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Updated: Dec 15, 2025
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
Pathway identification through transcriptome analysis
Takeshi Terabayashi1, Gregory G Germino1, Luis F Menezes1
1Kidney Disease Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health (NIH), Bethesda, MD, United States.
Abstract:
Systems-based, agnostic approaches focusing on transcriptomics data have been employed to understand the pathogenesis of polycystic kidney diseases (PKD). While multiple signaling pathways, including Wnt, mTOR and G-protein-coupled receptors, have been implicated in late stages of disease, there were few insights into the transcriptional cascade immediately downstream of Pkd1 inactivation. One of the consistent findings has been transcriptional evidence of dysregulated metabolic and cytoskeleton remodeling pathways. Recent technical developments, including bulk and single-cell RNA sequencing technologies and spatial transcriptomics, offer new angles to investigate PKD. In this article, we review what has been learned based on transcriptional approaches and consider future opportunities.
Insights
Transcriptomics reveal key metabolic and cytoskeleton changes in polycystic kidney disease (PKD) pathogenesis. This review explores insights into the transcriptional cascade following Pkd1 inactivation and future research directions.
Area of Science:
- Genomics and Molecular Biology
- Nephrology and Urology
Background:
- Polycystic kidney diseases (PKD) pathogenesis is often studied using transcriptomics.
- While late-stage pathways like Wnt and mTOR are implicated, early transcriptional events post-Pkd1 inactivation remain unclear.
- Metabolic and cytoskeleton remodeling pathways consistently show dysregulation in PKD.
Purpose of the Study:
- To review current understanding of PKD pathogenesis derived from transcriptomic approaches.
- To highlight the transcriptional cascade immediately downstream of Pkd1 inactivation.
- To discuss future research opportunities in PKD using advanced transcriptomic technologies.
Main Methods:
- Analysis of transcriptomics data from PKD models and patients.
- Review of studies implicating signaling pathways in PKD.
- Consideration of bulk and single-cell RNA sequencing, and spatial transcriptomics.
Main Results:
- Transcriptional evidence points to dysregulated metabolic and cytoskeleton remodeling pathways in PKD.
- Limited insights into the immediate transcriptional cascade following Pkd1 inactivation.
- Identification of key pathways involved in disease progression.
Conclusions:
- Transcriptomics provides valuable insights into PKD pathogenesis, particularly metabolic and cytoskeletal alterations.
- Advanced sequencing technologies offer new avenues for investigating PKD.
- Further research is needed to fully elucidate the early transcriptional events in PKD.
