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Table 2 Summary of omics-based technologies used for target discovery and validation for protozoan pathogens

From: Advances in omics-based methods to identify novel targets for malaria and other parasitic protozoan infections


Tools used




In vitro evolution and whole-genome analysis

- Tiling microarrays

- Whole-genome sequencing

- Identifying the targets of compounds

- Analyzing the mechanisms of resistance

- Can determine the targets of compounds from phenotypic screens

- Simultaneously enables the assessment of mechanisms of resistance

- High specificity

- Resistance mutations may obscure mutations in the gene encoding the target

- Inability to generate in vitro resistance to some compounds, particularly fast-killing compounds

Genome-wide essentiality studies

- piggyBac transposon system

- Targeted barcode gene knockouts

- Determining essential pathways, thereby identifying potentially druggable pathways

- Assesses the entire genome at once

- A gene or pathway can be directly linked to a particular phenotype

- Transposition may occur in essential genes

- Assessment is limited to annotated genes

- Some genes are more amenable to transposon mutagenesis or gene knockout

Transcriptomic analysis

- RNA-seq of the pathogen

- Dual RNA-seq of host cells and the pathogen

- Identifies pathogen gene pathways that are upregulated during infection

- Identifies host pathways that are important in response to infection

- Provides information about the upregulation of genes relative to other pathways

- Assessment is limited to annotated genes

- High sequencing coverage is needed to detect meaningful changes resulting from low-level infection


- Mass spectrometry

- Nuclear magnetic resonance-based structure guidance

- Target identification

- Target validation

- Understanding mechanisms of resistance

- Can identify the cellular location of a target or mechanism of resistance

- Targeting protein-protein interactions increases the number of potential inhibitor-binding locations

- Multiple proteins are typically identified in initial studies

- Success is dependent on whether the inhibition is potent enough to cure the disease


- ATAC-seq (assay for transposase-accessible chromatin using sequencing)

- ChIP-seq (chromatin immunoprecipitation sequencing)

- Identifying which genes are expressed or silent at different stages of the parasite life cycle

- Can help to interpret whole-genome data by assessing whether intergenic mutations are in regulatory regions

- ATAC-seq is biased against AT-rich sequences