title: Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Université Laval, Division de Microbiologie, Centre de Recherche en Infectiologie, boulevard Laurier, Québec, G1V 4G2, Canada. Jean-Michel.Ubeda@crchul.ulaval.ca
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Ubeda
authors.forename: Danielle
authors.initials: D
authors.lastname: Légaré
authors.forename: Frédéric
authors.initials: F
authors.lastname: Raymond
authors.forename: Amin Ahmed
authors.initials: AA
authors.lastname: Ouameur
authors.forename: Sébastien
authors.initials: S
authors.lastname: Boisvert
authors.forename: Philippe
authors.initials: P
authors.lastname: Rigault
authors.forename: Jacques
authors.initials: J
authors.lastname: Corbeil
authors.forename: Michel J
authors.initials: MJ
authors.lastname: Tremblay
authors.forename: Martin
authors.initials: M
authors.lastname: Olivier
authors.forename: Barbara
authors.initials: B
authors.lastname: Papadopoulou
authors.forename: Marc
authors.initials: M
authors.lastname: Ouellette
mesh_terms: D000782:Aneuploidy; D000818:Animals; D027321:Anion Transport Proteins / Q000235:genetics; D004351:Drug Resistance / Q000235:genetics*; D005784:Gene Amplification; D017353:Gene Deletion; D020869:Gene Expression Profiling; D017125:Genes, Protozoan; D007891:Leishmania / Q000187:drug effects* / Q000235:genetics*; D018314:Leishmania infantum / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D018320:Leishmania major / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D008727:Methotrexate / Q000494:pharmacology; D009097:Multienzyme Complexes / Q000235:genetics; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D010088:Oxidoreductases / Q000235:genetics; D015800:Protozoan Proteins / Q000235:genetics*; D013762:Tetrahydrofolate Dehydrogenase / Q000235:genetics; D013940:Thymidylate Synthase / Q000235:genetics
chemical_list: D027321:Anion Transport Proteins; D009097:Multienzyme Complexes; D015800:Protozoan Proteins; C497355:folate transporter 1, Leishmania infantum; C056930:thymidylate synthase-dihydrofolate reductase; D010088:Oxidoreductases; C085592:pteridine reductase; D013762:Tetrahydrofolate Dehydrogenase; D013940:Thymidylate Synthase; D008727:Methotrexate