Table 2 Summary of omics-based technologies used for target discovery and validation for protozoan pathogens
| Technology | Tools used | Application | Advantages | Disadvantages |
|---|---|---|---|---|
| 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 |
| Proteomics |
- 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 |
| Epigenomics |
- 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 |