Impact of Zika Virus Infection on Human Neural Stem Cell MicroRNA Signatures
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. Infection
2.3. Plaque-Forming-Assay
2.4. MiRNAs: Sequencing and Data Analysis
2.5. Microarray-Based Gene Expression Analysis
2.6. Real-Time Quantitative PCR
2.7. Oxyblot
2.8. Immunofluorescence Microscopy
2.9. Statistical Analysis
3. Results
3.1. ZIKV Uganda and French Polynesia Alter Gene Expression in lt-NES® Cells
3.2. Dysregulated miRNAs Play a Role in Neurodevelopment and Cell Cycle
3.3. ZIKV Modifies the Host miRNA Cargo in Secreted EVs
3.4. Dysregulated miRNAs and mRNAs Involved in Oxidative Stress
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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GeneSymbol | Fold Change ZIKV Uganda | p-Value ZIKV Uganda | Fold Change ZIKV Polynesia | p-Value ZIKV Polynesia |
---|---|---|---|---|
COL4A1 | −2.1 | 0.0093 | −1.2 | 0.635 |
MIR17HG | −2.3 | 0.0497 | −1.3 | 0.749 |
TUBA1A | −2.2 | 2.56 × 10−4 | −1.5 | 0.256 |
SLC2A1 | −2.3 | 0.0239 | 1.0 | 0.806 |
ASNS | 9.6 | 0.0314 | 2.9 | 0.006 |
STAMBP | 2.5 | 1.07 × 10−4 | 1.4 | 0.975 |
GeneSymbol | Fold Change ZIKV Uganda 24 hpi | Fold Change ZIKV Uganda 48 hpi | Fold Change ZIKV Uganda 72 hpi |
---|---|---|---|
OASL | 1.6 | 49.9 | 766.7 |
CH25H | 2.5 | 46.8 | 611.3 |
IFNB1 | 2.3 | 37.9 | 554.3 |
CXCL10 | −1.3 | 40.8 | 521.3 |
IFIT2 | 1.0 | 30.7 | 218.8 |
IFIH1 | 2.1 | 38.1 | 176.4 |
PRDM16 | 8.1 | 23.5 | 141.9 |
CCL5 | −1.3 | 10.3 | 117.1 |
CXCL11 | 1.1 | 12.8 | 104.1 |
GSC | 1.2 | 9.0 | 60.4 |
BST2 | 1.8 | 26.6 | 59.0 |
IFI44 | 2.4 | 20.8 | 55.5 |
PKD1L2 | 2.8 | 9.6 | 49.9 |
DHX58 | 1.3 | 8.3 | 46.3 |
ATP4A | 1.1 | 3.7 | 38.3 |
TMEM71 | 2.5 | 8.7 | 35.8 |
CEACAM1 | 1.4 | 6.8 | 35.8 |
NEURL3 | 1.2 | 10.5 | 34.0 |
IFI6 | 1.0 | 9.1 | 33.8 |
GeneSymbol | Fold Change ZIKV Polynesia 24 hpi | Fold Change ZIKV Polynesia 48 hpi | Fold Change ZIKV Polynesia 72 hpi |
---|---|---|---|
BST2 | 1.2 | 10.2 | 459.5 |
OAS1 | −1.0 | 2.7 | 261.2 |
IFIH1 | 1.5 | 11.8 | 219.1 |
IFNB1 | 1.4 | 4.3 | 211.2 |
OASL | −1.1 | 6.3 | 193.1 |
CXCL10 | 1.0 | 4.2 | 147.1 |
IFITM1 | 1.4 | 4.8 | 133.1 |
HERC6 | 1.1 | 3.2 | 130.7 |
CH25H | 1.5 | 3.0 | 126.7 |
IFI44 | 2.1 | 11.6 | 124.7 |
IFI6 | −1.0 | 3.7 | 118.3 |
SAMD9L | −1.0 | 6.2 | 105.6 |
IFIT2 | 1.3 | 5.1 | 96.8 |
MX1 | 1.1 | 4.3 | 90.2 |
ISG15 | −1.0 | 5.1 | 67.5 |
OAS2 | −1.1 | 2.4 | 54.4 |
DDX60 | 1.0 | 4.3 | 52.0 |
GO Category | p-Value | #Genes |
---|---|---|
Gene expression | 2.49 × 10−5 | 12 |
Cellular nitrogen compound metabolic process | 0.00013 | 37 |
Macromolecular complex assembly | 0.00162 | 13 |
Protein complex assembly | 0.01012 | 11 |
Cellular component assembly | 0.01986 | 14 |
Biosynthetic process | 0.02673 | 28 |
Biological process | 0.02901 | 90 |
Negative regulation of oxidoreductase activity | 0.03821 | 2 |
In utero embryonic development | 0.03821 | 7 |
DEG | Fold Change ZIKV Polynesia |
---|---|
PNPT1 | 3.36 |
FOS | 5.18 |
XBP1 | 2.06 |
PPARGC1A | 2.06 |
KLF4 | 6.28 |
PML | 3.76 |
TNFAIP3 | 4.96 |
STAT1 | 17.09 |
SLC7A11 | 2.11 |
JUN | 2.10 |
DEG | Fold Change ZIKV Polynesia |
---|---|
XBP1 | 2.06 |
EIF2AK2 | 4.72 |
ASNS | 2.13 |
TRIB3 | 2.84 |
DDIT3 | 5.17 |
ATF3 | 5.56 |
HERPUD1 | 2.48 |
PPP1R15A | 2.31 |
FBXO6 | 2.33 |
CHAC1 | 4.46 |
miRNA ID | Gene Targets (ID) |
---|---|
hsa-miR-26b-5p | TRIB3, FOS, HERPUD1, TNFAIP3, JUN, ASNS, CHAC1, ATF3 |
hsa-let-7g-5p | TRIB3, FBXO6, CHAC1 |
hsa-miR-17-5p | FOS, TNFAIP3, JUN, KLF4 |
hsa-miR-221-3p | FOS, PPP1R15A |
hsa-miR-16-5p | HERPUD1, PML, EIF2AK2, JUN, ASNS, PPP1R15A, CHAC1, STAT1 |
hsa-miR-106b-5p | TNFAIP3 |
hsa-miR-374a-5p | TNFAIP3, EIF2AK2 |
hsa-miR-93-5p | TNFAIP3, JUN |
hsa-miR-20a-5p | TNFAIP3 |
hsa-miR-186-5p | EIF2AK2, JUN, ASNS, CHAC1 |
hsa-miR-32-5p | JUN, KLF4 |
hsa-miR-218-5p | CHAC1 |
hsa-miR-340-5p | PPARGC1A |
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Tabari, D.; Scholl, C.; Steffens, M.; Weickhardt, S.; Elgner, F.; Bender, D.; Herrlein, M.-L.; Sabino, C.; Semkova, V.; Peitz, M.; et al. Impact of Zika Virus Infection on Human Neural Stem Cell MicroRNA Signatures. Viruses 2020, 12, 1219. https://doi.org/10.3390/v12111219
Tabari D, Scholl C, Steffens M, Weickhardt S, Elgner F, Bender D, Herrlein M-L, Sabino C, Semkova V, Peitz M, et al. Impact of Zika Virus Infection on Human Neural Stem Cell MicroRNA Signatures. Viruses. 2020; 12(11):1219. https://doi.org/10.3390/v12111219
Chicago/Turabian StyleTabari, Denna, Catharina Scholl, Michael Steffens, Sandra Weickhardt, Fabian Elgner, Daniela Bender, Marie-Luise Herrlein, Catarina Sabino, Vesselina Semkova, Michael Peitz, and et al. 2020. "Impact of Zika Virus Infection on Human Neural Stem Cell MicroRNA Signatures" Viruses 12, no. 11: 1219. https://doi.org/10.3390/v12111219