Extrachromosomal DNA amplicons in antimalarial-resistant Plasmodium falciparum.

Jennifer M Mcdaniels,Sabrina Lingeman,Molly Congdon,Jennifer L Guler,Webster Santos,Pradipsinh K Rathod,Audrey Francis,Sabrina A Carter,Adam C Huckaby

doi:10.1111/mmi.14624

Jennifer M Mcdaniels, Sabrina Lingeman + Show 7 more

Open Access

https://doi.org/10.1111/mmi.14624

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Abstract

Extrachromosomal (ec) DNAs are genetic elements that exist separately from the genome. Since ecDNA can carry beneficial genes, they are a powerful adaptive mechanism in cancers and many pathogens. For the first time, we report ecDNA contributing to antimalarial resistance in Plasmodium falciparum, the most virulent human malaria parasite. Using pulse field gel electrophoresis combined with PCR‐based copy number analysis, we detected two ecDNA elements that differ in migration and structure. Entrapment in the electrophoresis well and low susceptibility to exonucleases revealed that the biologically relevant ecDNA element is large and complex in structure. Using deep sequencing, we show that ecDNA originates from the chromosome and expansion of an ecDNA‐specific sequence may improve its segregation or expression. We speculate that ecDNA is maintained using established mechanisms due to shared characteristics with the mitochondrial genome. Implications of ecDNA discovery in this organism are wide‐reaching due to the potential for new strategies to target resistance development.

Highlights

A major factor that contributes to genome plasticity in a variety of organisms is extrachromosomal DNA
We have identified ecDNA in DSM1-resistant P. falciparum parasites
Using electrophoresis-based methods, we made a number of important observations about these molecules including their confinement to H clones and the existence of two distinct ecDNA elements (Figures 3 and 4)

Summary

| INTRODUCTION

A major factor that contributes to genome plasticity in a variety of organisms is extrachromosomal (ec) DNA. EcDNA contains extra gene copies that exist outside of the genome and are often observed at high copy numbers in organisms under strong selection As evidence for their contribution to genome plasticity, genes that confer fitness benefits are enriched in ecDNA (Albertson, 2006; Beverley, 1988; Dillon et al, 2015; Genois et al, 2014; Hastings et al, 2009; Leprohon et al, 2014; McGill et al, 1993; Møller et al, 2015; Shibata et al, 2012; Verhaak et al, 2019; Wagner and So, 1992). TA B L E 1 Details of primers used in Southern blot analysis and Digital Droplet PCR (ddPCR)

Method

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| DISCUSSION

Findings

| EXPERIMENTAL PROCEDURES