Active transcriptome remodeling underlies antimony-induced drug tolerance in persister-like Leishmania parasites

Persistence - characterized by the transient ability of subpopulations of Leishmania parasites to survive exposure to drugs - is a major driver of treatment failure and clinical relapses in leishmaniasis. Persisters are characterized by non-dividing or slow-growing state and increased drug tolerance. However, the molecular mechanisms governing formation of persisters remain poorly understood in Leishmania parasites. Here, we developed a model to explore persistence in Leishmania mexicana. Viable promastigote persister-like subpopulations were enriched using Ficoll density gradient centrifugation following lethal exposure to potassium antimonyl tartrate (PAT) that killed 80% of parasites. The surviving parasites exhibited delayed growth in drug-free medium that is characteristic for persisters, and higher drug tolerance upon rechallenge. Transcriptomic profiling across acute stress, drug-free recovery, and rechallenge phases revealed a global remodeling in persister-like cells under all tested conditions. Induction was characterized by downregulation of several biological processes and a robust upregulation of nucleolar pathways, supporting epitranscriptomic changes during the formation of persister-like cells. Upon drug removal, this profile rapidly reverted, initiating ribosome biogenesis to exit latency and resume proliferation. Resuscitation phase exhibited active protein synthesis and upregulation in biological processes associated with metabolic and mitochondrial functions. Furthermore, persister-like parasites displayed distinct drug response profiles compared to parental parasites by rapidly implementing a highly conserved, coordinated survival reprogramming, where 316 genes were uniquely downregulated, and 241 genes were upregulated. The distinct features of the drug response in rechallenged persister-like cells were characterized by the downregulation of mitochondrial function and protein synthesis to induce dormant state, and the upregulation of drug-response and stress-tolerance genes to survive immediate toxicity. In contrast, parental parasites displayed a broad and disorganized drug response. Additionally, rechallenged persisters exhibited distinct transcriptomic features that transiently phenocopies stable genetic resistance. This pre-adapted state is characterized by the targeted upregulation of epigenetic and epitranscriptomic modulators, heavy metal transporters, and catabolic enzymes to maintain viability. These findings demonstrate that drug persistence in Leishmania is not merely a metabolic collapse, but rather a sophisticated survival strategy involving active transcriptome remodeling, downregulation of translation and epigenetic/epitranscriptomic changes. This transient state constitutes an initial evolutionary step toward permanent drug resistance and highlights new molecular vulnerabilities for therapeutic interventions aimed at preventing clinical relapse.