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Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection

Nicoletta Bivi12, Milena Romanello1, Richard Harrison3, Ian Clarke2, David C Hoyle2, Luigi Moro4, Fulvia Ortolani5, Antonella Bonetti5, Franco Quadrifoglio1, Gianluca Tell1 and Daniela Delneri2*

Author Affiliations

1 Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe, 33100, Udine, Italy

2 Faculty of Life Science, University of Manchester, Oxford Road, M13 9PT, Manchester, UK

3 School of Biological Sciences, Institute of Evolutionary Biology, King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK

4 The Center for the Study of Metabolic Bone Diseases, via Vittorio Veneto, 34170, Gorizia, Italy

5 Department of Medical and Morphological Research, University of Udine, Piazzale Kolbe, 33100, Udine, Italy

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Genome Biology 2009, 10:R93  doi:10.1186/gb-2009-10-9-r93

Published: 10 September 2009



Nitrogen-containing bisphosphonates are the elected drugs for the treatment of diseases in which excessive bone resorption occurs, for example, osteoporosis and cancer-induced bone diseases. The only known target of nitrogen-containing bisphosphonates is farnesyl pyrophosphate synthase, which ensures prenylation of prosurvival proteins, such as Ras. However, it is likely that the action of nitrogen-containing bisphosphonates involves additional unknown mechanisms. To identify novel targets of nitrogen-containing bisphosphonates, we used a genome-wide high-throughput screening in which 5,936 Saccharomyces cerevisiae heterozygote barcoded mutants were grown competitively in the presence of sub-lethal doses of three nitrogen-containing bisphosphonates (risedronate, alendronate and ibandronate). Strains carrying deletions in genes encoding potential drug targets show a variation of the intensity of their corresponding barcodes on the hybridization array over the time.


With this approach, we identified novel targets of nitrogen-containing bisphosphonates, such as tubulin cofactor B and ASK/DBF4 (Activator of S-phase kinase). The up-regulation of tubulin cofactor B may explain some previously unknown effects of nitrogen-containing bisphosphonates on microtubule dynamics and organization. As nitrogen-containing bisphosphonates induce extensive DNA damage, we also document the role of DBF4 as a key player in nitrogen-containing bisphosphonate-induced cytotoxicity, thus explaining the effects on the cell-cycle.


The dataset obtained from the yeast screen was validated in a mammalian system, allowing the discovery of new biological processes involved in the cellular response to nitrogen-containing bisphosphonates and opening up opportunities for development of new anticancer drugs.