural network

Cited by 338 publications

References 25 publications

mGluR7 facilitates extinction of aversive memories and controls amygdala plasticity

mGluR7 facilitates extinction of aversive memories and controls amygdala plasticity

Topoisomerase levels determine chemotherapy response in vitro and in vivo

Silencing the Activity and Proliferative Properties of the Human EagI Potassium Channel by RNA Interference

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