Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms

Abstract

The relatively high post-treatment relapse rates of paromomycin (PMM) in visceral leishmaniasis treatment and the swift emergence of experimental drug resistance challenge its broad application and urge for rational use and monitoring of resistance. However, no causal molecular mechanisms to Leishmania PMM resistance have been identified so far. To gain insights into potential resistance mechanisms, twelve experimentally selected Leishmania donovani clonal lines and the non-cloned preselection population, with variable degrees of PMM resistance, were subjected to whole genome sequencing. To identify genomic variations potentially associated with resistance, SNPs, Indels, chromosomal somy and gene copy number variations were compared between the different parasite lines. A total of 11 short nucleotide variations and the copy number alterations in 39 genes were correlated to PMM resistance. Some of the identified genes are involved in transcription, translation and protein turn-over (transcription elongation factor-like protein, RNA-binding protein, ribosomal protein L1a, 60S ribosomal protein L6, eukaryotic translation initiation factor 4E-1, proteasome regulatory non-ATP-ase subunit 3), virulence (major surface protease gp63, protein-tyrosine phosphatase 1-like protein), mitochondrial function (ADP/ATP mitochondrial carrier-like protein), signaling (phosphatidylinositol 3-related kinase, protein kinase putative and protein-tyrosine phosphatase 1-like protein) and vesicular trafficking (ras-related protein RAB1). These results indicate that, in Leishmania, the aminoglycoside PMM affects protein translational processes and underlines the complex and probably multifactorial origin of resistance.

Tandem mass tag-based quantitative proteomics analyses of a chicken-original virulent and its attenuated Histomonas meleagridis strain in China

“…The 60s subunit ribosomal protein of Trypanosomatid has the potential to be a novel pharmaco therapeutic target (53). In visceral Leishmaniasis, the 60S ribosomal protein L6 was suggested to be potentially associated with its resistance to paromomycin (54). Meanwhile its 40S ribosomal protein S12 has the highest sensitivity and specificity as an ELISA assay to detect the target antigen (55).…”

The critical role of mode of action studies in kinetoplastid drug discovery

“…Generation of resistant clonal lines starting from a sensitive clonal line of parasites accompanied by whole genome sequencing is another powerful tool in target identification. This has been widely used in elucidating the targets and modes of action of drugs and experimental compounds in African trypanosomes and leishmania (Coelho et al, 2012;Jones et al, 2015;Wyllie et al, 2016a;Wyllie et al, 2018;Yasur-Landau et al, 2018;Bhattacharya et al, 2020;Hendrickx et al, 2021;Paradela et al, 2021;Rosa-Teijeiro et al, 2021;Alpizar-Sosa et al, 2022;Hefnawy et al, 2022). This approach involves stepwise exposure of wild-type kinetoplastid clonal lines to increasing (sublethal) drug concentrations over a period of weeks to months to obtain lines capable of proliferating normally in concentrations (generally >10 × EC 50 ) that would be lethal for the original parental line (Jones et al, 2015;Wyllie et al, 2016a;Wyllie et al, 2018).…”

Antileishmanial and Antitrypanosomes Drugs for the Current Century

“…However, no causal molecular mechanisms for Leishmania PMM resistance have been identified so far. A relevant contribution in this Special Issue [ 41 ] addresses this aspect by investigating genomic variations found in twelve experimentally selected L. donovani clonal lines resistant to PMM compared to sensitive lines. Whole genome sequencing allowed identification of eleven short nucleotide variations and copy number alterations in 39 genes correlated to PMM resistance.…”