Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania

Aneuploidy causes broad-scale disruption in the stochiometric balances of transcripts, proteins, and metabolites. These disruptions often lead to detrimental effects for the organism, but for some organisms and in certain environments, it can also cause a fitness advantage. Understanding the complex trade-off between aneuploidy fitness gains and losses requires a systems biological comprehension of its molecular impact. The protozoan parasite Leishmania provides a unique study angle to this problem, as the pathogen lacks transcriptional regulation of individual protein-coding genes and has an unusually high tolerance for aneuploidy. Here, we present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. This 4 layer multi-omics analysis unambiguously establishes that despite this tolerance, aneuploidy in Leishmania globally and drastically impacts the transcriptome and proteome of affected chromosomes, ultimately explaining the degree of metabolic differences between strains. This impact appears to be present throughout the parasite’s life cycle as we observed it in both its proliferative and infectious life stages. We show that, through dosage compensation, protein complex subunits, secreted proteins, and non-cytoplasmic proteins responded less or even not at all to aneuploidy. In contrast to other Eukaryotes, we did not observe the widespread regulation at the transcript level that typically modulate some of the negative effects of aneuploidy. Instead, Leishmania features a surprisingly high number of regulated proteins encoded by non-aneuploid chromosomes, suggesting that aneuploidy results in extensive post-transcriptionally modulation of protein levels. Our results provide the foundation for the integrated molecular understanding of aneuploidy in Leishmania. They also highlight that the parasite is an attractive model to study processes of post-transcriptional modulation of protein levels in the context of aneuploidy and beyond.