Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from...

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• Host-pathogen transcriptomic studies are difficult due to low pathogen RNA levels.
• Candida species cause life-threatening infections, particularly in immunocompromised individuals.
• Understanding tissue-specific interactions of diverse Candida species is crucial.

Purpose of the Study:

• To develop a method for in vivo transcriptomic analysis of Candida species.
• To design and validate pan-Candida target capture probes for RNA enrichment.
• To enable accurate identification of infecting Candida strains.

Main Methods:

• Designed and validated pan-Candida target capture probes.
• Enriched protein-coding and non-coding transcriptomes from host-pathogen samples.
• Compared probe-based enrichment with differential lysis and existing capture methods.

Main Results:

• Probe-based enrichment outperformed differential lysis.
• Achieved similar enrichment performance to existing methods but with better expression fidelity.
• Enabled species multiplexing, lncRNA capture, and robust genotype-based strain identification.

Conclusions:

• The developed pan-Candida probes facilitate in vivo transcriptomic analysis.
• This approach enhances the study of host-pathogen interactions in Candida infections.
• The method allows for precise strain identification and characterization of fungal gene expression.