Table 1 Selected regulated genes in NHEK and SCC12B2 in response to UVB irradiation

From: Genome-wide comparison of human keratinocyte and squamous cell carcinoma responses to UVB irradiation: implications for skin and epithelial cancer

    Normal keratinocytes (NHEK) SCC12B2
Symbol Name Accession Nb.    0.5 h 3 h 6 h 12 h 24 h    6 h 12 h
1 Cell cycle (+/−)/oncogene/tumor suppressor
 (+) CCNA1 Cyclin A1 U66838   1.2 0.8 1.1 2.1 7.4    1.0 1.0
 (+) CCNB1 Cyclin B1 M25753   −1.1 −1.1 −1.4 −3.7 −4.3    −1.1 −1.7
 (+) CCNB2 Cyclin B2 AL060146   −1.6 −1.1 −1.3 −4.0 −4.3    −1.3 −1.6
 (+) CCNE1 Cyclin E1 M74093   −6.0 −1.7 −3.2 −7.2 −0.6    −1.7 −3.4
 (+) ODC1 Ornithine Decarboxylase 1 M33764   1.4 3.2 1.5 1.0 3.5    1.6 1.4
 (+) HRAS Ha-ras Oncogene J00277   6.9 1.3 2.3 1.7 2.6    −1.3 −1.7
 *(+) MDM2 MDM2 M92424    0.9 0.9 1.5 1.9 1.1    1.0 1.0
 (+/−) SFN 14-3-3 σ (Stratifin) X57348   1.4 1.5 2.2 2.0 1.1    −1.1 −1.1
 (+) FYN FYN oncogene M14333   −1.1 −1.3 −1.4 −4.9 −10.6    −1.8 −1.8
 (+) ABL1 c-abl oncogene X16416   9.9 −1.4 −2.8 −3.8 −8.1    −2.2 −3.0
 (+) ERBB3 c-erb-b2 Oncogene 3 M34309   −1.8 −1.5 −3.2 −3.4 −1.1    −1.6 −1.6
 (+) BCAR3 Breast Cancer Anti-Estrogen Resistance 3 U92715   −1.0 −2.4 −3.1 −12.1 −3.9    −2.6 −5.8
 (+) MK167 Antigen Ki-67 X65S50   −1.0 −1.3 −1.2 −2.9 −5.2    −2.3 −2.2
 (+) CSF2 CSF2 M13207    −1.1 −1.1 −1.1 −1.1 −1.1   4.6 4.7
 (−) PPP1R15A GADD34 U63981   9.8 1.0 1.4 2.2 5.1    −1.3 −1.1
 *(−) CDKN1A P21 CIP1 U03106    1.6 1.6 1.3 1.4 5.0    1.1 −1.2
 (−) CDKN1C P57 Kip2 064137   1.6 2.0 2.2 1.3 3.5   3.0 3.3
 (−) CDKN1B P27 Kip1 A1304854   −1.7 −3.0 −1.4 −1.3 −3.4    1.0 1.0
 (−) WEE1 WEE1 X62048   −1.6 −6.7 −14.9 −18.9 −4.5   −8.6 −0.8
 *(−) TP53 P53 tumor suppressor X02469    0.7 0.9 0.8 1.4 0.8    1.0 1.0
 (−) NF2 Neurofibromatosis 2 tumor suppressor AF122827   1.0 1.8 6.9 10.0 1.4   3.9 2.7
 (−) FUS1 FUS1 tumor suppressor AF055479    −1.1 −2.5 −2.7 −3.2 −1.7   −3.9 −3.6
 (−) FAT2 FAT2 tumor suppressor ABO11535   −1.3 −1.6 −3.6 −3.7 −7.9     
2 Apoptosis (+/−)
 (+) CRADD RAIDD U79115   0.7 1.7 1.5 3.1 2.4    1.1 1.3
 (+) TSSC3 Tumor suppressing STF 3 AF035444   1.5 4.1 3.4 4.1 4.4    1.5 1.4
 (+) PMAIP1 APR (NOXA) 090070   2.0 7.0 14.7 16.1 13.0   2.8 3.3
 (+) TNF TNFα X02910    1.5 1.4 1.8 2.2 1.4   10.5 10.4
 (−) BCL2 BCL-2 H14745   2.0 1.0 1.0 3.6 1.0    1.0 1.0
 (−) API5L1 Antiapoptosis 5-Like 1 Y15906   1.5 4.0 3.2 1.1 2.4    −1.1 −2.5
 (−) IER3 Radiation-inducible IER3 SB1914   1.5 5.2 5.1 5.4 4.5    1.4 1.2
 (−) TNFAIP3 TNFα-Induced Protein 3 M59465   1.0 0.7 1.2 2.4 6.8   −3.7 −4.3
 (−) HSPA2 HSP70 L26336   1.8 1.0 2.1 2.2 1.9    1.0 1.0
 (−) HSPCB HSP90 W28616   1.2 1.2 2.1 2.1 0.6   2.3 2.8
 (−) MCL1 Myeloid cell leukemia 1 L08246    0.8 0.4 0.4 0.4 1.6   −7.4 −8.9
 (−) BAG5 BCL2-Associated Athanogene 5 AB020680    1.0 0.6 0.4 0.5 1.1   −3.5 −5.7
3 DNA repair
GADD45A GADD45A MG0974   1.5 3.6 4.7 7.0 9.2   2.0 2.4
GADD45B GADD45B AF078077   1.6 2.3 2.2 2.8 4.8    1.2 1.5
ERCC1 ERCC1 Ml 31 94   1.2 2.0 1.4 1.1 3.9    1.3 1.3
ERCC2 ERCC2 AA079018   1.1 1.6 2.4 2.2 1.4    1.3 1.9
BTG1 B-cell Translocation Gene 1 X61123   1.1 1.3 1.7 2.2 3.4    1.1 −1.8
TOB1 Transducer of ErbB-2. 1 D38305   8.9 1.5 2.0 2.0 2.5   2.9 3.2
4 Oxydative stress/ROS metabolism (+/−)
 (+) CYBA Superoxide-Generating NADPH Oxidase M21186   1.3 1.0 1.7 2.5 2.8    −1.1 −1.3
 (−) MT1G Matallothionein 1G J03910   1.0 3.2 3.4 2.0 3.8    1.6 1.3
 (−) MT2A Matallothionein 2A A1547258    2.3 0.7 0.8 1.9 0.6   −4.4 −3.6
 (−) PRDX3 Peroxiredoxin 3 D49396    0.7 0.9 0.8 0.9 0.7   2.2 2.4
5 Extra cellular matrix/protease (+/−)
 *(+) MMP1 Collagenase M13509    0.8 1.4 1.3 1.8 3.3    1.5 1.8
 (+) MMP10 Stromelysin 2 X07820   1.8 2.5 2.2 2.1 4.5    1.0 1.8
 (+) PRSS4 Trypsin 4 X71345   1.4 2.2 1.4 1.9 7.0    1.0 1.0
6 Growth factor/chemokine/cytokine/inflammation (+/−)
 (+) IL8 IL-8 (CXC) M28130   2.0 10.6 36.8 48.1 71.7   12.5 11.9
 (+) IL6 IL-6 X04430   1.0 1.3 4.1 3.7 1 9   4.3 4.0
 (+) IL1B IL-1B X04500   1.0 1.3 1.4 1.6 1.9   2.9 2.3
 (+) GRO1 Small Inducible Cytokine B1 (MGSA) (CXC) X54489   2.2 1.7 2.2 3.1 3.2   2.9 2.0
 (+) GRO2 Small Inducible Cytokine B2 (CXC) M36820   1.4 3.9 5.8 6.0 5.1   11.6 8.9
 (+) GRO3 Small Inducible Cytokine B3 (CXC) M36821   2.0 2.4 6.8 7.9 5.2   10.3 8.9
 (+) PPBP Small Inducible Cytokine B7 (NAP-2) (CXC) M54995   0.3 1.2 2.2 2.6 2.3    1.0 1.0
 (+) SCYA20 Small Inducible Cytokine A20 (CC) U64197   1.9 3.7 11.5 21.5 17.0   3.5 4.0
 (+) PTGS2 Cyclooxygenase (COX-2) U04636   6.8 2.8 4.8 13.5 24.7   5.5 7.8
 (+) HB-EGF HB-EGF-Like M60278   1.7 1.5 3.2 4.6 9.9    1.3 7.9
 (+) S100A9 Calgranulin B W72424   1.1 1.5 1.6 2.2 6.0    1.3 1.7
 INSL4 Insulin-like 4 (IGF family) L34838   1.0 12.0 13.4 20.2 26.1    −1.1 1.9
 CTGF IGFBP8 X78947   1.3 3.8 5.6 6.3 1.3    1.1 1.1
 CYR61 IGFBP10 Y11307   1.3 2.8 3.4 2.4 3.6   −9.8 −6.5
9 Development/differentiation (+/−)
 (+) TP63 p63(ΔNp63) Y16961   −0.9 −1.0 −2.0 −3.7 −16.0   −2.4 −4.3
 (+) PUM1 Pumilio 1 D43951   −1.6 −3.2 −6.6 −23.7 −2.4   −6.0 −10.3
 (+) PUM2 Pumilio 2 D87078   −1.3 −2.1 −3.1 −5.7 −2.8    −1.8 −2.5
11 Transcription (+/−)/replication
 (+) FOS FOS V01512   5.4 4.7 4.7 2.1 0.6   16.1 27.6
 (+) JUN JUN J04111   2.9 7.9 5.7 2.9 1.1    1.2 −1.1
 (+) JUNB JUNB M29039   2.0 4.5 3.6 4.0 3.4    1.3 −1.4
 (+) JUND JUND X56681   1.3 2.2 3.7 3.0 2.6   3.7 2.0
 (+) TLS/CHOP GADD153 AA633221   2.5 3.8 1.6 0.2 1.1    1.6 1.0
 (+) MYC MYC V00568   −1.5 −3.5 −3.2 −4.9 −4.2   −6.9 −5.6
 (+) E2F3 E2F3 D38550   −1.4 −2.0 −3.6 −3.5 −2.9   −3.3 −3.3
 (+) E2F5 E2F5 U31556   −1.2 −1.6 −1.3 −3.2 −6.3    −1.2 −1.1
 *(+) RELA NFkB (p65 subunit) L19067    1.3 1.4 1.6 1.3 1.4    −1.3 −1.4
 (−) TSC22 TGF β-Stimulated Protein AJ222700   1.2 2.3 4.0 3.1 1.6    −1.1 −1.5
 (−) DRAP1 DR1-Associated Protein 1 U41843   1.3 1.7 4.2 0.7 5.3   2.6 3.7
 (−) ATF3 ATF3 L19871   1.3 3.8 4.7 10.8 17.1   2.4 5.6
 (−) ATF4 ATF4 AL022312   1.2 1.7 2.1 2.2 3.1    1.2 1.0
 (−) SAP18 Sin3-associated Polypeptide W27641   1.8 1.5 2.1 2.1 0.8    1.3 1.6
 (−) ID2 Inhibitor of DNA Binding 2 D13891   1.9 6.0 3.8 2.1 2.1   14.6 22.0
12 Histone/chromatin
 H1FX Histone H1X D64142   0.8 1.4 3.5 3.5 4.5    1.0 −1.1
 H2AFA Histone H2A A AI039144   1.1 4.6 9.4 13.4 12.4    1.0 1.0
 H2AFG Histone H2A G ZB0776   2.4 1.8 1.8 4.3 6.3    3.9 1.3
 H2AFO Histone H2A O L19779   1.5 3.2 2.1 3.0 18.0    1.9 2.0
 H2AFX Histone H2A X XI4850   1.0 2.5 0.7 1.3 3.2    1.2 1.0
 H2BFA Histone H2B A AJ223352    1.1 0.9 1.2 1.1 2.4   3.0 2.9
 H2BFC Histone H2B C AL009179   1.0 2.2 3.2 6.5 5.5    1.0 1.0
 H2BFG Histone H2B G Z80779   1.6 5.3 5.3 7.1 12.1    1.6 2.1
 H2BFQ Histone H2B Q X57985          1.1 1.3
 MORF Histone Acetyltransferase AB002381   −0.9 −1.4 −1.4 −5.4 −6.7    −2.6 −1.7
 BAZ1A Br Domain adj. to ZF1A (hist acetyltransferase) AL050089   −1.3 −1.9 −2.0 −3.9 −5.1    −1.1 −1.6
 BAZ1B Br Domain adj. to ZF1B (hist acetyltransferase) AF072810   −0.8 −1.1 −5.5 −3.4 −2.5    −1.7 −2.8
  1. All genes that changed expression and passed the filtering threshold (see Figure 4) were classified into 14 functional categories as listed in Figure 6 and given in supplemental data in Tables 2 and 3. The list in Table 1 was selected from 9 categories of these lists (not including categories 7, 8, 10, 13 and 14) and illustrates the major changes in gene expression. Numbers show fold change of expression. Symbols ‘+’ or ‘−’ stand for positive or negative functional regulators, and ‘↑’, or ‘↓’ for UVB-induced up- or downregulation, respectively. The symbol ‘*’ stands for six genes that are at the margin of the filtering threshold, but discussed in the Results and discussion section. Online Supplemental Data: Table 2 and 3 containing full lists of up- and downregulated genes are available at http://www.weizmann.ac.il/~ligivol/