Table 3.
Common genes, responding to irradiation in U87 and HEL cell lines and U87 xenografts
Access. no. | Group and name | U87-C
|
HEL-C
|
U87-X
|
Comments | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 Gy | 3 Gy | 10 Gy | 1 Gy | 3 Gy | 10 Gy | 1 Gy | 3 Gy | 10 Gy | |||
1. Homeostasis/self defense | |||||||||||
AA464246 | HLA-C | 1.28 | 1.20 | 0.51 | 0.98 | 0.91 | 2.65 | 1.71 | 1.74 | 1.53 | ↓ D |
AA434117 | HLA-B-assot. G9a | 0.89 | 0.57 | 0.51 | 0.72 | 0.78 | 0.61 | $ | |||
AA670408 | β2-Microglobulin | 1.02 | 2.14 | 0.53 | 1.43 | 1.82 | 5.78 | 1.80 | 1.93 | 1.24 | $ * D |
AA778663 | 4-1BB ligand | 1.67 | 1.38 | 0.35 | 4.43 | 10.70 | 12.1 | * A | |||
AA136271 | CD58 (LFA3) | 1.06 | 0.89 | 0.20 | 0.51 | 0.90 | 0.59 | $ | |||
R77293 | ICAM1 | 1.22 | 0.99 | 0.42 | 2.00 | 1.47 | 2.46 | ↓ B | |||
AA130584 | CEACAM5 | 1.77 | 1.28 | 1.88 | 3.22 | 18.63 | 3.64 | * A | |||
N51018 | Biglycan | 1.33 | 1.22 | 1.64 | 0.47 | 0.74 | 1.69 | * E | |||
AA399674 | SPRR2C | 0.85 | 0.89 | 0.43 | 0.82 | 0.84 | 1.79 | ↓ | |||
T49657 | K+ channel TASK | 2.09 | 1.61 | 2.36 | 1.60 | 1.89 | 1.68 | 4.62 | 3.90 | 5.36 | $ * A |
AA069770 | K+ channel KCNB1 | 0.56 | 1.53 | 1.59 | 10.07 | 7.12 | 6.79 | ↓ C | |||
H14808 | Na+/K+ ATPase β2 | 1.46 | 0.93 | 2.11 | 3.07 | 2.43 | 6.45 | * A | |||
H24316 | Aquaporin | 1.03 | 1.63 | 1.44 | 24.56 | 12.25 | 5.84 | * C | |||
H57136 | PLM Cl− channel | 1.23 | 1.80 | 1.60 | 0.87 | 0.84 | 0.53 | 2.72 | 4.17 | 4.44 | ↓ * C |
AA402891 | Transporter ENT2 | 1.08 | 1.19 | 1.60 | 6.07 | 36.08 | 2.61 | * C | |||
AA191488 | Cu2+ uptake protein CTR1 | 1.72 | 1.00 | 2.46 | 2.42 | 3.20 | 4.39 | 1.05 | 1.27 | 1.80 | $ * E |
AA490459 | Transcobalamin II | 0.76 | 0.61 | 0.55 | 0.47 | 0.83 | 0.31 | $ | |||
H72723 | MT1B | 1.12 | 0.61 | 0.57 | 2.04 | 2.93 | 5.46 | ↓ D | |||
H23187 | Carbonic anhydrase II | 0.84 | 1.10 | 0.59 | 4.41 | 2.50 | 2.26 | ↓B | |||
2. Cell–cell communications/signaling | |||||||||||
R56211 | PDGFRβ | 1.02 | 1.12 | 1.87 | 0.92 | 1.37 | 1.85 | $ | |||
AA486393 | IL-10 receptor β | 1.72 | 1.19 | 1.60 | 6.12 | 3.84 | 3.78 | * A | |||
AA485226 | Vitamin D receptor | 2.31 | 0.69 | 0.64 | 6.54 | 9.35 | 3.34 | * A | |||
H54023 | MIR-10 (LILRB2) | 1.71 | 1.00 | 1.35 | 0.48 | 0.63 | 1.98 | ↓ E | |||
AA400973 | Lipocalin 2 | 1.16 | 0.56 | 0.49 | 0.68 | 0.62 | 0.53 | $ | |||
AA485922 | Copine I | 1.65 | 1.06 | 1.08 | 3.84 | 3.74 | 4.24 | * A | |||
R73545 | Flotillin 2 | 1.18 | 0.94 | 0.61 | 1.11 | 1.17 | 1.89 | ↓ | |||
N20203 | BMP receptor II | 0.60 | 0.79 | 0.97 | 5.54 | 2.88 | 2.00 | ↓ B | |||
AA450062 | BMP, placental | 1.45 | 1.49 | 1.60 | 1.35 | 0.82 | 1.62 | $ | |||
AA489383 | BMP 2 | 1.71 | 1.61 | 1.80 | 0.61 | 2.14 | 1.61 | 1.77 | 1.69 | 1.06 | $ * F |
T55558 | CSF 1 | 0.92 | 1.29 | 0.56 | 0.83 | 0.61 | 0.52 | $ | |||
AA486072 | RANTES | 1.14 | 0.67 | 0.42 | 4.92 | 2.79 | 3.74 | ↓ A | |||
R43320 | G-protein GNAO1 | 1.79 | 1.05 | 1.83 | 0.61 | 0.82 | 1.65 | * E | |||
R56046 | G-protein GNAZ | 0.74 | 0.87 | 0.49 | 0.85 | 0.93 | 1.77 | 0.73 | 0.67 | 1.75 | ↓ E |
AA458785 | Guanylate cyclase β1 | 1.74 | 1.45 | 1.86 | 3.89 | 3.75 | 4.07 | * A | |||
R37953 | Adenylyl cyclase associated protein | 1.31 | 1.23 | 0.59 | 1.04 | 1.04 | 2.60 | ↓ | |||
N28497 | PP2A (PPP2R1B) | 1.16 | 1.35 | 2.00 | 0.78 | 0.77 | 0.33 | 7.81 | 6.84 | 5.31 | ↓ * B |
H15718 | Protein kinase AXL | 0.76 | 0.59 | 0.80 | 0.48 | 0.57 | 0.52 | $ | |||
AA453789 | Protein kinase 7 | 0.94 | 1.19 | 0.60 | 0.69 | 1.04 | 0.53 | $ | |||
R59598 | Protein kinase Syk | 0.56 | 0.64 | 0.48 | 0.54 | 0.61 | 0.76 | $ | |||
R80779 | Protein kinase MLK-3 | 1.15 | 1.50 | 1.66 | 10.99 | 6.73 | 4.43 | * B | |||
AA890663 | Protein kinase PAK1 | 0.64 | 1.95 | 1.80 | 0.90 | 1.06 | 0.56 | ↓ | |||
N52958 | SLP-76 | 1.38 | 2.21 | 1.72 | 1.07 | 1.32 | 1.80 | * | |||
H73724 | CDK6 | 1.76 | 1.53 | 2.08 | 0.47 | 0.81 | 2.01 | *E | |||
AA464731 | Calgizzarin | 1.01 | 0.96 | 0.33 | 1.06 | 1.07 | 2.35 | ↓ | |||
N63940 | Acetylcholinesterase | 0.83 | 0.61 | 0.87 | 0.65 | 0.62 | 0.84 | $ | |||
3. Cytoskeleton/motility | |||||||||||
AA703141 | Protein 4.1 (EBP41) | 0.60 | 0.63 | 0.64 | 0.61 | 0.81 | 1.34 | $ | |||
AA877166 | Myosin light chain 2 | 0.83 | 1.01 | 0.57 | 0.83 | 0.86 | 0.49 | $ | |||
AA504625 | Kinesin heavy chain | 0.62 | 1.34 | 0.59 | 4.42 | 12.29 | 0.25 | * C | |||
AA868929 | Troponin T1 | 1.01 | 0.53 | 0.27 | 0.18 | 0.12 | 1.98 | * | |||
R44290 | β-Actin (ACTB) | 1.13 | 0.60 | 0.55 | 1.32 | 1.47 | 3.48 | 1.79 | 1.93 | 1.43 | ↓ D |
AA634006 | Actin α-2 (ACTSA) | 1.51 | 0.80 | 0.51 | 1.01 | 1.30 | 3.16 | 1.55 | 1.55 | 1.52 | ↓ D |
AA629189 | Keratin 4 (KRT4) | 1.08 | 1.08 | 1.62 | 1.02 | 1.32 | 0.39 | ↓ | |||
4. RNA synthesis/modifications | |||||||||||
H99588 | LAF4 | 3.15 | 1.23 | 2.62 | 3.62 | 2.70 | 4.83 | 0.59 | 0.82 | 1.65 | $ * E |
N47099 | SMAD2 | 1.12 | 1.64 | 2.04 | 0.94 | 1.90 | 0.55 | $ | |||
AA478268 | CTBP 1 | 1.17 | 1.63 | 1.44 | 3.99 | 5.34 | 2.77 | * B | |||
AA394127 | NF-AT3 | 1.24 | 0.96 | 0.36 | 1.15 | 0.90 | 2.19 | ↓ | |||
AA258001 | RELB | 1.02 | 1.10 | 0.59 | 5.12 | 7.57 | 2.33 | ↓ C | |||
AA253434 | Transcription factor HSF2 | 1.08 | 0.60 | 1.06 | 5.09 | 2.64 | 1.86 | ↓ C | |||
AA457155 | ZNF212 | 0.49 | 0.68 | 1.32 | 2.02 | 0.87 | 2.45 | ↓ | |||
R02346 | U1 snRNP 70 | 2.57 | 1.32 | 2.59 | 1.33 | 1.51 | 1.98 | 6.29 | 5.46 | 8.60 | $* A |
AA496879 | RNP S1 | 1.58 | 1.70 | 2.43 | 1.18 | 1.02 | 0.47 | 7.72 | 7.05 | 4.26 | $* B |
N26026 | Gemin 2 (SIP1) | 2.31 | 2.94 | 3.88 | 5.00 | 4.38 | 3.32 | * A | |||
AA126911 | hnRNP A1 | 0.99 | 0.57 | 0.39 | 1.65 | 1.81 | 4.53 | ↓ | |||
AA431440 | hnRNP-E2 | 0.81 | 0.64 | 0.61 | 0.83 | 1.09 | 2.01 | ↓ | |||
T60163 | RNase L | 1.13 | 1.09 | 1.64 | 6.84 | 8.45 | 3.32 | * B | |||
5. Protein synthesis/modifications | |||||||||||
R43973 | EF1γ | 2.23 | 1.22 | 0.54 | 1.69 | 1.30 | 3.83 | $ | |||
R54097 | elF-2b | 0.91 | 0.63 | 0.50 | 0.55 | 0.98 | 2.15 | ↓ | |||
AA873351 | RP L35a | 0.97 | 2.30 | 1.61 | 0.93 | 0.91 | 2.28 | 1.91 | 1.67 | 1.34 | $* D |
T69468 | RPS4Y | 0.51 | 1.01 | 0.89 | 1.95 | 1.87 | 3.26 | ↓ | |||
AA490011 | RPL38 | 1.43 | 0.92 | 0.22 | 0.99 | 1.40 | 2.97 | ↓ | |||
T67270 | RPL10 | 1.97 | 1.29 | 0.61 | 1.22 | 1.31 | 2.75 | ↓ | |||
AA464743 | RPL21 | 1.09 | 1.31 | 0.52 | 0.87 | 0.91 | 1.73 | ↓ | |||
AA680244 | RPL11 | 1.01 | 1.18 | 0.25 | 0.84 | 1.18 | 2.94 | ↓ | |||
W96450 | aa-tRNA synthetase FARSL | 1.10 | 1.67 | 1.46 | 1.97 | 1.84 | 1.36 | * F | |||
AA599158 | aa-tRNA synthetase EPRS | 0.97 | 0.89 | 0.56 | 2.20 | 1.84 | 1.31 | ↓ F | |||
AA664241 | α-NAC | 0.60 | 0.83 | 2.07 | 0.89 | 1.09 | 1.68 | $ | |||
AA424786 | Golgin-95 | 0.90 | 0.99 | 0.57 | 10.02 | 19.14 | 2.95 | ↓ C | |||
AA457114 | Protein B94 | 1.85 | 1.14 | 1.95 | 4.01 | 2.33 | 6.45 | * D | |||
AA504455 | LDLC | 1.71 | 1.92 | 1.62 | 2.43 | 1.88 | 1.50 | * F | |||
R78585 | Calumenin | 0.99 | 1.02 | 0.53 | 1.02 | 1.26 | 2.89 | 1.06 | 1.44 | 1.14 | ↓D |
T71316 | ADP-ribosylation factor 4 | 1.25 | 0.79 | 0.48 | 0.94 | 1.05 | 3.12 | ↓ | |||
AA455301 | Protein GPAA1 | 0.58 | 0.58 | 0.93 | 2.43 | 2.11 | 1.57 | ↓ B | |||
N78843 | CYP-33 (PPIE) | 1.79 | 1.47 | 1.69 | 8.57 | 5.27 | 3.85 | * C | |||
H98666 | PCOLN3 | 0.80 | 0.60 | 0.50 | 0.78 | 0.61 | 0.60 | $ | |||
AA430524 | ACE | 1.17 | 1.70 | 1.99 | 1.78 | 2.85 | 1.66 | * A | |||
AA410517 | Serpin PTI | 0.91 | 1.47 | 1.79 | 1.31 | 1.60 | 2.72 | $ | |||
W61361 | Serpin CAP2 | 1.24 | 1.76 | 1.27 | 6.67 | 8.93 | 3.52 | * C | |||
AA430512 | Serpin CAP3 | 1.22 | 1.53 | 1.69 | 6.45 | 5.37 | 4.20 | * B | |||
AA402874 | Protective protein | 1.15 | 0.76 | 0.55 | 1.20 | 1.21 | 1.42 | ↓ D | |||
6 & 8. Metabolism/energy/oxidative stress | |||||||||||
N33331 | PPARδ | 1.15 | 1.62 | 1.45 | 34.35 | 50.10 | 95.30 | * C | |||
AA465366 | Leukotriene A4 hydrolase | 1.69 | 2.28 | 0.85 | 4.58 | 7.54 | 3.17 | * C | |||
R55046 | MpV17 (peroxisome) | 0.75 | 0.60 | 0.57 | 1.30 | 1.69 | 2.18 | ↓ | |||
W49667 | Fatty acid desaturase | 1.08 | 0.43 | 1.08 | 4.36 | 4.38 | 3.79 | ↓ A | |||
W95082 | 11β-hydroxysteroid dehydrogenase | 1.07 | 0.80 | 0.45 | 0.45 | 0.82 | 0.44 | 16.25 | 5.88 | 3.48 | $ B |
T73294 | P450 reductase | 1.78 | 1.05 | 2.01 | 0.80 | 0.71 | 2.69 | * | |||
AA708298 | H+ ATP synthase | 1.20 | 1.02 | 0.49 | 1.11 | 1.62 | 5.38 | 1.85 | 1.46 | 1.30 | ↓D |
H61243 | Uncoupling protein 2 | 0.93 | 0.82 | 0.53 | 1.07 | 0.93 | 1.81 | ↓ | |||
W96179 | Glutamate-cysteine ligase | 2.67 | 2.03 | 3.18 | 6.69 | 4.97 | 4.54 | * A | |||
AA463458 | Glutathione synthetase | 0.94 | 0.73 | 0.32 | 1.73 | 0.94 | 1.43 | ↓ | |||
AA290738 | GSTM4 | 1.10 | 0.93 | 0.46 | 4.34 | 2.92 | 2.00 | ↓ B | |||
R52548 | SOD-1 | 0.92 | 0.84 | 0.60 | 6.58 | 3.01 | 2.12 | ↓ B | |||
R39463 | Aldolase C | 0.98 | 0.90 | 0.58 | 0.62 | 0.77 | 0.47 | $ | |||
H05914 | LDHA | 0.84 | 1.27 | 0.59 | 1.15 | 1.12 | 2.68 | ↓ | |||
AA629567 | HSP73 | 1.07 | 0.86 | 0.49 | 1.00 | 1.39 | 2.40 | ↓ | |||
7. DNA metabolism/chromatin structure | |||||||||||
H15112 | Uracil-DNA glycosylase 1 | 0.45 | 0.58 | 1.64 | 0.85 | 1.36 | 1.70 | $ | |||
N26769 | DNA glycosylase (MPG) | 0.89 | 0.94 | 0.55 | 5.88 | 3.06 | 1.70 | ↓B | |||
AA608557 | XPE1 (DDB1) | 1.61 | 1.16 | 1.98 | 0.68 | 0.77 | 1.76 | * E | |||
AA035095 | BCR protein 1 | 0.99 | 0.74 | 0.52 | 0.65 | 0.93 | 0.54 | $ | |||
AA460927 | Translin | 0.53 | 1.29 | 2.49 | 0.99 | 1.51 | 2.37 | $ | |||
AA442991 | Prothymosin α (PTMA) | 2.56 | 2.01 | 1.06 | 2.19 | 1.61 | 2.66 | $ | |||
AA456077 | Centromere protein p27 | 0.86 | 0.72 | 0.44 | 0.62 | 0.88 | 0.41 | $ | |||
R56871 | Chromatin assembly factor-I | 0.69 | 0.98 | 1.82 | 0.94 | 0.30 | 0.60 | ↓ | |||
9. Unclassified | |||||||||||
AA683321 | PAR-5 | 1.72 | 1.27 | 1.38 | 2.26 | 2.62 | 8.38 | 0.44 | 0.72 | 1.61 | ↓ $ E |
R06254 | Protein D54 | 1.62 | 0.92 | 1.68 | 1.26 | 1.29 | 1.87 | $ | |||
AA406064 | BPY1 | 1.78 | 1.86 | 2.12 | 1.68 | 2.57 | 1.02 | * D | |||
AA448289 | Protein D123 | 1.14 | 1.05 | 2.08 | 9.12 | 10.66 | 9.06 | * C | |||
N34095 | FEZ2 | 1.14 | 1.55 | 1.69 | 2.86 | 3.20 | 3.70 | * A | |||
R87497 | 2.19 gene | 1.85 | 2.70 | 1.71 | 4.32 | 3.50 | 5.08 | * A | |||
AA452826 | Purkinje cell protein 4 | 0.60 | 0.80 | 0.59 | 5.26 | 3.82 | 3.32 | ↓ D |
Genes that responded to irradiation in both U87 and HEL cell lines in vitro or U87 grown in cell culture (U87-C) or transplanted in xenografts (U87-X) are shown. Genes distributed according cell functions. Numbers are average ratios of significant up- or down-regulation for each dose tested at 5 h after irradiation. $, consistent up- or down-regulation in both U87 and HEL in vitro;
, consistent up- or down-regulation in both U87 in vitro and U87 xenografts; ⇅, opposite response in either U87/HEL or U87-C/U87-X cell types; A–F, cluster of expression in U87 xenografts (see Fig. 1).