Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways
- Creators
- Yi, Lynn
- Pimentel, Harold
- Pachter, Lior
Abstract
Background: A recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and identified cell cycle-related pathways that are affected by infection. However deeper exploration of the information present in the RNA-Seq data can be used to further elucidate the manner in which Zika infection of hNPCs affects the transcriptome, refining pathway predictions and revealing isoform-specific dynamics. Methodology/Principal findings: We analyzed data published by Tang et al. using state-of-the-art tools for transcriptome analysis. By accounting for the experimental design and estimation of technical and inferential variance we were able to pinpoint Zika infection affected pathways that highlight Zika's neural tropism. The examination of differential genes reveals cases of isoform divergence. Conclusions: Transcriptome analysis of Zika infected hNPCs has the potential to identify the molecular signatures of Zika infected neural cells. These signatures may be useful for diagnostics and for the resolution of infection pathways that can be used to harvest specific targets for further study.
Additional Information
© 2017 Yi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: October 11, 2016; Accepted: March 30, 2017; Published: April 27, 2017. Data Availability Statement: The data analysis can be repeated using the provided scripts at http://www.github.com/pachterlab/zika/. The preloaded sleuth Shiny app can be found via http://128.32.142.223/tang16/. These links direct to all the information necessary to replicate the study. LY was supported by funding from the UCLA/Caltech Medical Scientist Training Program, The Walter and Sylvia Treadway Endowment, and the NIH T32 (NRSA). LP was partially funded by NIH R01 DK094699. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author Contributions: Conceptualization: LP. Data curation: LY HP. Formal analysis: LY HP LP. Funding acquisition: LP. Investigation: LY. Methodology: HP LY. Project administration: LP. Resources: LP. Software: HP LY. Supervision: LP. Validation: LY. Visualization: LY HP. Writing – original draft: LY LP. Writing – review & editing: LY HP LP. The authors have declared that no competing interests exist.Attached Files
Published - journal.pone.0175744.pdf
Submitted - 072439.full.pdf
Supplemental Material - journal.pone.0175744.s001.csv
Supplemental Material - journal.pone.0175744.s002.csv
Supplemental Material - journal.pone.0175744.s003.csv
Supplemental Material - journal.pone.0175744.s004.xls
Supplemental Material - journal.pone.0175744.s005.xls
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Additional details
- PMCID
- PMC5407828
- Eprint ID
- 77219
- Resolver ID
- CaltechAUTHORS:20170505-103858288
- UCLA-Caltech Medical Scientist Training Program
- Walter and Sylvia Treadway Endowment
- R01 DK094699
- NIH
- Created
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2017-05-05Created from EPrint's datestamp field
- Updated
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2023-06-01Created from EPrint's last_modified field