A genome-wide CRISPR base-editing resource for functional genomics and drug-response mapping in Leishmania mexicana

Abstract

We present a CRISPR/Cas9 cytosine base editing library for genome-wide loss-of-function screening in L. mexicana and apply it to dissect the genetics of Leishmania drug response. The results, accessible at https://www.LeishBASEeditDB.net, revealed novel response biomarkers for SbIII, miltefosine, amphotericin B, pentamidine, and the arylmethylaminosteroid 1c. We identified hundreds of loci linked to altered drug responses, including opposing effects among paralogs, cross-resistance, and collateral sensitivity. Among 41 validated candidates, we identified sterol defects in two novel amphotericin B markers, discovered a regulator of intracellular miltefosine transporter complex localization, and uncovered evidence that flagellar-associated defects reduce drug sensitivity. Parallel viability and motility screens revealed, for the first time, genome-wide fitness contributions of unique and multi-copy genes in Leishmania promastigotes. Our approach enables powerful reverse genetic screens across Leishmania species, advancing drug mechanism studies and guiding combination therapy designs. The library is available for others to screen a multitude of additional loss-of-function phenotypes.