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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

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