Caractérisation multi-omique des mécanismes de manipulation des voies de signalisation de la cellule hôte par des effecteurs parasitaires : identification des stratégies de subversion communes à Leishmania et Eimeria

Leishmania donovani, the causative agent of visceral leishmaniasis, resides within parasitophorous vacuoles (PV) inside host macrophages, where it modulates immunity, cell death and major signalling cascades such as MAPK and JAK-STAT. While previous studies have explored host transcriptomic and proteomic changes during infection, phosphoproteomic modulation has been overlooked. Given its rapid and reversible nature, phosphorylation likely plays a key role in the dynamic subversion of macrophages to support parasite survival. In my PhD, I used a multi-omics approach to study host signalling modulation in L. donovani-infected macrophages. I observed time-dependent changes including global dephosphorylation and reduced protein levels affecting MAPK signalling, lysosomal function and iron homeostasis. I focused on iron homeostasis due to the critical role of host iron in parasite growth, and after detecting a significant upregulation of Ftl1, a subunit of ferritin. As free iron is toxic, ferritin storage is vital for L. donovani-infected macrophages, located in iron-rich organs (liver and spleen). I showed parasite-dependent colocalization of ferritin with NCOA4 at the PV, without triggering known ferritin degradation pathways. L. donovani altered ferritin composition toward Ftl1 enrichment, a profile typical of high iron, priming the macrophage for iron-rich conditions. However, Ftl1 knockdown did not impair infection due to compensatory mechanisms allowing parasite adaptation to oxidative stress such as upregulation of HSPB1, which prevents lipid peroxidation by inhibiting the Fenton reaction. It nevertheless comes at the cost of reducing iron import. These findings reveal that L. donovani hijacks the ferritin degradation pathway to sequester ferritin within the PV, safeguarding its iron content while blocking macrophage-mediated iron release that could otherwise trigger ferroptosis. To study the role of parasite effectors driving the observed host signalling changes, I focussed on Leishmania casein kinase 1.2 (L-CK1.2), an essential secreted kinase. I investigated whether L-CK1.2 contributes to the host modulations seen during infection, using selective inhibitors and systems level analyses. Inhibition of L-CK1.2 affected host pathways such as phagosome maturation, mRNA processing, MAPK signalling and translation. These findings also identified potential host substrates targeted by L-CK1.2. Since Leishmania modulates these pathways, L-CK1.2 involvement highlights its role as a key parasitic effector manipulating host functions. Finally, I assessed whether the host subversion strategy used by Leishmania via L-CK1.2 is conserved across diverse parasites by comparing Leishmania and Eimeria tenella, an evolutionarily distant apicomplexan causing coccidiosis in poultry. Omics-based comparison revealed modulation of key host pathways, p53 signalling, apoptosis, and mRNA splicing, across both infections. Both parasitic effectors L-CK1.2 and EtROP1 (Eimeria) modulated host cell apoptosis, RNA processing, and metabolism, revealing a shared host subversion strategy. These results suggest evolutionary pressure to control vital host functions during infection, offering opportunities for pan-parasitic therapies targeting these shared pathways. In conclusion, my PhD integrates multi-omics approaches with mechanistic studies to investigate host subversion by Leishmania. This work revealed effector-specific host modulations, uncovered novel strategies such as ferritin sequestration, and offered cross-parasite comparative insights by examining evolutionarily distinct parasites, Leishmania and Eimeria, thereby highlighting conserved mechanisms of host-parasite interaction. This work lays the foundation for future studies to dissect effector functions, novel mechanistic pathways, and guide targeted therapies against parasitic diseases.