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Related Experiment Video

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Low-volume Plasmodium blood sample processing protocols for untargeted transcriptomics optimized using Plasmodium

Erin Sauve1, Johanna Helena Kattenberg1, Pieter Moris1

  • 1Malariology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, 155 Nationalestraat, 2000 Antwerp, Belgium.

Microbial Genomics
|November 20, 2025
PubMed
Summary

Optimizing sample processing for Plasmodium transcriptomics is crucial. Combining white blood cell and globin depletion with mRNA library preparation significantly improves parasite RNA enrichment in low-volume samples.

Keywords:
Plasmodiumfield studiesparasitologysample processingtranscriptomicswhite blood cell depletion

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Area of Science:

  • Malariology and Parasitology
  • Genomics and Transcriptomics
  • Molecular Biology

Background:

  • Studying Plasmodium non-falciparum species is challenging due to reliance on natural infections and low parasite densities.
  • Existing transcriptomic research is complicated by high proportions of human genetic material in samples.
  • Optimized sample processing protocols are needed to overcome limitations in low-volume Plasmodium studies.

Purpose of the Study:

  • To develop an optimized protocol for low-volume Plasmodium sample processing for transcriptomic analysis.
  • To compare the efficacy of different white blood cell (WBC), rRNA, and globin depletion methods.
  • To evaluate various RNA-seq library preparation kits for parasite RNA enrichment.

Main Methods:

  • Utilized a Plasmodium knowlesi culture in whole blood as a mock Plasmodium vivax infection model.
  • Compared white blood cell (WBC), rRNA, and globin depletion techniques.
  • Assessed different RNA-seq library preparation kits for their impact on parasite RNA yield and quality.

Main Results:

  • White blood cell (WBC) depletion significantly increased mapped Plasmodium paired-end (PE) reads from 5.4% to 37.2-54.5%.
  • Globin RNA and rRNA depletion reduced human globin and rRNA gene counts by up to 90%.
  • mRNA library preparation kits showed high correlation and enriched protein-coding genes, outperforming total RNA kits dominated by rRNA.

Conclusions:

  • Combining WBC and globin depletion with mRNA library preparation kits optimizes Plasmodium transcriptomic sequencing output.
  • This optimized protocol enhances parasite RNA enrichment in low-parasite density and low-volume samples.
  • The findings facilitate untargeted Plasmodium transcriptomics in resource-limited settings, enabling new biological insights.