Table 1.
Literature findings on cross-comparison of significantly mutated genes in recessive dystrophic epidermolysis bullosa (RDEB)-squamous cell carcinoma (SCC) and cutaneous SCC in the general population.
| Significantly Mutated Genes | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Reference | Disease Model (Sample Size) |
CASP8 | NOTCH1 | TP53 | CDKN2A | FAT1 | ARID2 | HRAS | KMT2B | ARHGEF6 | FAM114A2 | LRRC8A | PHF13 | SPTBN4 | NOTCH2 | SMARCA4 | EGFR | NF2 | NOTCH4 | PRDM9 | Other Genes |
| Cho R.J. et al. Sci. Transl. Med. 2018 (PMID: 30135250) [31] | RDEB SCCs (n = 31) |
38.7 | 54.8 | 45 | 32.2 | 22.5 | 12.9 | 12.9 | 19.3 | ||||||||||||
| Sans-DeSanNicolas L. et al. J. Invest. Dermatol. 2018 (PMID: 29291383) [30] | RDEB SCC1 (n = 1) |
+ | VAF 20% | VAF 15.9% | |||||||||||||||||
| RDEB SCC2 (n = 1) |
+ | + | + | + | + | VAF 36.47% | VAF 9.02% | ||||||||||||||
| Inman G.J. et al. Nat. Commun. 2018 (PMID: 30202019) [7] | non-EB SCCs (n = 40) |
75 | 70 | 45 | 22.5 | 50 | ATP1A1, CACNA1C, CLCN3, CRY1, FLNB, GLIS3, GRHL2, HERC6, LCLAT1, MAP3K9, MAPK1IP1L, PTEN, SF3B1, TMEM51, TRAPPC9, VSP41, WHSC1. | ||||||||||||||
| Li Y.Y. et al. Clin. Cancer. Res. 2015 (PMID: 25589618) [33] | metastatic SCCs (n = 29) |
N/P | 48 | 79 | 45 | N/P | N/P | N/P | N/P | N/P | N/P | N/P | 28 | 14 | 17 | N/P | |||||
| Pickering C.R. et al. Clin. Cancer. Res. 2014 (PMID: 25303977) [32] | aggressive UV-induced SCCs (n = 39) |
23.1 | 59 | 94.9 | 43.6 | 43.6 | 20.5 | 51.3 | AJUBA, BBS9, BF2D, COBLL1, DCLK1, DCLRE1A, FBX021, KMT2C, OPN3, PARD3, PEG10, RASA1, RBM46, SEC31A, SNX25, ZNF644. | ||||||||||||
[31]: Significantly mutated genes with a false discovery rate (FDR) q < 0.001 after analysis with MuSiC algorithm are indicated. Mutated genes are shown from the most (CASP8) to the least (KMT2B) significant. A different statistical analysis performed using MutSigCV algorithm identified only three genes (CDKN2A, CASP8, and TP53) as significantly mutated. [30]: The sign plus (+) indicates the genes mutated in two RDEB-SCCs, RDEB-SCC1 and RDEB-SCC2, with variant allele frequency (VAF) > 45%. The complete list of significantly mutated genes with VAF > 20% is available in Ref. 30 as supplementary material. Values within the cells indicate VAF for NOTCH pathway members and PRDM9; the only mutated gene shared between RDEB-SCC1 and RDEB-SCC2. [7]: Significantly mutated genes were identified by at least two out of three algorithms used (MutSigCV, Oncodrive-FM and Oncodrive-CLUST). [33]: Targeted sequencing using the OncoPanelv2 platform. Significantly mutated genes were determined by MutSigCV (q-value ≤ 0.1). N/P = Not Profiled. [32]: Genes were identified as significant by MutSigCV algorithm or by at least two out of three other algorithms.