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Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy

Jean-Michel Ubeda1, Danielle Légaré1, Frédéric Raymond12, Amin Ahmed Ouameur1, Sébastien Boisvert2, Philippe Rigault2, Jacques Corbeil12, Michel J Tremblay1, Martin Olivier3, Barbara Papadopoulou1 and Marc Ouellette1*

Author Affiliations

1 Université Laval, Division de Microbiologie, Centre de Recherche en Infectiologie, boulevard Laurier, Québec, G1V 4G2, Canada

2 Université Laval, Centre de Recherche en Endocrinologie Moléculaire et Oncologique, boulevard Laurier, Québec, G1V 4G2, Canada

3 McGill University, Department of Microbiology and Immunology, Lyman Duff Medical Building, University Street, Montreal, H3A 2B4, Canada

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Genome Biology 2008, 9:R115  doi:10.1186/gb-2008-9-7-r115

Published: 18 July 2008



Drug resistance can be complex, and several mutations responsible for it can co-exist in a resistant cell. Transcriptional profiling is ideally suited for studying complex resistance genotypes and has the potential to lead to novel discoveries. We generated full genome 70-mer oligonucleotide microarrays for all protein coding genes of the human protozoan parasites Leishmania major and Leishmania infantum. These arrays were used to monitor gene expression in methotrexate resistant parasites.


Leishmania is a eukaryotic organism with minimal control at the level of transcription initiation and few genes were differentially expressed without concomitant changes in DNA copy number. One exception was found in Leishmania major, where the expression of whole chromosomes was down-regulated. The microarrays highlighted several mechanisms by which the copy number of genes involved in resistance was altered; these include gene deletion, formation of extrachromosomal circular or linear amplicons, and the presence of supernumerary chromosomes. In the case of gene deletion or gene amplification, the rearrangements have occurred at the sites of repeated (direct or inverted) sequences. These repeats appear highly conserved in both species to facilitate the amplification of key genes during environmental changes. When direct or inverted repeats are absent in the vicinity of a gene conferring a selective advantage, Leishmania will resort to supernumerary chromosomes to increase the levels of a gene product.


Aneuploidy has been suggested as an important cause of drug resistance in several organisms and additional studies should reveal the potential importance of this phenomenon in drug resistance in Leishmania.