Table 3.
MS analysis of identified proteins in cells reprogrammed with MYCL-WT and c-MYC-ΔMB0 compared with MYCL-ΔMB0.
| (i) Proteins enriched more than two-fold in MYCL-WT compared with MYCL-ΔMB0 (EpiP) | |||||
|---|---|---|---|---|---|
| UBQLN2 | DYNLRB1 | EXOC2 | KRT17 | NANS | ARL1 |
| REEP5 | RAB11B | ARPC2 | TPM1 | UTP15 | TMPO |
| SGCD | WDR46 | CD47 | SLC44A2 | RASA1 | CETN2 |
| TUBB2A | ALDH6A1 | STRN3 | FBXW10 | BAP18 | SNW1 |
| HMGB1 | POTEF | PDHA1 | CAMK2D | TM9SF3 | NFS1 |
| PPIC | COMMD4 | SCP2 | MT-ATP6 | YIPF5 | MPI |
| HMGB3 | TUSC3 | COL3A1 | ARF4 | ATP5PB | MPDU1 |
| PCNP | MYD88 | GNB2 | NUCKS1 | LIMS1 | USP15 |
| SYAP1 | RAC1 | COG6 | TMED2 | LRBA | OVCA2 |
| CHMP4B | MACF1 | SOX2 | PRKACA | MAPK14 | CALD1 |
| UTP3 | SRSF11 | SSR1 | MID1 | DUSP12 | GBP1 |
| BLOC1S1 | EXOC5 | CSTF3 | PCID2 | THOC3 | ANP32B |
| ST6GALNAC1 | DNAJC9 | CACNA2D1 | TRIP12 | SRSF5 | USP48 |
| MAP3K20 | MICAL1 | NRDC | GADD45GIP1 | VAC14 | PDIA4 |
| KNTC1 | POLR2L | MSRB3 | GTF2I | PDXDC1 | SF3A3 |
| BAG5 | SFXN3 | NOL11 | ERLIN2 | ZNF462 | NUCB2 |
| CD320 | CRIP1 | OSTC | DBNL | ITGB1 | AGK |
| MRPL11 | NAA10 | RPL37A | STT3A | CTTN | PPIL3 |
| TFG | ARF6 | LZIC | PAFAH1B1 | EEF1B2 | IDI1 |
| THYN1 | CCDC43 | BMP1 | SLC25A24 | UGP2 | ELN |
| NDRG3 | NEK7 | PDCL3 | HOOK3 | LSM2 | COL4A2 |
| TMX4 | TUBB4B | UGP2 | LAS1L | ACTB | BUD31 |
| SEPHS1 | MYO1E | TNS3 | HLA-H | RABL3 | MAP2 |
| RPL36A | FNTA | VPS26B | DCN | RWDD1 | PAIP1 |
| MYDGF | SRBD1 | EHD1 | PUM1 | TOMM20 | ITGA5 |
| OPTN | DBI | ANKFY1 | PUS7 | CRABP2 | GPX8 |
| GNAQ | SUGP2 | KBTBD3 | KPNA4 | VDAC3 | TXLNG |
| ACSL4 | MTA1 | SCPEP1 | METTL26 | EDIL3 | ATP5MG |
| ATP5ME | MAP7D1 | FBLN2 | B4GALT4 | PLA2G4A | PIK3R4 |
| ABI3BP | ACTG1 | LDLR | MBD5 | CTNNA1 | PLBD2 |
| ASAH1 | HINT1 | EXOSC7 | CSRP1 | RPL23A | ZYX |
| GNS | HMGN1 | DIP2B | GNB1 | TMEM165 | COX7C |
| WDR61 | PTGR1 | PITRM1 | SNRPB2 | DNAH6 | H3-3A,H3-3B |
| ARL8A | TMSB4X | METTL14 | CNN2 | DPP9 | NCKAP1 |
| MAP3K20 | FAM114A1 | TMSB10 | PPIB | ENDOD1 | AHNAK |
| NDRG1 | FTH1 | CNPY3 | S100A10 | NDUFB11 | PGM2 |
| PITPNA | SGTA | HABP2 | C1orf198 | NAA50 | PODXL |
| NIF3L1 | SGPL1 | SRP9 | MARCKSL1 | DNAJC8 | CFL2 |
| NME2 | CD59 | NDUFB9 | TOR1AIP1 | NXN | STAT6 |
| PFDN1 | DHRS4 | RBPJ | NDUFA4 | MRPS17 | TP53BP1 |
| ATG3 | GSPT1 | DCTN5 | ACSS2 | REXO2 | ATAD1 |
| ACIN1 | BLOC1S3 | TMED1 | GSTK1 | PEBP1 | EIF3K |
| RAB14 | RFC3 | AKR1B1 | ISLR | S100A13 | GPX7 |
| SNAP23 | CD55 | TALDO1 | NOP14 | SLC25A6 | TRIO |
| EMC2 | RPS15A | DSTN | POLR2A | OSBPL3 | TSPYL5 |
| (ii) Proteins enriched more than wo-fold in c-MYC-ΔMB0 compared with MYCL-ΔMB0 (EpiP) | |||||
|---|---|---|---|---|---|
| UBQLN2 | ACIN1 | NEK7 | PITRM1 | PDLIM5 | CAMK2D |
| HMGB1 | SRSF11 | RAB11B | ITGA1 | H3-3A,H3-3B | CRABP2 |
| REEP5 | OPTN | ANKFY1 | ISLR | C1orf198 | NCKAP1 |
| NDRG1 | KNTC1 | CD47 | SRSF5 | LUZP1 | HMGN1 |
| SGCD | PAIP1 | PRKACA | ERLIN2 | IDI1 | MAP2 |
| MAP3K20 | NIF3L1 | SCRN3 | MRPS17 | HABP2 | TOR1AIP1 |
| TUBB2A | POTEF | FAM114A1 | TOMM20 | PAFAH1B1 | ARL1 |
| CCDC43 | COG6 | NOLC1 | UGP2 | ITGA5 | OSBPL3 |
| PCNP | TSPYL5 | COMMD4 | LSM2 | CHIC1 | ANP32B |
| TMX4 | DYNLRB1 | EHD1 | UTP15 | SMTN | STT3A |
| BLOC1S1 | STRN3 | PPP4C | PUM1 | DUSP12 | VPS26B |
| SYAP1 | ASAH1 | FNTA | MYO1E | MEAF6 | APP |
| PPIC | ATP5ME | GNAQ | TP53RK | NMT1 | GALNT1 |
| NME2 | OVCA2 | SEMA7A | POLR2L | NDUFA4 | SSR1 |
| ACSL4 | RAC1 | RPL36A | MYO6 | LIMS1 | YIF1A |
| HMGB3 | OSTC | FTH1 | PUS7 | CLASP2 | UGP2 |
| FBXW10 | DBI | PTGR1 | PIK3R4 | ILF3 | USP48 |
| MAP3K20 | PDHA1 | KRT17 | MYD88 | RASA1 | PPIB |
| NDRG3 | SFXN3 | ARPC2 | REXO2 | GALE | METTL26 |
| GNS | TNS3 | ABI1 | DBNL | TXLNG | MYO1D |
| UTP3 | DHRS4 | PAIP1 | USP15 | PPIL3 | NDUFS6 |
| SEPHS1 | MPDU1 | PCID2 | SRBD1 | RFC3 | PPIF |
| BAG5 | DNAJC9 | SEC24A | ACTG1 | SCLY | SMARCC2 |
| ATG3 | MAPK14 | UBQLN1 | LZIC | MPV17 | STAM2 |
| SCPEP1 | MRPS24 | MTA1 | TRIP12 | VAC14 | BMP1 |
| TFG | PLA2G4A | BAP18 | THOC3 | DCTN5 | PGM2 |
| MT-ATP6 | NOL11 | METTL14 | SCP2 | COG7 | CERS2 |
| MRPL11 | SUGP2 | EXOC5 | POLR2A | MCRIP1 | SLIT3 |
| CHMP4B | TUSC3 | BLOC1S3 | CSTF3 | CTNNA1 | HOOK3 |
| SGPL1 | DIP2B | DUSP23 | GNB2 | SENP3 | COL3A1 |
| MICAL1 | PFDN1 | SOX2 | GSPT1 | EIF2B1 | ITGB1 |
| DCN | NRDC | LDLR | GADD45GIP1 | SETD7 | AGK |
| CUL4A | SGTA | CNPY3 | KPNA4 | DNASE2 | MPHOSPH10 |
| ARF6 | PODXL | MPI | FADS2 | RAI14 | BOLA2,BOLA2B |
| HLA-H | ARL8A | HINT1 | NSA2 | TPMT | IMPACT |
| MACF1 | PDXDC1 | GSTK1 | ATAD1 | EDIL3 | USP9X |
| THYN1 | CD320 | CD59 | METAP1 | IGF2R | OCIAD2 |
| MYDGF | PITPNA | FBLN2 | TPM1 | NAA50 | CACNA2D1 |
| NACA4P | MAP7D1 | NANS | MBD5 | EEF1B2 | YIPF5 |
| NAA10 | WDR46 | TM9SF3 | DCTD | EEA1 | TMSB10 |
| NDUFB9 | LRRC17 | YAP1 | GTF2I | CD55 | SNAP23 |
| ABI3BP | WDR61 | RABL3 | PRKRA | DNAJC8 | EIF3H |
| SNW1 | LMCD1 | KLF4 | PSMD4 | S100A10 | KBTBD3 |
| SNRPB2 | COL4A2 | CFL2 | LSM5 | FBXO22 | ACYP1 |
| ARF4 | VDAC3 | ALDH6A1 | CYP51A1 | CBX3 | SNX27 |
| ATP5MG | CNN1 | CLINT1 | ACSS2 | EIF2B3 | SLC25A24 |
| CTTN | CALD1 | DYNC1LI1 | NDUFAF2 | S100A13 | CDC42BPB |
| TMPO | EWSR1 | ANTXR2 | TP53BP1 | RBM17 | IDH3G |
| RPL37A | SPATS2L | PHLDB1 | CARHSP1 | CFAP74 | EMC2 |
| PLS1 | HSD17B7 | FAP | NXN | TUBB4B | SF3A3 |
| MTR | OSTF1 | TMSB4X | SRP9 | VASP | EXOC2 |
| NCBP1 | SFXN4 | NUCKS1 | RPS29 | MANF | COPS6 |
| VPS4B | AHNAK | CSRP1 | SLC25A6 | CARM1 | FKBP2 |
| TMOD3 | RBPJ | TALDO1 | ATP5PB | PRPF4B | TBC1D15 |
| GPX7 | B4GALT4 | MSRB3 | DNAH6 | COX7C | OGFR |
| ALDH1L2 | CRIP1 | AP3M1 | SCAMP2 | C1orf50 | ELN |
| TSN | TOR1B | PDS5A | PDIA4 | RWDD1 | GABPA |
| DYNLL1 | USP47 | ENDOD1 | NUCB2 | GINS4 | DR1 |
| FKBP5 | OAS2 | MRTO4 | NFS1 | NPC2 | ABI2 |
| SERPINE2 | NDUFAF4 | ZYX | HACD3 | EXOSC7 | |
| (iii) Commonly enriched proteins in (i) and (ii) | |||||
|---|---|---|---|---|---|
| WDR46 | TUSC3 | RBPJ | NFS1 | NIF3L1 | DNAJC8 |
| MYO1E | MYD88 | FBXW10 | ARF4 | TM9SF3 | TMPO |
| RAC1 | SFXN3 | CAMK2D | MPDU1 | CTNNA1 | EEF1B2 |
| TMSB10 | MACF1 | NUCKS1 | OVCA2 | CHMP4B | COL3A1 |
| LDLR | DBNL | PRKACA | ANP32B | PCNP | S100A10 |
| CRABP2 | EXOC5 | TRIP12 | SLC25A24 | PAIP1 | NEK7 |
| NOL11 | DNAJC9 | GADD45GIP1 | SF3A3 | ARL1 | MICAL1 |
| POLR2L | CRIP1 | GTF2I | AGK | PODXL | S100A13 |
| TOMM20 | CCDC43 | AHNAK | PPIL3 | REXO2 | STT3A |
| CFL2 | SRBD1 | ENDOD1 | IDI1 | FNTA | H3-3A,H3-3B |
| POTEF | SUGP2 | PDHA1 | ELN | FBLN2 | SCPEP1 |
| TSPYL5 | MTA1 | HOOK3 | COL4A2 | NDRG3 | TXLNG |
| SGTA | TMSB4X | HLA-H | MAP2 | EXOC2 | MPI |
| REEP5 | ACTG1 | PUM1 | ATP5MG | SOX2 | HMGN1 |
| SGCD | HINT1 | KPNA4 | PIK3R4 | DBI | UBQLN2 |
| HMGB3 | PTGR1 | METTL26 | COX7C | TUBB2A | NDUFB9 |
| SYAP1 | EMC2 | B4GALT4 | NCKAP1 | SRP9 | PDXDC1 |
| UTP3 | RPL36A | MBD5 | ASAH1 | FAM114A1 | TOR1AIP1 |
| BLOC1S1 | CD59 | SNRPB2 | PGM2 | CD55 | MAP7D1 |
| MAP3K20 | NUCB2 | C1orf198 | TP53BP1 | SNAP23 | COG6 |
| KNTC1 | BLOC1S3 | ACSS2 | ATAD1 | UGP2 | TNS3 |
| BAG5 | STRN3 | GSTK1 | RPL37A | KRT17 | SGPL1 |
| CD320 | SCP2 | NANS | RFC3 | DCTN5 | CSRP1 |
| TFG | GNB2 | UTP15 | TALDO1 | USP48 | ATG3 |
| THYN1 | SSR1 | BAP18 | ISLR | NDUFA4 | EDIL3 |
| TMX4 | CSTF3 | YIPF5 | POLR2A | ITGB1 | ZYX |
| ARL8A | CACNA2D1 | LIMS1 | OSBPL3 | ATP5PB | PCID2 |
| GNAQ | NRDC | THOC3 | GPX7 | PUS7 | RASA1 |
| ACSL4 | MSRB3 | SRSF5 | PPIC | SRSF11 | DNAH6 |
| ATP5ME | OSTC | VAC14 | MYDGF | USP15 | ALDH6A1 |
| ABI3BP | LZIC | ARF6 | HMGB1 | MT-ATP6 | COMMD4 |
| GNS | BMP1 | UGP2 | ERLIN2 | NAA10 | CNPY3 |
| MAP3K20 | VPS26B | LSM2 | FTH1 | ITGA5 | HABP2 |
| NDRG1 | ANKFY1 | RABL3 | DUSP12 | CD47 | DHRS4 |
| NME2 | KBTBD3 | RWDD1 | CTTN | MRPL11 | SNW1 |
| PFDN1 | EHD1 | PLA2G4A | PPIB | OPTN | ARPC2 |
| MAPK14 | EXOSC7 | SLC25A6 | SEPHS1 | WDR61 | TPM1 |
| ACIN1 | DIP2B | NAA50 | DCN | PDIA4 | GSPT1 |
| DYNLRB1 | PITRM1 | NXN | PAFAH1B1 | VDAC3 | TUBB4B |
| RAB11B | METTL14 | MRPS17 | PITPNA | CALD1 | |
Three groups are described: (i) proteins whose peptide counts increased more than two-fold in MYCL-WT compared to MYCL-ΔMB0; (ii) proteins whose peptide counts increased more than two-fold in c-MYC-ΔMB0 compared to MYCL-ΔMB0; and (iii) commonly identified proteins. n = 3.