TABLE 1.
List of genes in which induction by CCCP is PRC-dependent
| Gene symbol | Gene name | Control shRNA +/− CCCPa |
PRC shRNA#1 +/− CCCPb |
Control/sh1e | ||
|---|---|---|---|---|---|---|
| -Fold inductionc,d | Adjusted p value | -Fold inductionc,d | Adjusted p value | |||
| Inflammation/stress | ||||||
| SPRR2D | Small proline-rich protein 2D | 43.3 (1206.6) | 1.36E-15 | 1.6 (34.2) | 6.80E-03 | 27.1 (35.3) |
| IL8 | Interleukin 8 | 6.5 (2.7) | 2.65E-09 | −2.0 (0.8) | 1.32E-03 | 13.0 (3.4) |
| SPRR2F | Small proline-rich protein 2F | 9.0 (890.7) | 3.10E-15 | 1.1 (17.8) | 5.83E-01 | 9.0 (50.0) |
| IL1A | Interleukin 1α | 5.7 (170.0) | 2.30E-13 | 1.1 (9.5) | 4.62E-01 | 5.7 (17.9) |
| CCL20 | Chemokine (C-C motif) ligand 20 | 10.0 (29.1) | 5.80E-14 | 2.9 (5.6) | 4.57E-08 | 3.5 (5.2) |
| CHRNA9 | Cholinergic receptor, nicotinic, α9 | 3.5 (41.6) | 4.95E-09 | 1.4 (3.3) | 1.46E-02 | 3.5 (12.6) |
| PTGS2 | Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) | 3.1 | 1.88E-12 | 1.1 | 4.87E-01 | 3.2 |
| LCN2 | Lipocalin 2 | 3.1 (9.5) | 2.09E-06 | 1.2 (4.6) | 5.15E-01 | 3.1 (2.1) |
| PHLDA1 | Pleckstrin homology-like domain, family A, member 1 | 3.0 | 4.67E-03 | 3.0 | ||
| ESM1 | Endothelial cell-specific molecule 1 | 2.9 (23.1) | 4.01E-04 | 1.2 (5.3) | 6.03E-01 | 2.9 (4.4) |
| NFKBIZ | Nuclear factor of κ light polypeptide gene enhancer in B-cells inhibitor, ζ | 2.4 | 9.34E-06 | 1.1 | 7.08E-01 | 2.4 |
| ERRFI1 | ERBB receptor feedback inhibitor 1 | 2.4 (4.1) | 6.95E-06 | −1.0 (1.2) | 9.25E-01 | 2.4 (3.4) |
| IL13RA2 | Interleukin 13 receptor, α2 | 2.3 | 9.94E-11 | 2.3 | ||
| GDF15 | Growth differentiation factor 15 | 15.5 | 5.67E-14 | 7.4 | 6.53E-11 | 2.1 |
| DDIT4 | DNA damage-inducible transcript 4 | 8.0 | 2.01E-09 | 4.0 | 1.51E-06 | 2.0 |
| Signaling/proliferation | ||||||
| DUSP5 | Dual specificity phosphatase 5 | 5.9 | 3.36E-10 | 5.9 | ||
| RND3 | Rho family GTPase 3 | 3.5 | 8.46E-06 | 1.6 | 6.11E-02 | 3.5 |
| GNG11 | Guanine nucleotide-binding protein (G protein), γ 11 | 3.0 (5.0) | 5.08E-03 | 2.0 (2.5) | 9.37E-02 | 3.0 (2.0) |
| BMP6 | Bone morphogenetic protein 6 | 2.7 (2.9) | 1.72E-07 | −1.1 (0.8) | 6.80E-01 | 2.7 (3.6) |
| ZFP36L1 | Zinc finger protein 36, C3H type-like 1 | 2.4 | 2.07E-04 | 2.5 | ||
| OSCAR | Osteoclast-associated, immunoglobulin-like receptor | 2.3 | 2.57E-08 | 1.1 | 4.02E-01 | 2.3 |
| FBXL13 | F-box and leucine-rich repeat protein 13 | 3.6 | 6.31E-12 | 1.6 | 3.69E-05 | 2.3 |
| VIP | Vasoactive intestinal peptide | 2.2 | 2.73E-07 | 1.1 | 6.08E-01 | 2.3 |
| MYCT1 | Myc target 1 | 2.2 | 1.61E-07 | 2.2 | ||
| SUNC1 | Sad1 and UNC84 domain-containing 1 | 3.6 | 1.48E-05 | 1.8 | 2.50E-02 | 2.0 |
| ATF4 | Activating transcription factor 4 (tax-responsive enhancer element B67) | 4.1 | 5.73E-08 | 2.1 | 4.10E-04 | 2.0 |
| NAD/glucose metabolism | ||||||
| OLAH | Oleoyl-ACP hydrolase | 4.9 | 1.31E-12 | 1.7 | 5.00E-05 | 2.9 |
| NAMPT | Nicotinamide phosphoribosyltransferase | 2.6 | 3.03E-08 | 1.7 | 2.52E-04 | 2.6 |
| GK | Glycerol kinase | 2.4 | 1.15E-07 | 1.2 | 1.91E-01 | 2.4 |
| HK2 | Hexokinase 2 | 3.7 | 6.15E-10 | 1.9 | 2.43E-05 | 2.0 |
| Cell structure | ||||||
| CLDN1 | Claudin 1 | 3.5 | 1.35E-07 | 1.4 | 4.74E-02 | 3.5 |
| KRT33B | Keratin 33B | 2.5 | 1.30E-08 | 2.5 | ||
| TMEM154 | Transmembrane protein 154 | 4.7 | 1.14E-09 | 2.0 | 1.60E-04 | 2.4 |
| LAMB3 | Laminin, β3 | 2.2 | 7.50E-05 | 2.2 | ||
| KRT34 | Keratin 34 | 4.9 | 1.10E-08 | 2.4 | 6.03E-05 | 2.0 |
| Other | ||||||
| ST6GALNAC3 | ST6 (α-N-acetyl-neuraminyl-2,3-β-galactosyl-1,3)-N-acetylgalactosaminide α-2,6-sialyltransferase 3 | 3.3 (6.0) | 4.88E-11 | 1.0 (0.9) | 9.40E-01 | 3.3 (6.7) |
| SPINK1 | Serine peptidase inhibitor, Kazal type 1 | 7.1 | 8.94E-09 | 2.4 | 5.15E-04 | 3.0 |
| AADAC | Arylacetamide deacetylase (esterase) | 2.8 (13.3) | 1.65E-08 | 1.1 (4.7) | 4.30E-01 | 2.9 (2.8) |
| TM6SF1 | Transmembrane 6 superfamily member 1 | 2.7 | 1.36E-11 | 1.2 | 2.54E-02 | 2.3 |
| CT45A5 | Cancer/testis antigen family 45, member A5 | 2.2 | 1.24E-07 | 1.2 | 8.25E-02 | 2.3 |
| C12orf39 | Chromosome 12, open reading frame 39 | 2.2 | 2.65E-09 | 1.2 | 5.77E-02 | 2.2 |
| UBR4 | Ubiquitin-protein ligase E3 component n-recognin 4 | 2.1 | 1.29E-02 | 2.1 | ||
| DEFB103B | Defensin, β 103B | 2.0 | 3.93E-03 | 2.0 | ||
| ALOX5AP | Arachidonate 5-lipoxygenase-activating protein | 2.0 | 1.33E-03 | 2.0 | ||
| EPHB1 | EPH receptor B1 | 2.0 | 9.14E-03 | 1.5 | 1.49E-01 | 2.0 |
| Tfam | Mitochondrial transcription factor A | (1.7) | (1.2) | (1.4) | ||
a Total RNA was isolated from CCCP-treated and untreated U2OS lentiviral transductants expressing the control shRNA. Fold induction values were derived by normalizing the expression of the indicated gene in CCCP-treated cells to that in the untreated cells (+/−).
b Total RNA was isolated from CCCP-treated and untreated U2OS lentiviral transductants expressing the PRC shRNA-1. Fold induction values were derived by normalizing the expression of the indicated gene in CCCP-treated cells to that in the untreated cells (+/−).
c Numbers are derived from microarray analysis using a Illumina HT12 gene chip.
d Numbers in parentheses are values derived from quantitative real time PCR.
e Numbers represent the ratio of the fold induction of the listed gene in the control shRNA transductant to that in the PRC shRNA-1 transductant derived from either microarray analysis or quantitative real time PCR (in parentheses).