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Plasmodium falciparum genetic crosses in a humanized mouse model

Nature Methods volume 12, pages 631–633 (2015)Cite this article

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Abstract

Genetic crosses of phenotypically distinct strains of the human malaria parasite Plasmodium falciparum are a powerful tool for identifying genes controlling drug resistance and other key phenotypes. Previous studies relied on the isolation of recombinant parasites from splenectomized chimpanzees, a research avenue that is no longer available. Here we demonstrate that human-liver chimeric mice support recovery of recombinant progeny for the identification of genetic determinants of parasite traits and adaptations.

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Figure 1: The FRG huHep mouse for P. falciparum genetic crosses.
Figure 2: Analysis of recombinant progeny from P. falciparum crosses.

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Acknowledgements

We thank the Center for Infectious Disease Research (formerly Seattle BioMed) insectary and vivarium for mosquito and rodent care, respectively, as well as R. Garcia and M. McDew-White at the Texas Biomedical Research Institute for technical assistance. We thank S. Mikolajczak, E. Wilson and J. Bial for ongoing FRG huHep mouse discussions and M. Macarulay and K. Ushimaru for help with parasite cloning. Thanks also to A. Kaushansky for help with graphics. NIH grants R21 AI 115194–01 to A.M.V. and M.T.F., R37 AI 048071 to T.J.C.A. and Chemistry-Biochemistry-Biology Interface Training Fellowship T32 GM075762 to R.S.P. supported this work, as did Seattle BioMed internal funds to S.H.I.K. The AT&T Genomics Computing Center at Texas Biomedical Research Institute is supported by the AT&T Foundation and the US National Center for Research Resources (NCRR) grant number S10 RR029392, and laboratory work was conducted in facilities constructed with support from Research Facilities Improvement Program grant C06 RR013556 and RR017515 from NCRR.

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Authors and Affiliations

  1. Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington, USA

    Ashley M Vaughan, Nelly Camargo, Matthew Fishbaugher & Stefan H I Kappe

  2. Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA

    Richard S Pinapati, Lisa A Checkley, Carolyn A Hutyra & Michael T Ferdig

  3. Texas Biomedical Research Institute, San Antonio, Texas, USA

    Ian H Cheeseman, Shalini Nair & Timothy J C Anderson

  4. Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Mae Sot, Thailand

    François H Nosten

  5. Department of Global Health, University of Washington, Seattle, Washington, USA

    Stefan H I Kappe

Authors
  1. Ashley M Vaughan
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  2. Richard S Pinapati
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  4. Nelly Camargo
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  6. Lisa A Checkley
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  9. François H Nosten
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  11. Michael T Ferdig
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Contributions

A.M.V., S.H.I.K. and M.T.F. conceived, initiated and supervised the project. A.M.V., S.H.I.K., T.J.C.A., R.S.P. and M.T.F. designed experiments and wrote the manuscript. A.M.V., N.C., M.F., L.A.C., R.S.P., I.H.C., S.N. and C.A.H. carried out the experiments. F.H.N. and T.J.C.A. supplied parasites. A.M.V., S.H.I.K., I.H.C., T.J.C.A., R.S.P. and M.T.F. analyzed results.

Corresponding authors

Correspondence to Michael T Ferdig or Stefan H I Kappe.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Proof of recombination from the NF54HT-GFP–luc × GB4 cross.

Progeny from the NF54HT-GFP–luc (N) × GB4 (G) cross were cloned after selection with WR99210 (NF54HT-GFP–luc is resistant) and chloroquine (GB4 is resistant). Primers specific for the GFP–luc integration and the chloroquine resistance-associated (CQR) allele pfcrt were used to amplify genomic DNA from ten progeny (1 through 10). Agarose gel electrophoresis shows the presence of both the GFP-luc integration (a) and following ApoI digestion, the presence of the CQR allele, in all progeny (b). Full gels are presented to the right of each panel.

Supplementary Figure 2 Segregation of 7,536 SNPs and microsatellites (MSs) in 14 progeny from the P. falciparum NF54HT-GFP–luc × NHP* experimental genetic cross.

As an example, chromosome 11 is shown in the main body of the text (Fig. 2). Each row represents an individually sequenced chromosome from one of the 14 progeny. Haplotypes inherited from NHP* are shown in black and those from NF54HT-GFP–luc in red, while microsatellite markers from NHP* are shown in yellow and those from NF54HT-GFP–luc in blue. Seventeen of the 22 MS developed for the study are shown; the remaining five were invariant in the two parents. Chromosome regions in white mark the position of recombination breakpoints. Chromosomes are shown from the first to the last genotyped marker, and therefore do not start at zero base pairs. The grey tick marks along the top of each chromosome indicate the position of the segregating SNPs, while the scale (in base pairs) is shown at the base of the figure.

Supplementary Figure 3 Pairwise allele sharing among 14 progeny from the P. falciparum NF54HT-GFP–luc × NHP* experimental genetic cross.

With Mendelian segregation, progeny are expected to share on average 50% of markers that are identical by descent. We calculated the proportion of segregating SNPs at which each of 91 pair-wise combinations of progeny genotypes differ, and plotted the frequency distribution of these values. Segregation was normally distributed and centered on 52% (mean = 52%, s.d. = 8.03, Shapiro-Wilk test, P = 0.27, W = 0.98).

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Vaughan, A., Pinapati, R., Cheeseman, I. et al. Plasmodium falciparum genetic crosses in a humanized mouse model. Nat Methods 12, 631–633 (2015). https://doi.org/10.1038/nmeth.3432

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