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Updated: Apr 16, 2026
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
Temporal SILAC-based quantitative proteomics identifies host factors involved in chikungunya virus replication
Emmely E Treffers1,2, Ali Tas1, Florine E M Scholte1
1Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, The Netherlands.
Abstract:
Chikungunya virus (CHIKV) is an arthropod-borne reemerging human pathogen that generally causes a severe persisting arthritis. Since 2005, the virus has infected millions of people during outbreaks in Africa, Indian Ocean Islands, Asia, and South/Central America. Many steps of the replication and expression of CHIKV's 12-kb RNA genome are highly dependent on cellular factors, which thus constitute potential therapeutic targets. SILAC and LC-MS/MS were used to define the temporal dynamics of the cellular response to infection. Using samples harvested at 8, 10, and 12 h postinfection, over 4700 proteins were identified and per time point 2800-3500 proteins could be quantified in both biological replicates. At 8, 10, and 12 h postinfection, 13, 38, and 106 proteins, respectively, were differentially expressed. The majority of these proteins showed decreased abundance. Most subunits of the RNA polymerase II complex were progressively degraded, which likely contributes to the transcriptional host shut-off observed during CHIKV infection. Overexpression of four proteins that were significantly downregulated (Rho family GTPase 3 (Rnd3), DEAD box helicase 56 (DDX56), polo-like kinase 1 (Plk1), and ubiquitin-conjugating enzyme E2C (UbcH10) reduced susceptibility of cells to CHIKV infection, suggesting that infection-induced downregulation of these proteins is beneficial for CHIKV replication. All MS data have been deposited in the ProteomeXchange with identifier PXD001330 (http://proteomecentral.proteomexchange.org/dataset/PXD001330).
Insights
Chikungunya virus (CHIKV) infection impacts host cell proteins, including RNA polymerase II degradation. Downregulation of Rnd3, DDX56, Plk1, and UbcH10 aids CHIKV replication, offering potential therapeutic targets.
Area of Science:
- Virology
- Molecular Biology
- Proteomics
Background:
- Chikungunya virus (CHIKV) is a reemerging arthropod-borne pathogen causing severe arthritis.
- CHIKV outbreaks have affected millions globally since 2005.
- Viral replication relies on host cellular factors, presenting potential therapeutic targets.
Purpose of the Study:
- To define the temporal dynamics of the cellular proteome during CHIKV infection.
- To identify host proteins crucial for CHIKV replication.
- To explore potential therapeutic targets against CHIKV.
Main Methods:
- Stable Isotope Labeling by Amino acids in Cell culture (SILAC) coupled with Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) were employed.
- Proteomic analysis was performed on infected cells at 8, 10, and 12 hours postinfection.
- Differential protein expression analysis identified host factors affected by CHIKV.
Main Results:
- Over 4700 proteins were identified, with 2800-3500 quantified per time point.
- A significant number of proteins, including RNA polymerase II subunits, showed decreased abundance over time.
- Downregulation of Rho family GTPase 3 (Rnd3), DEAD box helicase 56 (DDX56), polo-like kinase 1 (Plk1), and ubiquitin-conjugating enzyme E2C (UbcH10) was observed.
Conclusions:
- CHIKV infection leads to host transcriptional shut-off, partly via RNA polymerase II degradation.
- Overexpression of downregulated proteins (Rnd3, DDX56, Plk1, UbcH10) reduced CHIKV susceptibility, indicating their importance for viral replication.
- These host factors represent promising targets for developing CHIKV therapeutics.
