# Harnessing the Power of Experimental Genetic Crosses to Probe Drug Resistance in Malaria

> **NIH NIH P01** · UNIVERSITY OF NOTRE DAME · 2024 · $2,430,648

## Abstract

ABSTRACT
Genetic crosses coupled with linkage mapping have provided an outstandingly successful approach for locating
the genetic determinants of biomedically important traits such as drug resistance and host specificity in P.
falciparum malaria. In the initial funding period of this Program Project (P01), we made great strides in
transitioning Plasmodium crosses from the original model using chimpanzees to the human-liver chimeric mouse
infused with human red blood cells (the FRG huHep/huRBC mouse) to generate more than 30 crosses in a span
of 5 years. This included many replicate crosses of 6 different parental combinations that produced nearly a
thousand new cloned progeny. This capacity allowed for optimizations that drove our development of the bulk
segregant analysis (BSA) methodology and put within reach the ability to use experimental crosses of new
clinical isolates to test specific hypotheses about emerging drug resistance. The combination of routine and
replicated experimental crosses with BSA has shifted the challenge from making crosses and identifying genetic
loci to instead prioritizing the rapid identification of genes and mechanisms underling parasite drug resistance
and fitness. Our capstone discovery identified the role of pfaat1 as an epistatic partner with pfcrt in the evolution
of chloroquine resistance that influences the balance between resistance and compensatory fitness, a crucial
determinant of how new drug resistances emerge and spread. The overall goal of this P01 renewal proposal is
to continue to advance this technology to track in real-time the alarming emergence of artemisinin resistance
(ART-R) and its partner drugs used in artemisinin combination therapies (ACTs) in East Africa, an imminent
threat to reverse decades of progress against morbidity and mortality due to malaria on the continent where
more than 90% of malaria deaths occur. Coding mutations in the kelch13 gene that are strongly associated with
ART-R and serve as the only markers for surveillance. However, mutations in kelch13 generate a wide range of
resistance levels and fitness effects, and how these effects are compensated by other structural or regulatory
changes in the genome remains unknown. Relying on 3 Research Projects, supported by 2 Scientific Cores, we
will use targeted experimental genetic crosses to (i) dissect the genetic complexity of ART-R, (ii) clarify the role
of kelch13, (iii) define the regulators and partner genes that control ART-R and emerging resistance to
lumefantrine, the predominant ACT partner drug in Africa and (iv) establish a sustainable and user-centric
valuable community resource including our methodological pipeline, data and biological materials. In the
process, we will expand our BSA drug selection protocols to include cutting edge single cell RNAseq as the next
step in building this powerful community resource for real-time solutions to clinically urgent questions.

## Key facts

- **NIH application ID:** 10863147
- **Project number:** 2P01AI127338-06A1
- **Recipient organization:** UNIVERSITY OF NOTRE DAME
- **Principal Investigator:** Michael T Ferdig
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $2,430,648
- **Award type:** 2
- **Project period:** 2017-08-01 → 2029-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10863147

## Citation

> US National Institutes of Health, RePORTER application 10863147, Harnessing the Power of Experimental Genetic Crosses to Probe Drug Resistance in Malaria (2P01AI127338-06A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10863147. Licensed CC0.

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