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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
André Nicolau Aquime Gonçalves1, Vanessa Escolano Maso2, Ícaro Maia Santos de Castro3
1Laboratory of Pathology of Infectious Diseases, Department of Pathology, Medical School, University of São Paulo; Scientific Platform Pasteur USP.
Journal of Visualized Experiments : Jove
|March 21, 2022
Summary
Researchers can analyze host-pathogen interactions using RNA sequencing (RNA-seq) data. This protocol details a pipeline for analyzing RNA-seq data to understand disease mechanisms and identify potential drug targets.
Area of Science:
- Genomics
- Infectious Diseases
- Bioinformatics
Background:
- Pathogens cause infectious diseases, with host biological responses dictating disease severity.
- Host transcriptome analysis via RNA sequencing (RNA-seq) offers insights into infection dynamics.
- Understanding host responses is crucial for identifying therapeutic targets.
Purpose of the Study:
- To present a comprehensive pipeline for analyzing host RNA-sequencing data in host-pathogen interaction studies.
- To enable a deeper understanding of disease mechanisms at the molecular level.
- To facilitate the discovery of novel drug targets and treatments.
Main Methods:
- A five-step pipeline for RNA-sequencing data analysis: quality control, gene mapping and annotation, differential and co-expression analysis, molecular perturbation assessment, and functional analysis.
- Quality control to remove technical artifacts.
- Statistical methods to identify differentially expressed and co-expressed genes.
- Assessment of sample variability and outlier detection.
- Functional analysis to determine disease-associated pathways.
Main Results:
- The pipeline effectively processes raw RNA-seq reads into meaningful biological insights.
- Identification of differentially expressed and co-expressed genes in infected versus non-infected samples.
- Characterization of molecular perturbations and associated pathways.
Conclusions:
- The presented pipeline provides a robust framework for analyzing host responses in infectious diseases using RNA-seq.
- This approach aids researchers in understanding molecular mechanisms of infection.
- The findings support the development of future in vitro and in vivo experiments for therapeutic discovery.
