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Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

Yi, Lynn and Pimentel, Harold and Pachter, Lior (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLoS ONE, 12 (4). Art. No. e0175744. ISSN 1932-6203. PMCID PMC5407828. https://resolver.caltech.edu/CaltechAUTHORS:20170505-103858288

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1371/journal.pone.0175744DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407828/PubMed CentralArticle
https://doi.org/10.1371/journal.pone.0175744.s001DOIS1 Table
https://doi.org/10.1371/journal.pone.0175744.s002DOIS2 Table
https://doi.org/10.1371/journal.pone.0175744.s003DOIS3 Table
https://doi.org/10.1371/journal.pone.0175744.s004DOIS4 Table
https://doi.org/10.1371/journal.pone.0175744.s005DOIS5 Table
https://doi.org/10.1101/072439DOIDiscussion Paper
ORCID:
AuthorORCID
Yi, Lynn0000-0003-4575-0158
Pachter, Lior0000-0002-9164-6231
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.
Funders:
Funding AgencyGrant Number
UCLA-Caltech Medical Scientist Training ProgramUNSPECIFIED
Walter and Sylvia Treadway EndowmentUNSPECIFIED
NIHR01 DK094699
Issue or Number:4
PubMed Central ID:PMC5407828
Record Number:CaltechAUTHORS:20170505-103858288
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170505-103858288
Official Citation:Yi L, Pimentel H, Pachter L (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLoS ONE 12(4): e0175744. https://doi.org/10.1371/journal.pone.0175744
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:77219
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:05 May 2017 18:01
Last Modified:09 Mar 2020 13:19

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