Pascale Pescher

Vector-borne, protist parasites have evolved complex developmental programs to adapt to very distinct host environments. How these important pathogens transition between insect and mammalian stages is only poorly understood. Here, we investigated stage differentiation in Leishmania donovani , a trypanosomatid parasite with constitutive gene transcription, offering a model to study post-transcriptional regulation. Using a five-layer integrative systems analysis (genome to metabolome), we compared hamster-derived amastigotes and culture-derived promastigotes. Genomic adaptation was excluded as a major driver of differentiation, while differential mRNA turnover emerged as a key mechanism of stage-specific gene expression. Transcriptomic and proteomic comparisons revealed a broad dynamic range of protein abundance changes that correlated poorly with mRNA levels. This discrepancy was linked to (i) altered snoRNA expression and rRNA modifications, indicating stage-specific tuning of translation, and (ii) differential protein degradation, supported by proteomics following proteasome inhibition with lactacystin. Lactacystin impaired amastigote-to-promastigote differentiation, highlighting the importance of proteasomal activity. Overall, our analysis links Leishmania development to coordinated post-transcriptional regulatory networks. Our findings provide a powerful new resource for research programs that aim to dissect the emergent properties of regulatory networks and feedback loops underlying Leishmania stage differentiation, serving as a blueprint for other vector-borne pathogens that rely on disease-associated developmental transitions.

Vector-borne, protist parasites have evolved complex developmental programs to adapt to very distinct host environments. How these important pathogens transition between insect and mammalian stages is only poorly understood. Here we investigate stage differentiation in the trypanosomatid parasite Leishmania that shows constitutive gene transcription, thus providing a unique model system to assess how development is governed by post-transcriptional mechanisms. Using a five-layer integrative systems analysis (from genome to metabolome), we examined hamster-isolated Leishmania donovani amastigotes and culture-derived, insect-stage promastigotes. This approach enabled us to rule out genomic adaptation as a key driver of parasite stage differentiation, while confirming the pivotal role of differential mRNA turnover in stage-specific gene expression. Assessing transcriptomic against proteomic expression changes uncovered an unexpectedly broad dynamic range of stage-regulated changes in protein abundance that only poorly correlated with mRNA levels. This discrepancy correlated with (i) alterations in snoRNA expression and changes in rRNA modification they guide suggesting stage-specific adaptation of the protein translation apparatus that can uncouple mRNA from protein abundancies, and (ii) differential protein degradation as revealed by quantitative proteomics of parasites treated with the proteasomal inhibitor lactacystin. Lactacystin treatment stalled the transition of spleen-derived amastigotes into promastigotes in culture, further underscoring the role of proteasomal activity in stage differentiation. Integration of our five-layer systems analysis established the first link between Leishmania development and the expression of co-regulated genetic networks encompassing mRNA turnover, protein translation, phosphorylation, and degradation. Our findings provide a powerful new resource for research programs that aim to dissect the emergent properties of regulatory networks and feedback loops underlying Leishmania stage differentiation, serving as a blueprint for other vector-borne pathogens that rely on disease-associated developmental transitions.

The basis for differential susceptibility to Leishmania donovani infection observed in individuals remains poorly understood. Here we address this important open question comparing bone marrow–derived macrophages (BMDMs) from susceptible hamsters (hamBMDMs) and resistant mice (mBMDMs) to identify intrinsic cellular features that may contribute to host-specific outcomes. We first optimized and validated an experimental protocol for generating hamBMDMs, which closely resemble classical mBMDMs in terms of morphology, marker gene expression, and phagocytic activity. Comparative transcriptomic analysis uncovered rodent-specific intrinsic differences in the expression of metabolic and immune-related pathways known to influence susceptibility to intracellular Leishmania infection. Notably, hamBMDMs were characterized by the expression of Lyve1, a marker of tissue-resident macrophages involved in extracellular matrix homeostasis, which may contribute to their distinct functional profile. In vitro infection assays confirmed the microbicidal capacity of hamBMDMs and also revealed their increased permissiveness to Leishmania proliferation. In conclusion, the combined use of murine and hamster macrophage systems provides a powerful platform to dissect the molecular mechanisms underlying L. donovani survival and host resistance. Our improved protocol allows for the generation of large quantities of functionally validated hamster macrophages, enabling systems-level investigations in this important rodent model that more accurately reflects human infection dynamics than mice. This addresses a major bottleneck in experimental infections with L. donovani, but also other clinically relevant pathogens, such as Mycobacterium spp. and SARS-CoV-2, for which hamsters have been used to model human infection.

Hybridization, the merging of distinct genomes, is increasingly recognized as a major evolutionary force among eukaryotic pathogens, including facultatively sexual protist parasites like Leishmania and Trypanosoma. While it may contribute to pathogen virulence and drug resistance, hybridization remains poorly characterized, particularly how genetic distance between parental cells influences genomic compatibility and which compensatory mechanisms ensure hybrid viability. Here, we report the in vitro generation of an unusual sexual hybrid between Leishmania species infecting mammals (L. infantum) and reptiles (the Sauroleishmania L. tarentolae), and used this unique genetic model system to address these open questions. Our data provide evidence of genomic compatibility between even highly divergent Leishmania species, offering new insights into the evolutionary potential of Leishmania and related pathogens. We demonstrate that the genomic shock caused by the fusion of distinct genomes can be mitigated by two key mechanisms: (i) at the genomic level, chromosome loss allows the establishment of mosaic aneuploidy in the newly formed hybrid, and (ii) at the post-transcriptional level, preferential mono-parental allelic expression acts as a secondary compensatory mechanism. Our findings establish genome instability and post-transcriptional regulation as central processes in Leishmania hybridization, which may be of broad relevance to other biological systems undergoing genetic exchange.

The basis for differential susceptibility to Leishmania ( L. ) donovani infection observed in individuals remains poorly understood. Here we address this important open question comparing bone marrow-derived macrophages from susceptible hamsters (hamBMDMs) and resistant mice (mBMDMs) to identify intrinsic cellular features that may contribute to host-specific outcomes. We first optimized and validated an experimental protocol for generating hamBMDMs, which closely resemble classical mouse BMDMs in terms of morphology, marker gene expression and phagocytic activity. Comparative transcriptomic analysis uncovered rodent-specific, intrinsic differences in the expression of metabolic and immune-related pathways known to influence susceptibility to intracellular Leishmania infection. In vitro infection assays confirmed the microbicidal capacity of hamBMDMs, while also revealing their increased permissiveness to Leishmania proliferation. In conclusion, the combined use of murine and hamster macrophage systems provides a powerful platform to dissect the molecular mechanisms underlying L. donovani survival and host resistance. Our improved protocol allows for the generation of large quantities of functionally validated hamster macrophages, enabling systems-level investigations in this important rodent model that more accurately reflects human infection dynamics than mice. This addresses a major bottleneck in experimental infections with L. donovani, but also other clinically relevant pathogens, such as Mycobacterium spp. and SARS-CoV-2, for which hamsters have been used to model human infection.

Vector-borne, protist parasites have evolved complex developmental programs to adapt to very distinct host environments. How these important pathogens transition between insect and mammalian stages is only poorly understood. Here we investigate stage differentiation in the trypanosomatid parasite Leishmania that shows constitutive gene transcription, thus providing a unique model system to assess how development is governed by post-transcriptional mechanisms. Using a five-layer integrative systems analysis (from genome to metabolome), we examined hamster-isolated Leishmania donovani amastigotes and culture-derived, insect-stage promastigotes. This approach enabled us to rule out genomic adaptation as a key driver of parasite stage differentiation, while confirming the pivotal role of differential mRNA turnover in stage-specific gene expression. Assessing transcriptomic against proteomic expression changes uncovered an unexpectedly broad dynamic range of stage-regulated changes in protein abundance that only poorly correlated with mRNA levels. This discrepancy correlated with (i) alterations in snoRNA expression and changes in rRNA modification they guide suggesting stage-specific adaptation of the protein translation apparatus that can uncouple mRNA from protein abundancies, and (ii) differential protein degradation as revealed by quantitative proteomics of parasites treated with the proteasomal inhibitor lactacystin. Lactacystin treatment stalled the transition of spleen-derived amastigotes into promastigotes in culture, further underscoring the role of proteasomal activity in stage differentiation. Integration of our five-layer systems analysis established the first link between Leishmania development and the expression of co-regulated genetic networks encompassing mRNA turnover, protein translation, phosphorylation, and degradation. Our findings provide a powerful new resource for research programs that aim to dissect the emergent properties of regulatory networks and feedback loops underlying Leishmania stage differentiation, serving as a blueprint for other vector-borne pathogens that rely on disease-associated developmental transitions.

Summary: Leishmania parasites can enter a cryptic sexual reproductive cycle generating hybrid genotypes that can lead to unpredictable clinical outcomes and transmission cycles. Despite the importance of hybrids in Leishmania epidemiology, the mechanisms involved in their formation - including the impact of parental genetic distance - remain poorly understood. We report the in vitro generation of a hybrid between Leishmania (Leishmania) infantum and Leishmania (Sauroleishmania) tarentolae, two species from sister phylogenetic clades circulating across Southern Italy, providing evidence of genomic compatibility. Whole-Genome Sequencing indicates that, while the hybrid is largely tetraploid, its genome is not just the sum of its parental content. RNA-seq analysis of the hybrid transcriptome uncovers significant differences in the abundance of orthologous transcripts expressed from both parental genomes, driven by either parent-specific gene copy number variations or differential mRNA turnover. These results demonstrate that, beyond genomic restructuring, post-transcriptional regulation may serve as an additional mechanism shaping viable hybrid phenotypes, potentially enhancing parasite adaptability and fitness.

Trypanosomatid pathogens are transmitted by blood-feeding insects, causing devastating human infections. These parasites show important phenotypic shifts that often impact parasite pathogenicity, tissue tropism, or drug susceptibility. The evolutionary mechanisms that allow for the selection of such adaptive phenotypes remain only poorly investigated. Here, we use Leishmania donovani as a trypanosomatid model pathogen to assess parasite evolutionary adaptation during experimental sand fly infection. Comparing the genome of the parasites before and after sand fly infection revealed a strong population bottleneck effect as judged by allele frequency analysis. Apart from random genetic drift caused by the bottleneck effect, our analyses revealed haplotype and allelic changes during sand fly infection that seem under natural selection given their convergence between independent biological replicates. Our analyses further uncovered signature mutations of oxidative DNA damage in the parasite genomes after sand fly infection, suggesting that Leishmania suffers from oxidative stress inside the insect digestive tract. Our results propose a model of Leishmania genomic adaptation during sand fly infection, with oxidative DNA damage and DNA repair processes likely driving haplotype and allelic selection. The experimental and computational framework presented here provides a useful blueprint to assess evolutionary adaptation of other eukaryotic pathogens inside their insect vectors, such as Plasmodium spp, Trypanosoma brucei , and Trypanosoma cruzi .