Table 5.
Mutations identified using NGS in CTCL.
| Mutation category | Mutation | Reference |
|---|---|---|
| Tumor suppressor genes | ARID1A, DNMT3A, MSH2, PDCD1, TMCC1, NR3C1, ATXN1, HLA-B/C, TNFA/P3, FOXO3, AHR, LATS1, EGR3, CDKN2A, HNPRNK, TGFBR1, ZEB1, AGAP6, FAS/PTEN, MGMT, WT1, ATM, CDKN1B, SOCS2, RB1, ZFPM1, TP53, GRAP, ZBTB7A, SBNO2, MAP4K1, PD1, FUBP1, ANO6, BACH2, NFKB2, CTCF, FAT1, FAT3 | (117, 121) |
| Oncogenes | IRF4, CARD11, PTPRN2, JAK2/PD-L1/PD-L2, PRKCQ, TP53, PLCG1, FAS, POT1, DNMT3A, KIT, TNFRSF1B, RHOA | (121, 122) |
| Hotspot point mutations | NFKB1, KLF2, JUNB, TBL1XR1 | (121) |
| Enrichment of mutational signatures | Signature 1 (related to aging), Signature 7 (related to UV induced mutations), Signature 11 (related to alkylating agents), Signature 17 (possibly related to oxidative damage) | (121, 123) |
| Chromosome arm-level somatic copy number variants (SCNVs) | 17p deletion, 10q deletion, 17q amplification in Leukemic CTCLs | (121) |
| Signaling pathways | • Receptor Tyrosine Kinase (IRS2, FOXO3) • JAK/STAT (JAK3, STAT5A/B, SOCS1) • NOTCH (NOTCH1, NOTCH2) • NF-kB pathway (PLCG1, CARD11, TNFRSF1B, KIT) • TP53 pathway • PI3K-serine/threonine protein kinases (AKT) • Fibroblast growth factor receptors (FGFR) • Peroxisome proliferator-activated receptors (PPAR) • T-cell–specific pathways (MAP4K1, ANO6, GRAP, NR3C1, SBNO2, SOCS2, BACH2, NFKB1, KLF2, JUNB, AHR, ZFMP1, ZBTB7A) |
(117, 121, 122, 124) |
| DNA damage repair and epigenetic | ATM, MDC1, MSH3, ARID1B, MLL2, MLL3, KDM6A, DNMT1 | (117) |
| Miscellaneous | Androgen Receptor (AR) (subclonal level) | (117) |