The genes that were evaluated were BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2
, NRAS, PTPN11, RAF1, and SHOC2.
The Ion Torrent PGM system was used to sequence exons and splicing sites of 29 genes of the RAS MAPK signaling pathway involved in Noonan syndrome and other rasopathies, i.e.,: the commonly mutated PTPN11, SOS1, RAF1, KRAS, BRAF, NRAS, HRAS, MAP2K1, MAP2K2
, SHOC2, CBL, SPRED1 genes and less common ones such as LZTR1 (more details about the complete list of genes are provided under request).
Recurring false-positive variants in HRAS and MAP2K2
were identified (Supplemental Table 4).
We analyzed the characteristics of the gene partners (see details in Supplementary Table 1) to potentially define the molecular functions of the identified fusions, and we observed that chromatin modifiers (KMTA2-MLL, RCOR1, and KAT6A), kinases (RPS6KA, MUSK, TRIM28, MPZL1, and MAP2K2
), and phosphates (LPAR1, PICALM, RPS6KB1, DLG2, PPP6RB, TPTA, and PI4KA) were frequently present.
miR-148a might modulate fat deposition by targeting MAPKAPK5, MAPK3, and MAP2K2
, and miR-148 has been shown to affect obesity and modulates adipocyte differentiation [40, 41].
Meanwhile, MAPK signaling pathway molecules including MEKK1, ASK1 (MAP3K5), MLK2 (MAP3K10), MLK3, NIK, MEK1 (MAP2K1), MEK2 (MAP2K2
), MEK4 (MAP2K4), MEK7 (MAP2K7), ERK1 (MAPK3), JNK1 (MAPK8) and JNK2 (MAPK9) were significantly up-regulated and revealed 2.00-4.09 fold increases in expression level (Table 1).
AKT1 CTNNB1 FGFR1 GNAS KRAS NRAS PIK3R5 STAT1 AKT2 EGFR FGFR2 HRAS MAP2K1 NTRK1 PKHD1 TEC AKT3 ERBB2 FGFR3 IDH1 MAP2K2
NTRK2 PRKCB1 TP53 (HER2) ALK ERCC6 FGFR4 IDH2 MAP2K7 NTRK3 RAF1 BRAF FBX4 FOXL2 IGF1R MET PDGFRA RET CDK4 FBXW7 GNA11 KDR MYC PIK3R1 SMO CSF1R FES GNAQ KIT NEK9 PIK3R4 SOS1
Triptolide downregulated the cell cycle-related genes E2F2 E2F3, E2F5, CDKN2C, CDK7, CDC23, and SMAD3; the MAPK signaling pathway genes FOS, CASP3, JUND, KRAS, MAP2K2
; and the Wnt signaling pathway genes WNT4, MYC, and AXIN2.
Eight percent of melanomas showed gain-of-function mutations in the MAP2K1 (encoding MEK1) and MAP2K2
(encoding MEK2) genes, (476) resulting in constitutive activation of downstream ERK MAPK.