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Hao Y, Li X, Qin K, Shi Y, He Y, Zhang C, Cheng B, Zhang X, Hu G, Liang S, Tang Q, Chen X. Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network. Angewandte Chemie (International ed. in English) 2023 36852467
Abstract:
Self-renewal and differentiation of embryonic stem cells (ESCs) are influenced by protein O-linked β-N-acetylglucosamine (O-GlcNAc) modification, but the underlying mechanism remains incompletely understood. Herein, we report the identification of 979 O-GlcNAcylated proteins and 1340 modification sites in mouse ESCs (mESCs) by using a chemoproteomics method. In addition to OCT4 and SOX2, the third core pluripotency transcription factor (PTF) NANOG was found to be modified and functionally regulated by O-GlcNAc. Upon differentiation along the neuronal lineage, the O-GlcNAc stoichiometry at 123 sites of 83 proteins-several of which were PTFs-was found to decline. Transcriptomic profiling reveals 2456 differentially expressed genes responsive to OGT inhibition during differentiation, of which 901 are target genes of core PTFs. By acting on the core PTF network, suppression of O-GlcNAcylation upregulates neuron-related genes, thus contributing to mESC fate determination.
O-GlcNAc proteins:
AMRA1, SETX, SKT, BCORL, AGRIN, MGAP, ARI1A, KANL3, CHD6, PHRF1, ZCH24, EP300, KIF7, KI67, CE350, ANR11, NUMA1, TPR, MORC3, TAF4B, KMT2B, EMD, AKAP1, TCOF, DCTN1, MNT, NCOA3, ATN1, ECP3, DPOD2, CTND2, PIAS3, AF10, ACK1, GET3, DSG2, ESS2, ATX2, PDLI1, ULK1, BARD1, KDM6A, ZN106, NSD1, ZFR, HIPK1, SETB1, LAMC1, MYCN, GCR, EGR1, RC3H2, ATX1L, DERPC, K2C8, HSPB1, JUND, FGFR1, G3P, ATF2, COF1, HEXB, VIME, PO5F1, CBL, CCNB1, PO2F1, RS2, NFKB1, MAX, PABP1, NEDD1, PTN12, FMR1, ELK1, FOXK1, STAT3, SOX15, PLIN2, CBP, NEDD4, YAP1, RFX1, SOX2, LMNA, ROA1, S1PR2, ARNT, RD23A, PLTP, KMT2A, KLF16, FOXP1, TB182, GMEB2, SENP1, YTHD1, MRTFB, DOCK4, STIM1, TBX3, NCOA1, ERF, SIAE, NACAM, ATF1, WNK1, G3BP2, DNLI3, G3BP1, RLA2, GABPA, S30BP, ZEP1, ENAH, SOX13, CAPR2, APLP2, CLUS, TLE3, GATA4, MITF, CHD8, ZCH18, TANC1, CDK12, SAP25, LIN41, MLXIP, HROB, VRTN, CO039, PDLI7, SMCA4, PRC2C, MILK2, MIDN, YETS2, PBIP1, FUBP2, TFPT, SRBP2, GSE1, F117B, ZN865, WDR62, QRIC1, FOXK2, RREB1, TNR6C, DAB2P, TNR6A, RHG17, PKHA7, COBL1, FCHO2, TET1, ARMX5, GARL3, TET2, CDV3, PHAR4, C2CD3, LIN54, NPA1P, TAB3, TASO2, RESF1, NUFP2, UNKL, COBL, KDM6B, PRSR1, SMG7, RBM27, PHF12, ZDBF2, PUR4, SYNRG, UIMC1, SIN3A, NFAC2, SRC8, SKIL, ELF1, KLF4, NCOR1, KLF3, NCOA2, FOXD3, PAPOA, HCFC1, P3C2A, SIX4, ZFHX3, TOB1, AP180, GLI3, ATRX, MAFK, NPM, M3K7, DAG1, SPTB2, TAF6, TIF1B, SPT6H, SH3G1, ARI3A, TLE1, TLE4, IF4G2, MINT, ZIC3, ZYX, NUP62, PHC1, TFE3, TIF1A, SF01, DAZL, RBL1, KNL1, BCL9L, SBNO1, SLAI1, PKP4, CDK13, SH3R1, JHD2C, HECD1, ARMX2, LAR4B, RHG21, HELZ, SCAF8, UTF1, PKHG2, NIPBL, CCD66, F135A, RPRD2, WWC2, ZN532, KRBA1, TAF9B, RBM26, INT1, BCR, AHDC1, PTN23, PAPD7, KDM3A, KMT2D, CHD4, RN220, NUP98, NFRKB, GGYF2, LCOR, TEX2, PF21A, KDM3B, FNBP4, CNOT1, LARP1, RHG26, NU188, CNDD3, PICAL, SPAG5, HUWE1, SMAP2, CPEB3, MYCB2, PRC2B, PRR14, MACOI, ATX2L, CKP2L, PRC2A, MCAF1, SI1L2, KANL1, ERBIN, R3HD2, RERE, PUM2, PUM1, NU214, WNK4, TCAM1, SAS6, CAMP3, UBN2, TNC18, AGFG2, UBP2L, WNK3, ZN598, CTIP, SHAN2, NANOG, DDX42, RHG32, VGLU3, LPP, TET3, MYPT2, IF4B, CNO10, MISSL, TB10B, CARF, TGO1, ZN879, SP130, ZC3HE, ZNT6, SUN2, TNR6B, ARI5B, EMSY, BNC2, KAT6B, KMT2C, CLAP2, CNOT4, SRRM2, TOX4, GEPH, SYP2L, LARP4, KANK2, SALL4, YTHD3, TOIP2, KAT6A, ASXL2, POGZ, SREK1, TAF5, ZHX2, EPC2, SI1L1, CND2, RBM14, SUCO, CNOT2, DIDO1, SMAG1, LENG8, CDAN1, DPPA4, LRIF1, VCIP1, MB214, TAB1, SCYL2, ASPP2, LS14B, SYEP, F193A, BCOR, OGT1, SUGP1, NAV1, SYNJ1, ADNP2, RPGF2, BICRL, EP400, PHC3, VP37A, EPN2, P66A, PDLI5, ELYS, ZBT20, ANLN, AGFG1, MATR3, CASC3, I2BPL, PO121, ALMS1, SF3A1, GRHL2, ATF7, CACL1, DC1L1, MTSS1, SPART, TDIF2, HBP1, NUP58, RFIP5, BRD8, WIPI1, CDK8, CS047, ATX7, NUP35, LUZP1, RPAP2, NDC1, MAVS, AMOT, CSKI2, P66B, TAF9, IPO4, ZCH14, UBAP2, NCOA5, FUBP1, RBM47, AJUBA, VPS36, DCP1A, EGLN2, YTHD2, SRGP2, GRHL1, BCL7B, P4R3B, PLRG1, CIC, WAC, TRPS1, MED1, ACATN, NRBP, RP25L, NONO, TAB2, RBM10, EPN4, DDAH2, NOG2, ZN281, HGS, NASP, ARIP4, ANR17, ZN318, TRI33, MZT2, ZWINT, ECD, YIF1B, ROA0, DHRS7, TPD54, SSBP3, PSRC1, SARNP, BCL9, SP2, NOP56, SH24A, FIP1, PLIN3, MYPT1, KC1D, TCF20, TOR3A, SALL1, ZN704, RBP2, UBE4B, TBX20, AFF4, RBCC1, 4ET, PALLD, ELF2, TSSC4, NUDT3, HAKAI, ADRM1, NCOA6, FANCA, GIT2, BAG3, TOB2, ZN207, SON, TBL1X, PLEC, MACF1, GOGA5, QKI, GAB1, DMRT1, YLPM1, PCM1, RHG07, TAF7, FOXO1, ADA23, AKA12, UXT, MAN1, NCOR2, AKT3, COR1B, TNIP1, GANP, DEMA, CARM1, RGAP1, ITSN2, ZO2, KLF5, ADNP, ARI3B, BCL3, SE1L1, E41L1, ZN292
Species: Mus musculus
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Huynh VN, Wang S, Ouyang X, Wani WY, Johnson MS, Chacko BK, Jegga AG, Qian WJ, Chatham JC, Darley-Usmar VM, Zhang J. Defining the Dynamic Regulation of O-GlcNAc Proteome in the Mouse Cortex---the O-GlcNAcylation of Synaptic and Trafficking Proteins Related to Neurodegenerative Diseases. Frontiers in aging 2021 2 35822049
Abstract:
O-linked conjugation of ß-N-acetyl-glucosamine (O-GlcNAc) to serine and threonine residues is a post-translational modification process that senses nutrient availability and cellular stress and regulates diverse biological processes that are involved in neurodegenerative diseases and provide potential targets for therapeutics development. However, very little is known of the networks involved in the brain that are responsive to changes in the O-GlcNAc proteome. Pharmacological increase of protein O-GlcNAcylation by Thiamet G (TG) has been shown to decrease tau phosphorylation and neurotoxicity, and proposed as a therapy in Alzheimer's disease (AD). However, acute TG exposure impairs learning and memory, and protein O-GlcNAcylation is increased in the aging rat brain and in Parkinson's disease (PD) brains. To define the cortical O-GlcNAc proteome that responds to TG, we injected young adult mice with either saline or TG and performed mass spectrometry analysis for detection of O-GlcNAcylated peptides. This approach identified 506 unique peptides corresponding to 278 proteins that are O-GlcNAcylated. Of the 506 unique peptides, 85 peptides are elevated by > 1.5 fold in O-GlcNAcylation levels in response to TG. Using pathway analyses, we found TG-dependent enrichment of O-GlcNAcylated synaptic proteins, trafficking, Notch/Wnt signaling, HDAC signaling, and circadian clock proteins. Significant changes in the O-GlcNAcylation of DNAJC6/AUXI, and PICALM, proteins that are risk factors for PD and/or AD respectively, were detected. We compared our study with two key prior O-GlcNAc proteome studies using mouse cerebral tissue and human AD brains. Among those identified to be increased by TG, 15 are also identified to be increased in human AD brains compared to control, including those involved in cytoskeleton, autophagy, chromatin organization and mitochondrial dysfunction. These studies provide insights regarding neurodegenerative diseases therapeutic targets.
O-GlcNAc proteins:
TANC2, AMRA1, CAMP1, SKT, AGRIN, KANL3, TTLL3, NHSL2, CTTB2, CCDC6, SHAN1, SYGP1, DPYL2, STXB1, CLOCK, NOTC2, VIAAT, CTND2, TPD53, REPS1, NLK, ACK1, SYUA, ATX2, PDLI1, ZFR, HCN1, BSN, TOM1, SYN1, GCR, EGR1, NFL, NFM, ATX1L, DERPC, KCC2A, CNTN1, HSPB1, MAP1B, G3P, ATF2, MTAP2, RS2, FOXK1, STAT3, AINX, EPB41, RFX1, LMNA, INPP, VATA, DVL1, CNBP, ATX1, NCAN, GOGA3, PTPA, GCP3, TB182, GMEB2, YTHD1, PI5PA, MRTFB, LIPA3, NACAM, TNIK, WNK1, NPTN, NEO1, S30BP, ZEP1, APOC2, EMAL1, RELCH, PRC2C, YETS2, FUBP2, QRIC1, LIMC1, DAB2P, ZEP2, AAK1, TNR6A, FCHO2, DRC1, SRBS2, GRM5, PACS2, OXR1, PHAR4, LIN54, MLIP, UNKL, SMG7, RBM27, CYFP2, SYNRG, SRC8, SKIL, NCOR1, LAMA5, HCFC1, P3C2A, SAP, APC, TOB1, AP180, FXR1, HS71A, LASP1, MAFK, M3K7, TAF6, ASPP1, SRBS1, DBNL, SH3G1, TLE4, IF4G2, MINT, ZYX, NUP62, OMGP, TFE3, SYN2, TBR1, RBL2, SBNO1, SLAI1, PKP4, SH3R1, JHD2C, ABLM3, ARMX2, LAR4B, HELZ, S23IP, RBM26, BCR, AHDC1, PAPD7, MFF, KMT2D, ERC2, NFRKB, WDFY3, GGYF2, TEX2, CNOT1, IF2A, PICAL, PLPR3, PRC2B, C2CD5, TPPP, ATX2L, MAP6, NAV3, AUXI, RIMB2, AVL9, NU214, AP4E1, UBP2L, C2C2L, IF4G3, ZN598, SHAN2, LPP, MYPT2, PHIPL, TB10B, CCD40, ZC3HE, DLGP2, ZC21A, BAIP2, EMSY, CLAP2, LIPA2, SRRM2, PAMR1, GEPH, YTHD3, POGZ, EPC2, SI1L1, RBM14, HYCC2, ANK2, CDAN1, SYNPO, VCIP1, TAB1, MEF2C, F193A, OGT1, EP400, EPN2, P66A, PDLI5, GTPBA, ZBT20, RTN1, BRD3, AGFG1, ABLM1, MRTFA, DC1L1, SPART, RFIP5, NUP35, WASF1, SC6A8, SGIP1, AGAP3, P66B, TAF9, WDR13, LRP5, UBAP2, BASP1, DCP1A, SYUB, TRFE, TRIM7, CIC, S12A6, GORS2, TAB2, EPN4, RNF34, ANR17, NECP1, FLIP1, ROA0, RBM33, TPD54, ODO2, DLGP1, FIP1, TM263, PLIN3, LNEBL, KC1D, NBEA, INP4A, RIMS2, RBP2, RTN3, NUDT3, ATR, ADRM1, FMN2, NCOA6, SON, ULK2, ADDA, MAGD1, MAP1A, GRM3, PCLO, GAB1, FBX6, NPAS3, GUAD, NCOR2, ATRN, NFAT5, DEMA, E41L3, SLIT3, CARM1, DYR1B, MECP2, E41L1, HDAC6
Species: Mus musculus
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Deracinois B, Camoin L, Lambert M, Boyer JB, Dupont E, Bastide B, Cieniewski-Bernard C. O-GlcNAcylation site mapping by (azide-alkyne) click chemistry and mass spectrometry following intensive fractionation of skeletal muscle cells proteins. Journal of proteomics 2018 186 30016717
Abstract:
The O-linked-N-acetyl-d-glucosaminylation (O-GlcNAcylation) modulates numerous aspects of cellular processes. Akin to phosphorylation, O-GlcNAcylation is highly dynamic, reversible, and responds rapidly to extracellular demand. Despite the absolute necessity to determine post-translational sites to fully understand the role of O-GlcNAcylation, it remains a high challenge for the major reason that unmodified proteins are in excess comparing to the O-GlcNAcylated ones. Based on a click chemistry approach, O-GlcNAcylated proteins were labelled with azido-GalNAc and coupled to agarose beads. The proteome extracted from C2C12 myotubes was submitted to an intensive fractionation prior to azide-alkyne click chemistry. This combination of fractionation and click chemistry is a powerful methodology to map O-GlcNAc sites; indeed, 342 proteins were identified through the identification of 620 peptides containing one or more O-GlcNAc sites. We localized O-GlcNAc sites on proteins involved in signalling pathways or in protein modification, as well as structural proteins. Considering the recent role of O-GlcNAcylation in the modulation of sarcomere morphometry and interaction between key structural protein, we focused on proteins involved in the cytoarchitecture of skeletal muscle cells. In particular, several O-GlcNAc sites were located into protein-protein interaction domains, suggesting that O-GlcNAcylation could be strongly involved in the organization and reorganization of sarcomere and myofibrils.
O-GlcNAc proteins:
A2A7H5, MYOM3, CKAP5, BRWD3, A2AIR2, DCA10, A2AMY5, B1AXE9, B1AXR5, B1B0C9, B2RXQ9, B7ZC18, B8JJB2, D3YU08, D3YUW7, D3YVS1, D3YYR9, D3Z216, D3Z2W0, D3Z4C0, D3Z589, D3Z6H5, D3Z7Q3, D6RH90, D6RHQ6, E0CYM1, E9Q016, I2BP2, E9Q3W4, KIF23, E9Q616, E9Q6A3, E9Q6Q2, E9Q8K5, E9Q9Q7, E9QKG6, E9QNY8, E9QQ33, F6T0L5, F6UTU1, F6V513, F6WNS2, F6YRR2, F7AWU3, F7C957, F7D291, F8VQK3, F8WGN6, F8WIT2, G3UYW7, G3UZ19, G3X9H7, G3XA78, G5E8J9, H3BK97, CELR1, LNX1, PDLI1, UBB, HSPB1, VIME, CRYAB, CRYAA, TNR6, TLN1, DESM, AIMP1, RAB6A, FOXK1, CNR1, WN10B, LMNA, LIMK1, MRTFB, ACTB, HSP7C, IPKA, ACTC, RGRF2, MYBPH, NACAM, WNK1, STAC, CADH6, G3BP2, G3BP1, NOTC1, ENAH, NF1, INF2, Q3TBU7, MILK2, FOXK2, FCSD2, HERC2, TRI67, TAB3, FBXL7, MYPN, ICEF1, Q5SQY9, TLL1, SRBS1, DBNL, SH3G1, ZYX, M3K10, SH3R1, NCK5L, HYCCI, WDFY3, AKIB1, FHOD3, SI1L2, PKHH1, CYLD, DCAF1, TCPR1, DAPK1, MYPT2, CNOT4, Q8BUJ6, KANK2, IFFO1, ANKK1, VCIP1, CBPC2, TAB1, ASPP2, PDLI5, PP14C, KLH20, MARK1, SYNP2, UBP26, FLIP1, TX1B3, MYPT1, SYNCI, LIMA1, RBP2, LDB3, ADRM1, BAG3, LIMD1, MACF1, Q9Z1A1
Species: Mus musculus
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