Pathways Activated by Infected and Bystander Chondrocytes in Response to Ross River Virus Infection
Abstract
1. Introduction
2. Materials and Methods
2.1. Virus
2.2. Cells
2.3. RRV-GFP Infection of Differentiated Human Primary Chondrocytes for RNA-Seq
2.4. RNA Extraction and Preparation of cDNA Library
2.5. Differential Gene Expression Analysis of RNA-Seq Datasets
2.6. Gene Set Enrichment Analysis
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Relative Expression GFP+ Cells (Unique Genes) | Relative Expression GFP+ Cells (Overlapping Genes) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Symbol | Gene ID | log2FC | p-Value | FDR | Symbol | Gene ID | log2FC | p-Value | FDR | ||
Up-regulated | RIMS2 | 9699 | 13.27 | 4.21E-07 | 1.33E-05 | DNAH2 | 146754 | 15.87 | 9.07E-10 | 8.32E-07 | |
PTGER3 | 5733 | 12.75 | 1.06E-05 | 1.35E-04 | ACTN2 | 88 | 15.32 | 4.91E-08 | 3.33E-06 | ||
FOXJ1 | 2302 | 12.71 | 5.26E-07 | 1.60E-05 | HEATR9 | 256957 | 15.23 | 3.23E-09 | 1.04E-06 | ||
LOC400499 | 400499 | 12.71 | 4.22E-06 | 7.13E-05 | SCN3A | 6328 | 14.95 | 7.13E-09 | 1.34E-06 | ||
LRRC37A11P | 342666 | 12.53 | 1.78E-05 | 1.94E-04 | IL7R | 3575 | 14.93 | 4.90E-09 | 1.15E-06 | ||
INSM2 | 84684 | 12.51 | 3.16E-06 | 5.77E-05 | NEFM | 4741 | 14.73 | 1.10E-06 | 2.70E-05 | ||
GUCY2D | 3000 | 12.43 | 1.21E-05 | 1.48E-04 | IFIT1B | 439996 | 14.65 | 1.26E-07 | 6.23E-06 | ||
GAS2L2 | 246176 | 12.43 | 1.55E-04 | 9.98E-04 | MAFA | 389692 | 14.39 | 1.79E-07 | 7.77E-06 | ||
SLC9A2 | 6549 | 12.37 | 3.42E-05 | 3.16E-04 | ARHGAP9 | 64333 | 14.25 | 3.82E-09 | 1.09E-06 | ||
CATSPERD | 257062 | 12.31 | 2.81E-05 | 2.74E-04 | CXCL5 | 6374 | 14.19 | 2.48E-10 | 8.32E-07 | ||
Down-regulated | CGRRF1 | 10668 | −9.89 | 1.25E-03 | 5.04E-03 | GXYLT2 | 727936 | −11.22 | 1.21E-02 | 3.00E-02 | |
MTM1 | 4534 | −9.74 | 1.75E-03 | 6.59E-03 | GCHFR | 2644 | −11.14 | 5.39E-03 | 1.60E-02 | ||
MYPOP | 339344 | −9.69 | 5.54E-03 | 1.63E-02 | MRPL48 | 51642 | −10.87 | 3.60E-04 | 1.91E-03 | ||
TCEANC2 | 127428 | −9.60 | 8.73E-04 | 3.79E-03 | KIT | 3815 | −10.55 | 9.19E-03 | 2.43E-02 | ||
TMEM216 | 51259 | −9.54 | 2.26E-03 | 8.02E-03 | C22orf39 | 128977 | −10.54 | 4.03E-04 | 2.08E-03 | ||
ZNF415 | 55786 | −9.51 | 2.84E-03 | 9.64E-03 | MAP1LC3C | 440738 | −10.36 | 1.63E-03 | 6.22E-03 | ||
PLAG1 | 5324 | −9.39 | 4.69E-03 | 1.42E-02 | EPHX2 | 2053 | −10.31 | 6.55E-04 | 3.02E-03 | ||
ARL6 | 84100 | −9.37 | 1.97E-03 | 7.23E-03 | FBLN7 | 129804 | −10.19 | 1.33E-03 | 5.30E-03 | ||
PPP1R3D | 5509 | −9.36 | 2.17E-03 | 7.77E-03 | HOXA13 | 3209 | −10.03 | 1.80E-03 | 6.73E-03 | ||
FAM173B | 134145 | −9.35 | 7.11E-03 | 1.99E-02 | CYP4X1 | 260293 | −9.97 | 1.77E-02 | 4.09E-02 |
Relative Expression GFP− Cells (Unique Genes) | Relative Expression GFP− Cells (Overlapping Genes) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Symbol | Gene ID | log2FC | p-Value | FDR | Symbol | Gene ID | log2FC | p-Value | FDR | ||
Up-regulated | GABBR2 | 9568 | 11.02 | 1.94E-03 | 6.96E-03 | CXCL5 | 6374 | 15.56 | 1.15E-10 | 9.09E-07 | |
AIM2 | 9447 | 8.46 | 3.81E-04 | 2.01E-03 | CXCL10 | 3627 | 13.84 | 9.34E-07 | 3.17E-05 | ||
IFNL1 | 282618 | 8.27 | 1.06E-04 | 7.87E-04 | CXCL11 | 6373 | 13.79 | 8.81E-08 | 7.56E-06 | ||
CSF2 | 1437 | 8.02 | 2.13E-04 | 1.30E-03 | IL7R | 3575 | 13.45 | 1.02E-08 | 2.26E-06 | ||
KRTAP2-3 | 730755 | 8.00 | 2.16E-03 | 7.57E-03 | RSAD2 | 91543 | 13.27 | 5.82E-10 | 9.09E-07 | ||
C3AR1 | 719 | 7.92 | 3.93E-03 | 1.22E-02 | MMP1 | 4312 | 12.78 | 1.41E-09 | 9.30E-07 | ||
CCL8 | 6355 | 7.58 | 5.81E-04 | 2.74E-03 | ESM1 | 11082 | 12.68 | 6.28E-08 | 6.46E-06 | ||
RNY4 | 6086 | 6.36 | 2.01E-02 | 4.52E-02 | OASL | 8638 | 12.54 | 1.22E-09 | 9.09E-07 | ||
APOBEC3B | 9582 | 5.85 | 3.55E-04 | 1.90E-03 | BATF2 | 116071 | 12.38 | 1.98E-08 | 3.15E-06 | ||
HIST1H3F | 8968 | 5.84 | 1.76E-04 | 1.13E-03 | GBP5 | 115362 | 11.84 | 5.44E-07 | 2.20E-05 | ||
Down-regulated | FRMD7 | 90167 | −9.26 | 1.30E-05 | 1.76E-04 | KRT4 | 3851 | −11.66 | 1.84E-07 | 1.17E-05 | |
C1QTNF7 | 114905 | −8.85 | 7.21E-05 | 5.90E-04 | GDF10 | 2662 | −9.63 | 2.74E-05 | 2.97E-04 | ||
WSCD2 | 9671 | −8.74 | 1.09E-04 | 8.02E-04 | ATP1A2 | 477 | −8.34 | 2.83E-07 | 1.53E-05 | ||
CPAMD8 | 27151 | −7.75 | 5.38E-06 | 9.95E-05 | PRIMA1 | 145270 | −8.15 | 4.68E-07 | 2.00E-05 | ||
ALDH3A1 | 218 | −7.20 | 8.27E-06 | 1.29E-04 | ZBTB7C | 201501 | −7.63 | 4.12E-07 | 1.86E-05 | ||
SCN2B | 6327 | −6.37 | 4.61E-05 | 4.28E-04 | PTH1R | 5745 | −7.33 | 2.38E-05 | 2.69E-04 | ||
HLF | 3131 | −6.33 | 1.00E-05 | 1.47E-04 | YPEL1 | 29799 | −7.25 | 2.75E-05 | 2.98E-04 | ||
PRRT2 | 112476 | −6.30 | 7.39E-06 | 1.20E-04 | MAP1LC3C | 440738 | −7.18 | 3.62E-06 | 7.67E-05 | ||
RASSF2 | 9770 | −6.25 | 1.06E-05 | 1.54E-04 | TENT5C | 54855 | −6.60 | 1.72E-07 | 1.13E-05 | ||
REPS2 | 9185 | −6.10 | 4.11E-05 | 3.94E-04 | KLF15 | 28999 | −6.56 | 1.05E-08 | 2.28E-06 |
Symbol | Gene ID | Relative Expression GFP+ Cells | Relative Expression GFP− Cells | HPO (Increased Inflammatory Response) | HPO (Abnormal Joint Morphology) | HPO (Arthritis) | Associated with Alphavirus Infection | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
↑/↓ | log2FC | p-Value | FDR (Adjusted p-Value) | ↑/↓ | log2FC | p-Value | FDR (Adjusted p-Value) | ||||||
ASPN | 54829 | ↓ | −4.43 | 3.20E-06 | 5.84E-05 | ↓ | −6.43 | 1.88E-08 | 3.15E-06 | + | + | ||
CA2 | 760 | ↑ | 8.94 | 4.12E-06 | 7.01E-05 | ↑ | 5.25 | 1.50E-04 | 1.01E-03 | + | |||
EZH2 | 2146 | ↑ | 6.19 | 3.47E-09 | 1.05E-06 | ↑ | 1.91 | 1.54E-05 | 1.97E-04 | + | |||
FOXJ1 | 2302 | ↑ | 12.71 | 5.26E-07 | 1.60E-05 | ↑ * | 2.82 | 8.07E-02 | 1.38E-01 | + | |||
GCH1 | 2643 | ↑ | 5.87 | 3.30E-07 | 1.14E-05 | ↑ | 4.44 | 1.54E-06 | 4.41E-05 | + | + | ||
GORAB | 92344 | ↑ | 3.15 | 2.06E-07 | 8.34E-06 | ↑ | 0.68 | 6.65E-03 | 1.84E-02 | + | + | ||
HLA-B | 3106 | ↑ | 2.74 | 3.25E-07 | 1.13E-05 | ↑ | 3.22 | 6.46E-08 | 6.51E-06 | + | + | + | [27] |
IFIH1 | 64135 | ↑ | 7.32 | 7.49E-10 | 8.32E-07 | ↑ | 5.45 | 4.25E-09 | 1.28E-06 | + | + | + | [28] |
IL6 | 3569 | ↑ | 6.97 | 8.40E-08 | 4.70E-06 | ↑ | 6.35 | 1.21E-07 | 9.16E-06 | + | + | + | [29] |
IL7R | 3575 | ↑ | 14.93 | 4.90E-09 | 1.15E-06 | ↑ | 13.45 | 1.02E-08 | 2.26E-06 | + | [30] | ||
KDM6A | 7403 | ↑ | 3.62 | 5.06E-08 | 3.39E-06 | ↑ | 1.11 | 2.44E-04 | 1.43E-03 | + | + | ||
MAGI2 | 9863 | ↑ | 3.63 | 3.81E-07 | 1.27E-05 | ↓ | −1.45 | 1.82E-04 | 1.15E-03 | + | |||
MMP1 | 4312 | ↑ | 11.49 | 1.15E-08 | 1.76E-06 | ↑ | 12.78 | 1.41E-09 | 9.30E-07 | + | [31] | ||
MPDU1 | 9526 | ↑ | 4.17 | 4.96E-07 | 1.53E-05 | ↑ | 1.45 | 6.07E-04 | 2.84E-03 | + | |||
MSX1 | 4487 | ↑ | 5.32 | 9.80E-08 | 5.16E-06 | ↑ | 1.30 | 1.77E-03 | 6.50E-03 | + | |||
NFKB1 | 4790 | ↑ | 3.85 | 1.11E-07 | 5.67E-06 | ↑ | 1.03 | 1.21E-03 | 4.87E-03 | + | [32] | ||
NFKB2 | 4791 | ↑ | 4.52 | 1.71E-08 | 2.12E-06 | ↑ | 1.74 | 1.58E-05 | 2.02E-04 | + | [33] | ||
PNP | 4860 | ↑ | 4.03 | 1.11E-08 | 1.74E-06 | ↑ | 2.89 | 8.03E-08 | 7.25E-06 | + | |||
PRG4 | 10216 | ↓ | −3.35 | 5.25E-07 | 1.60E-05 | ↓ | −3.73 | 4.23E-08 | 5.20E-06 | + | + | + | |
RELB | 5971 | ↑ | 3.29 | 2.54E-07 | 9.68E-06 | ↑ | 2.66 | 4.54E-07 | 1.95E-05 | + | [34] | ||
RIPK1 | 8737 | ↑ | 4.37 | 2.16E-08 | 2.35E-06 | ↑ | 0.63 | 1.30E-02 | 3.16E-02 | + | [35] | ||
SALL4 | 57167 | ↑ | 10.92 | 1.65E-07 | 7.41E-06 | ↑ * | 2.42 | 4.60E-02 | 8.75E-02 | + | |||
SAMD9 | 54809 | ↑ | 3.82 | 2.46E-08 | 2.38E-06 | ↑ | 4.60 | 4.49E-09 | 1.28E-06 | + | |||
SERPINA1 | 5265 | ↑ | 5.27 | 1.40E-07 | 6.67E-06 | ↑ | 5.80 | 3.71E-08 | 4.85E-06 | + | |||
SLC39A8 | 64116 | ↑ | 4.41 | 2.31E-08 | 2.36E-06 | ↑ | 2.03 | 4.82E-06 | 9.23E-05 | + | |||
SLC40A1 | 30061 | ↓ | −4.95 | 2.11E-05 | 2.20E-04 | ↓ | −6.02 | 1.79E-07 | 1.16E-05 | + | + | ||
TAP1 | 6890 | ↑ | 3.26 | 4.03E-07 | 1.30E-05 | ↑ | 3.90 | 5.94E-08 | 6.19E-06 | + | [14] | ||
TNFAIP3 | 7128 | ↑ | 6.23 | 1.35E-09 | 8.33E-07 | ↑ | 5.30 | 3.22E-09 | 1.25E-06 | + | + | [36] | |
TNXB | 7148 | ↓ | −1.77 | 2.22E-02 | 4.88E-02 | ↓ | −4.71 | 1.28E-05 | 1.75E-04 | + | |||
VWF | 7450 | ↑ | 9.97 | 4.30E-08 | 3.17E-06 | ↑ | 2.10 | 1.45E-02 | 3.45E-02 | + | |||
WRAP53 | 55135 | ↑ | 5.13 | 1.72E-07 | 7.56E-06 | ↑ * | 0.68 | 5.37E-02 | 9.94E-02 | + |
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Lim, E.X.Y.; Webster, J.A.; Rudd, P.A.; Herrero, L.J. Pathways Activated by Infected and Bystander Chondrocytes in Response to Ross River Virus Infection. Viruses 2023, 15, 136. https://doi.org/10.3390/v15010136
Lim EXY, Webster JA, Rudd PA, Herrero LJ. Pathways Activated by Infected and Bystander Chondrocytes in Response to Ross River Virus Infection. Viruses. 2023; 15(1):136. https://doi.org/10.3390/v15010136
Chicago/Turabian StyleLim, Elisa X. Y., Julie A. Webster, Penny A. Rudd, and Lara J. Herrero. 2023. "Pathways Activated by Infected and Bystander Chondrocytes in Response to Ross River Virus Infection" Viruses 15, no. 1: 136. https://doi.org/10.3390/v15010136
APA StyleLim, E. X. Y., Webster, J. A., Rudd, P. A., & Herrero, L. J. (2023). Pathways Activated by Infected and Bystander Chondrocytes in Response to Ross River Virus Infection. Viruses, 15(1), 136. https://doi.org/10.3390/v15010136