Table 2 Critical aberrant pathways in penile cell lines
Cell line | Pathway | Involved gene variations |
|---|---|---|
Penl1 | Jak-STAT signaling pathway | Copy number gain (MYC, IL7R, LIFR, JAK2, IFNA4, IFNA2, IFNA5, IFNA7, IFNA8, IFNA14, IFNA16, IFNA21, IFNW1); Copy number loss (IL2RA, IL5RA, IL9R, IL15, IL10RB, IL21, PIAS2) |
TGF-beta signaling pathway | Copy number gain (MYC, BMP2, GDF5, RBL1, ID1); Copy number loss (TGFBR2, BMPR1B, ACVR2B, SMAD4, SMAD2, SMAD1, SMAD7, PITX2); TGFB3:NM_003239:exon1:c.202C>T:p.Q68X | |
MAPK signaling pathway | Copy number gain (MYC, FGF10); Copy number loss (TGFBR2, EGF, PDGFRA, NFKB1, IKBKB, RAF1, MAPK10, FGFR1, FGF2, FGF5, FGF17, MAP3K8, MAPKAPK3); TGFB3:NM_003239:exon1:c.202C>T:p.Q68X; IL1R2:NM_004633:exon8:c.989A>G:p.N330S; MAP2K3:NM_145109:exon3:c.118C>A:p.P40T; MAP3K3:NM_203351:exon11:c.934G>A:p.V312M | |
Notch signaling pathway | Copy number gain (JAG1); Copy number loss (MAML3); NOTCH1:NM_017617:exon8:c.1280G>A:p.G427D; NOTCH2:NM_024408:exon2:c.137A>G:p.N46SDTX2; NCOR2:NM_006312:exon46:c.6943G>A:p.A2315T; MAML3:NM_018717:exon2:c.1494_1504del:p.Q498fs, exon2:c.1506delG:p.Q502fs, exon4:c.2302_2304del:p.768_768del | |
Apoptosis | Copy number gain (BIRC3); Copy number loss (NFKB1, IKBKB, TNFRSF10B, TNFRSF10D, TNFRSF10A, BCL2, IRAK4, IRAK2); TP53:NM_001126118:exon7:c.731G>C:p.R244P, exon3:c.98C>G:p.P33R | |
Penl2 | MAPK signaling pathway | Copy number gain (MYC, FGF10, FGF12, FGF13, FGF14, MECOM, STK4, PRKCG, PAK2, MOS, RPS6KA6, RPS6KA3, ELK1, STK3, MAP3K13); Copy number loss (MAPK3, MAP2K2, FOS, FGFR1, FGF9, FGF22, FGF18, FGF17, PRKACA, NFATC4, MAPK12, MAPK11, MAPK13, RPS6KA2, MAPKAPK3, MKNK2, SRF, MAP3K14, CD14, FGFR4, ATF4, TAOK2); MAP2K3:NM_145109:exon3:c.118C>A:p.P40T; MAP3K4:NM_001301072:exon17:c.3554_3556del:p.1186_1186del |
Jak-STAT signaling pathway | Copy number gain (MYC, PIK3CA, STAT3, IL5, IFNA2, IFNA21, IL7, IFNW1, IL13RA1, IL13RA2); Copy number loss (PDGFRB, TGFB1, TGFB3, AKT2, CSF2, IL3, IL13, IL4R, IL9R, CSF2RB, IL2RB, GH1, GH2, LIF, OSM, STAT5A, JAK3, CBLC, IRF9); CSF2:NM_000758:exon4:c.356C>A:p.T119N; TGFBR2:NM_001024847:exon7:c.1564C>T:p.R522X; IL12RB1:splicing | |
TGF-beta signaling pathway | Copy number gain (MYC, E2F5, RBL1, GDF6); Copy number loss (MAPK3, TGFB1, TGFB3, BMP2, AMH, E2F4, ID3, SMAD9); TGFBR2:NM_001024847:exon7:c.1564C>T:p.R522X | |
Notch signaling pathway | Copy number gain (HES1); Copy number loss (KAT2A, NUMBL, NCOR2); NOTCH1:NM_017617:exon8:c.1400G>T:p.C467F; NOTCH2:NM_001200001:exon1:c.17_18del:p.P6fs,NOTCH2:NM_024408:exon1:c.17_18del:p.P6fs; DTX2:NM_020892:exon8:c.1151G>A:p.G384E; MAML3:NM_018717:exon2:c.1494_1504del:p.Q498fs, exon2:c.1506delG:p.Q502fs, exon4:c.2302_2304del:p.768_768del; NUMBL:NM_001289979:exon9:c.1182_1187del:p.394_396del; NCOR2:NM_006312:exon16:c.1531_1532insAGC:p.P511delinsQP, exon39:c.5517_5518insAGCAGCGGC:p.G1840delinsSSGG | |
Apoptosis | Copy number gain (PIK3CA, TNFSF10); Copy number loss (AKT2, IL3, CSF2RB, PRKACA,MAP3K14, TNFRSF10A, NFKBIA, RIPK1); TP53:NM_001126118:exon7:c.701G>A:p.R234H; ATM:NM_000051:exon55:c.8071C>T:p.R2691C | |
149RCa | MAPK signaling pathway | Copy number gain (MYC, EGFR, PDGFA, FGF13, FGF16, MOS, RPS6KA6, RPS6KA3, STK3, PRKX); Copy number loss (TNF, MAPK10); HRAS:NM_001130442:exon2:c.38G>T:p.G13V; FGFR4:NM_022963:exon4:c.535A>G:p.T179A; MAP2K3:NM_145109:exon3:c.118C>A:p.P40T; MAP3K4:NM_001301072:exon17:c.3554_3556del:p.1186_1186del; EGF:NM_001178130:exon1:c.46A>C:p.S16R; FGF6:NM_020996:exon1:c.251G>A:p.R84Q; FGF18:NM_003862:exon5:c.472C>T:p.R158W; TGFBR2:NM_001024847:exon5:c.959C>G:p.S320X |
Jak-STAT signaling pathway | Copy number gain (MYC, CSF2RA, IL3RA, IL6, CRLF2, IL7, IL13RA1, IL13RA2, IL5, IFNW1, IFNA2); STAT2:NM_005419:exon3:c.269T>C:p.F90S; EP300:NM_001429:exon6:c.1519A>G:p.S507G; LIFR:NM_001127671:exon2:c.116T>A:p.M39K; CSF3R:NM_000760:exon17:c.2197C>A:p.P733T | |
TGF-beta signaling pathway | Copy number gain (MYC, E2F5, INHBA); Copy number loss (TNF, BMP4, PITX2); EP300:NM_001429:exon6:c.1519A>G:p.S507G; TGFBR2:NM_001024847:exon5:c.959C>G:p.S320X; ACVRL1:NM_001077401:exon5:c.706G>A:p.E236K; LTBP1:NM_000627:exon15:c.2048C>A:p.P683Q | |
Notch signaling pathway | NOTCH2:NM_001200001:exon2:c.137A>G:p.N46S, exon4:c.660C>A:p.S220R, exon4:c.680C>A:p.P227H, exon4:c.703A>T:p.T235S; EP300:NM_001429:exon6:c.1519A>G:p.S507G; MAML3:NM_018717:exon2:c.1494_1504del:p.Q498fs, exon2:c.1506delG:p.Q502fs, exon3:c.1513_1514del:p.Q505fs, exon4:c.2302_2304del:p.768_768del; Copy number loss (DTX2) | |
Apoptosis | Copy number gain (IL3RA, BIRC3, PRKX, IRAK1); Copy number loss (TNF); TP53:NM_001126118:exon3:c.98C>G:p.P33R, exon3:c.211C>T:p.R71C, exon6:c.626G>A:p.R209Q; RIPK1:NM_003804:exon9:c.1335T>A:p.H445Q | |
149RM | MAPK signaling pathway | Copy number gain (MYC, EGFR, PDGFA, AKT3, MOS, STK3, TGFB2, FGF19, ELK4, MAP3K13); Copy number loss (MAPK10, AKT1, IKBKB, NFKB1, PDGFRA, TGFB3, FGFR1, FGF2, FGF5, FGF20, FGF17, FOS, RPS6KA5, RPS6KA1, MAPKAPK3, MAP3K6); HRAS:NM_001130442:exon2:c.38G>T:p.G13V; MAP2K3:NM_145109:exon3:c.118C>A:p.P40T; MAP2K6:NM_002758:exon4:c.139G>C:p.E47Q; MAP3K4:NM_001301072:exon17:c.3554_3556del:p.1186_1186del; EGF:NM_001178130:exon1:c.46A>C:p.S16R; FGF6:NM_020996:exon1:c.251G>A:p.R84Q; FGF18:NM_003862:exon5:c.472C>T:p.R158W; GFBR2:NM_001024847:exon5:c.959C>G:p.S320X |
Jak-STAT signaling pathway | Copy number gain (MYC, PIK3CA, IL6, IL7, IL5, AKT3); Copy number loss (AKT1, IL2, IL5RA, IL15, IL10RB, PIAS2); STAT2:NM_005419:exon3:c.269T>C:p.F90S; EP300:NM_001429:exon6:c.1519A>G:p.S507G; LIFR:NM_001127671:exon2:c.116T>A:p.M39K | |
TGF-beta signaling pathway | Copy number gain (MYC, E2F5, INHBA, TGFB2, LEFTY1, GDF6, LEFTY2); Copy number loss (TGFB3, ROCK1, BMPR1B, PITX2, ACVR2B, SMAD4, SMAD2, SMAD1, SMAD7, ID3); EP300:NM_001429:exon6:c.1519A>G:p.S507G; TGFBR2:NM_001024847:exon5:c.959C>G:p.S320X; ACVRL1:NM_001077401:exon5:c.706G>A:p.E236K; LTBP1:NM_000627:exon15:c.2048C>A:p.P683Q | |
Notch signaling pathway | NOTCH2:NM_001200001:exon2:c.137A>G:p.N46S; EP300:NM_001429:exon6:c.1519A>G:p.S507G; MAML3:NM_018717:exon2:c.1494_1504del:p.Q498fs, exon2:c.1506delG:p.Q502fs, exon4:c.2302_2304del:p.768_768del; Copy number loss (HDAC1, SNW1, RBPJ); Copy number gain (HES1) | |
Apoptosis | Copy number gain (BIRC3, AKT3, PIK3CA, TNFSF10); Copy number loss (AKT1, IKBKB, NFKB1, TNFRSF10B, TNFRSF10D, TNFRSF10C, TNFRSF10A, BCL2); TP53:NM_001126118:exon3:c.98C>G:p.P33R, exon3:c.211C>T:p.R71C, exon6:c.626G>A:p.R209Q; RIPK1:NM_003804:exon9:c.1335T>A:p.H445Q | |
LM156 | Jak-STAT signaling pathway | Copy number gain (MYC, IL7); Copy number loss (IFNA1, IFNA2, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA21, IFNB1, IFNGR1, IFNW1, IFNK); IL5RA:NM_175725:exon6:c.284C>G:p.S95X; PRL:NM_000948:exon4:c.391C>T:p.R131C; PIK3CA:NM_006218:exon12:c.1834C>T:p.R612X; JAK3:NM_000215:exon16:c.2062A>T:p.I688F |
MAPK signaling pathway | Copy number gain (MYC, MOS, STK3, STK4); Copy number loss (PRKCG, IKBKB, MAP3K7, FGFR1, FGF20, FGF17, MAP3K5, RPS6KA2, MAP3K4, TAOK2); HRAS:NM_176795:exon2:c.37G>C:p.G13R; NFATC2:NM_012340:exon4:c.1337A>G:p.H446R; MAP2K3:NM_145109:exon3:c.118C>A:p.P40T; MAP3K4:NM_005922:exon17:c.3566_3568del:p.1189_1190del; MAPKAPK5:NM_139078:exon14:c.1331G>A:p.R444H | |
Notch signaling pathway | NOTCH1:NM_017617:exon22:c.3598G>A:p.D1200N; NOTCH2:NM_024408:exon2:c.137A>G:p.N46S; KAT2A:NM_021078:exon8:c.1181_1186del:p.394_396del; MAML3:NM_018717:exon3:c.1513_1514del:p.Q505fs, exon4:c.2302_2304del:p.768_768del; Copy number gain (DTX2); Copy number loss (HDAC2) | |
TGF-beta signaling pathway | Copy number gain (MYC, E2F5, BMP2, GDF6, RBL1); Copy number loss (BMP6, ID4); BMP6:NM_001718:exon2:c.695A>C:p.Q232P | |
Apoptosis | TP53:NM_001126118:exon3:c.98C>G:p.P33R; PIK3CA:NM_006218:exon12:c.1834C>T:p.R612X; Copy number loss (IKBKB, TNFRSF10B, TNFRSF10D, TNFRSF10C, TNFRSF10A, BCL2) |
