Ontology Annotation

Abstract:
The synergistic approach of combining photodynamic immunotherapy with endogenous clearance of PD-L1 immune checkpoint blockade therapy holds promise for enhancing survival outcomes in glioblastoma (GBM) patients. The observed upregulation of O-GlcNAc glycolysis in tumors may contribute to the stabilization of endogenous PD-L1 protein, facilitating tumor immune evasion. This study presents a pH-adapted excited state intramolecular proton transfer (ESIPT)-isomerized β-ketoamide-based covalent organic framework (COF) nanoplatform (denoted as OT@COF-RVG). Temozolomide (TMZ) and OSMI-4 (O-GlcNAc transferase inhibitor) were integrated into COF cavities, then modified on the surface with polyethylene glycol and the rabies virus peptide RVG-29, showing potential for sensitizing TMZ chemotherapy and initiating photodynamic therapy (PDT). By inhibiting O-GlcNAc and promoting lysosomal degradation of PD-L1, OT@COF-RVG enhanced the effectiveness of immune checkpoint blockade (ICB) therapy. Additionally, treatment with OT@COF-RVG led to a notable elevation in reactive oxygen species (ROS) levels, thereby re-establishing an immunostimulatory state, inducing immunogenic cell death (ICD). In summary, our research unveiled a correlation between O-GlcNAc in GBM and the evasion of immune responses by tumors, while showcasing the potential of OT@COF-RVG in reshaping the immunosuppressive microenvironment of GBM and offering a more effective approach to immunotherapy in clinical settings.

Disease terms identified:
Neoplasms Death Glioblastoma

Cell lines identified:

Protein

Abstract:
Progranulin (PGRN) is overexpressed and implicated in hepatocellular carcinoma (HCC) development; however, its post-translational modifications and regulatory mechanisms in HCC remain largely unexplored. Here, the expression levels of PGRN, OGT, and O-GlcNAcylation were found to be elevated in both HCC samples and cell lines. LC-MS/MS analysis and immunoprecipitation revealed that PGRN underwent O-linked N-acetylglucosamine (O-GlcNAc) modification at threonine 272 (Thr272). Co-immunoprecipitation and confocal microscopy confirmed the interaction and colocalization of O-GlcNAc transferase (OGT) with PGRN. Reducing O-GlcNAcylation increased the ubiquitination of PGRN, while increasing O-GlcNAcylation inhibited ubiquitination and elevated PGRN stability, as measured by cycloheximide (CHX) chase experiments. This regulation of PGRN stability was directly linked to its expression levels. Moreover, mutation at the primary O-GlcNAc site Thr272 inhibited the activity of the PI3K/AKT/mTOR signaling pathway and suppressed HCC cell proliferation. Together, our findings indicate that O-GlcNAcylation at Thr272 is essential for PGRN-driven HCC cell proliferation.

Disease terms identified:
Carcinoma, Hepatocellular

Cell lines identified:

Protein
GRN

Abstract:
Polo-like kinase 1 (PLK1) is a crucial mitotic kinase that is implicated in various aspects of cell cycle. Many post-translational modifications have been identified on PLK1 to regulate its activation, stability, and localization. PLK1 has been shown previously to colocalize with the O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT), and OGT regulates PLK1 stability. In our recent work, we show that PLK1 is O-GlcNAcylated by click chemistry. Using stepped collisional energy/higher energy collision dissociation mass spectrometry, we mapped the PLK1 O-GlcNAc site to be T291. We further utilized fluorescent activated cell sorting and time-lapse microscopy to assess the mitotic defects of PLK1 O-GlcNAc mutants. In vivo studies in mouse xenograft demonstrated that it promoted uterine cancer tumorigenesis. In this chapter, we delineate the methodologies we used in studying PLK1 O-GlcNAcylation, including click chemistry, stepped collisional energy/higher energy collision dissociation mass spectrometry, fluorescent activated cell sorting, time-lapse microscopy, and mouse xenograft assays.

Disease terms identified:

Cell lines identified:

Protein
PLK1

Abstract:
V(D)J recombination secures the production of functional immunoglobulin (Ig) genes and antibody diversity during the early stages of B-cell development through long-distance interactions mediated by cis-regulatory elements and trans-acting factors. O-GlcNAcylation is a dynamic and reversible posttranslational modification of nuclear and cytoplasmic proteins that regulates various protein functions, including DNA-binding affinity and protein-protein interactions. However, the effects of O-GlcNAcylation on proteins involved in V(D)J recombination remain largely unknown. To elucidate this relationship, we downregulated O-GlcNAcylation in a mouse model by administering an O-GlcNAc inhibitor or restricting the consumption of a regular diet. Interestingly, the inhibition of O-GlcNAcylation in mice severely impaired Ig heavy-chain (IgH) gene rearrangement. We identified several factors crucial for V(D)J recombination, including YY1, CTCF, SMC1, and SMC3, as direct targets of O-GlcNAc modification. Importantly, O-GlcNAcylation regulates the physical interaction between SMC1 and SMC3 and the DNA-binding patterns of YY1 at the IgH gene locus. Moreover, O-GlcNAc inhibition downregulated DDX5 protein expression, affecting the functional association of CTCF with its DNA-binding sites at the IgH locus. Our results showed that locus contraction and long-range interactions throughout the IgH locus are disrupted in a manner dependent on the cellular O-GlcNAc level. In this study, we established that V(D)J recombination relies on the O-GlcNAc status of stage-specific proteins during early B-cell development and identified O-GlcNAc-dependent mechanisms as new regulatory components for the development of a diverse antibody repertoire.

Disease terms identified:

Cell lines identified:

Protein
MPEG1 CUL4B DHX8 RHG27 VIR PNISR FRPD1 RENT2 LAS1L ITIH4 THOC2 MMRN1 PYR1 YTDC2 PTPRB ANR44 RBM25 OSBL8 DAAF5 SAFB1 KI67 DESP YTDC1 UBE4A NUMA1 MORC3 HXK2 LEG9 KNG1 UBE3A DCTN1 DIAP1 U5S1 RL21 PHB2 CPSF2 DHX15 EXOC4 STAG2 AP1B1 PININ HNRH1 SP100 GP1BA ITB3 RL35A SPT5H DHX9 E41L2 BAZ1A ZFR ROA2 PRS6A FA5 AFAM COR1A SP1 C1QR1 COX2 AMY1 CO3 CO4B B2MG HBA HBB1 K1C10 K2C1 CFAB ALDOA TBA1B TBA3 ITAM K1C18 LDHA LCK APOA4 PTPRC CFAH TTHY ANXA2 ALBU A1AT1 SPA3K HS90A TRFL ENPL APOE MDHM GNAI2 RPB1 ITB1 PDIA1 NUCL APOA2 PTPRQ CALM2 EF1A1 4F2 PARP1 PERM FINC HS90B K2C8 ITA5 ITB2 TCPA RL7A GELS ICAM1 DNMT1 S10A6 RL27A RS16 RL7 RSSA LMNB1 ANXA6 RLA0 CD44 LEUK H12 CN37 AMPE HS71L G3P LAMP2 HSP72 ENOA PTBP1 PPIA TPIS LYZ1 PCNA PTPRA BASI KS6A1 KS6A3 COF1 FAS THRB RL13A BIP VIME PLMN VTDB A1AT2 CBL AP1G1 EIF3A EST1C ITAL CD11B MCM3 RS2 CD19 UBF1 TLN1 EZRI MOES KLKB1 H2AX VAV NCKP1 MUG1 KIF2A DPP4 PTN6 FETUA C5AR1 CEAM1 CD68 ANT3 SYWC KIF4 DPOLA RAB5C RAB18 CD22 TSP1 CALX RFC1 PRDX1 RL12 RL18 DNLI1 HSPA9 DYN2 RL28 MMP9 STAT1 STA5B EPS15 TCPQ MSH2 H14 H15 RAGP1 SIPA1 NSF PRS7 BRCC3 NEDD4 CAPZB RL6 RL5 RL13 RL36 KSYK PERE ROA1 MCM4 MCM5 SAHH K2C6A VATA PA2G4 RAB7A RL9 ADT2 IMA1 PON1 DPOD1 UBP10 KPYM STAT6 RL10A CEBPZ PIPNB MSH6 UBP5 ATPB UBP25 NICA ACTN4 EF2 OPA1 FOXP1 TPM2 WDHD1 ARPC4 RUVB1 PCBP1 ACTB IF4A1 RS20 UB2D3 ARF3 RL26 RL27 RL37A ARF4 HNRPK RS7 PRS4 RS8 RS15A RS14 RS23 RS18 RS11 RS13 SMD2 ARF6 PRS10 RS4X RL18A RL23A RS6 H4 VATB2 RAB1A RAN RL23 RS24 RS25 RS26 RL30 RL31 RS3 RL8 PROF1 RL40 HSP7C PHB1 RL22 RACK1 ACTS TBA4A TBB4B 1433F IMB1 M4K1 PKN1 STIM1 PYRG2 ROCK1 RAD50 PYRG1 TCPH TCPB TCPD TCPE TCPZ TCPG WNK1 RHOG RL19 H33 BACH2 MCM2 MCM6 RS3A ANX11 SMRC1 FUMH ARVC TBB5 APOA1 A1AT4 TYY1 HNRL2 LYAM3 TOP2A APOH TERA UBA1 PLAK ATPA IKZF1 SPA3M SMRCD TOP1 RAC2 PYC IF2P CBG ACADS AMBP PECA1 SSRP1 ZCH18 K2C80 PSA PTCD3 NSUN2 EDEM3 MCM9 TMC5 HMHA1 HP1B3 GUAA H2AV SMCA4 PRC2C MIDN K1C26 K22E PSMD1 BRE1B ESYT1 AAK1 RHG17 EDC4 UBP19 GPD1L ELNE SC31A IQGA2 K22O ITB2L C1TM UN13A PLCH1 PDS5B CENPJ DDX46 TR150 A16A1 EHMT1 MCTP2 RBM27 CYFP2 PSME4 MYO1G LC7L3 PUR4 MYH1 LEO1 SIN3A XRCC1 ODO1 HNRPD SAMH1 HELLS ARHG2 I17RA PML 2A5G PPM1G CFAI CERU CTCF PRDX2 EZH2 HCFC1 PA1B3 ARHG1 PLSL A2AP HSP74 DSG1A GSLG1 EWS RAD21 FSCN1 GDIB DDX5 HS105 ITIH2 ITA6 EI2BD SERA KINH PDCD4 PZP PRG2 MYH10 MCM7 NPM PCBP2 CTR9 DDX3X CD180 SPTB2 SPR1A TIF1B TFR1 RU17 SPT6H NDUA4 IF4G2 MINT RHG30 H2B1B TOP2B TPP2 AT2A3 H2A2C VINC PUR2 CLH1 SYMC GNPTA PDS5A CDC5L CE290 F120A UBP7 JADE3 K1C42 K2C72 SR140 K2C73 S23IP IF4G1 RBM26 P4R3A U520 ABCF1 SMHD1 UGGG1 XPO1 ANO6 KIF15 KIF11 FHOD1 FKB15 PTN23 LPPRC SMRC2 ECM29 CHD4 PK3C3 NUP98 GMIP NFRKB TEX2 UBE2O KDM3B CE162 CNOT1 CAND1 LARP1 VIP2 RS9 RL35 RS27L 2AAA SND1 ASAP2 IPO8 HUWE1 LC7L2 MBB1A INT7 CTDP1 PP6R1 ELP1 DCAF1 CLAP1 SCRIB PUM1 NU214 NAA15 FACD2 FBLL1 UBP2L SYMPK SIG10 DDX42 ANFY1 EFTU TNPO1 ROA3 PLD4 SYAC S2512 NU107 PTBP3 NRDC ERC6L GANAB SP130 NUP93 SUN2 RCC2 IPO5 EMSY ODP2 RBGPR SYLC SYQ ECHA RL24 CLAP2 CNDH2 PB1 FLNA SYIC IFIX CIP2A GEMI5 UBP47 CTL2 TBCD POGZ ANC2 KS6A5 EFL1 LCAP DOCK8 CND2 IWS1 RBM14 DOCK2 UBA6 MIC60 UFL1 VCIP1 NUP88 NED4L RPB2 AQR SMC4 SMC2 SYEP TCRG1 LONM OGT1 CHERP CCAR1 INT5 PYGB COPA PLCG2 INT4 EIF3B BCLF1 K319L URP2 DNM1L NEK9 FCHO1 PAF1 IPO11 CND1 MATR3 PLCL2 DP13A PO121 SF3A1 HNRPL NU133 EIF3C BST2 CD177 ADIPL CDC16 STPAP LRC8C ACSF2 EVI2B MYH9 UHRF1 VIGLN ADPGK PSMD2 HNRL1 AT1A1 MICA1 CCAR2 DX39A SRSF4 K2C79 RFA1 HNRPU S25A3 RBM39 SEC63 IPO4 SFPQ ACLY IF4A3 NDUS1 ATPG DDX1 UBAP2 HEMO IPO9 RBM5 PRP6 SMCA5 SP16H TADBP SF3B3 SYDC PP6R3 C1TC NOP2 PDE2A KIF2C K2C5 SIR1 XPO5 SMRD2 ECHB ARP3 EMIL1 UN45A ACON DPP3 HSP7E GTPB4 ARBK1 SRRT SF3B1 NU155 RRBP1 DHX30 RL17 NUDC2 6PGL COTL1 RM18 TRAP1 AT5F1 RL14 XPOT PRPS2 RRP44 SMC1A SMUF1 SMC3 PUR9 SNX2 ROA0 RL11 GARS RL15 MTREX MMS19 HNRPM SYRC NH2L1 RL34 GRIFN UB2V2 S10AE CORO7 STAG1 CUL5 SC23B CALL3 NOP56 RL4 EF1G PRP4 QCR2 PELP1 AP2B1 XRN2 NVL EIF3K 6PGD SYF1 EIF3F XPO7 IPO7 RENT1 BCAP PESC ERAP1 VPS35 EHD4 TFP11 XPO2 PKHA2 RBP2 UBE4B SHIP1 HRG XPO4 AN32B GTF2I DYHC1 STK4 COPB DDX21 ACINU FLII IQGA1 HYOU1 HIP1R FMNL1 SACS SART3 GIT2 MY18A ITA2B FAK2 CAF1A K1C17 FETUB PLEC PO210 ADDA PCLO COPG1 UBQL2 H2AY ZEB2 GALK1 SC11A MTA2 PR40A TIM MYO1C INSRR MD1L1 PDC6I PFKAP CXA10 GANP IF2G ADNP P5CS SAE2 ARI1 DX39B CLIC1 SYVC AP3B1 ILF3 USO1 HNRPC BAZ1B K1C16 SNUT1

Abstract:
O-GlcNAc transferase (OGT) is responsible for attaching O-linked N-acetylglucosamine (O-GlcNAc) to proteins, regulating diverse cellular processes ranging from transcription and translation to signaling and metabolism. This study focuses on the role and mechanisms of OGT in osteogenesis.

Disease terms identified:
Osteoporosis

Cell lines identified:

Protein
HDAC5 HDAC5

Abstract:
O-linked N-acetylglucosamine transferase (OGT)-catalyzed O-linked N-acetylglucosamine glycosylation (O-GlcNAcylation) is closely associated with diabetes progression. This study aims to investigate the mechanism of OGT in regulating endothelial dysfunction in gestational diabetes mellitus (GDM). Expressions of OGT, O-linked N-acetylglucosamine (O-GlcNAc), enhancer of zeste homolog 2 (EZH2), and HEK27me3 in human umbilical vein endothelial cells (HUVECs) and GDM-derived HUVECs (GDM-HUVECs) were assessed by western blot. RT-qPCR and western blot assays were used to test the OGT overexpression and EZH2 silencing levels. CCK-8, EdU, wound healing, and transwell invasion assays were used to analyze the cell proliferative, migratory, and invasive abilities. Tube formation assay was performed to evaluate angiogenesis ability of cells. Western blot assay was performed to estimate vascular endothelial growth factor (VEGF) and p-VEGFR2 levels in cells. The binding of O-GlcNAc and EZH2 after OGT overexpression was measured by Co-IP assay. The results showed that OGT, O-GlcNAc, EZH2, and HEK27me3 expressions were declined in GDM-HUVECs. OGT overexpression induced the proliferation, migration, and invasion of GDM-HUVECs, and also elevated angiogenesis and the expressions of VEGF and p-VEGFR2 in cells. O-GlcNAc, EZH2, and HEK27me3 expressions were upregulated after OGT overexpression. OGT upregulation induced the binding between O-GlcNAc and EZH2. EZH2 silencing attenuated the promotion of OGT overexpression on the proliferative, invasive, migratory, and angiogenic capacities of GDM-HUVECs. To be concluded, OGT overexpression stabilized EZH2 expression by promoting O-GlcNAcylation modification of EZH2, and further enhanced proliferation, migration, and invasion as well as angiogenesis of GDM-HUVECs. While these effects were decayed after EZH2 absenting. Overall, the modulation of OGT on endothelial dysfunction in GDM provides a novel perspective for the clinical treatment of GDM.

Disease terms identified:
Diabetes, Gestational Heart Diseases

Cell lines identified:

Protein
EZH2

Abstract:
Patients with estrogen receptor-positive breast cancer undergoing continuous adjuvant hormone therapy often experience delayed recurrence with tamoxifen use, potentially causing adverse effects. However, the lack of biomarkers hampers patient selection for extended endocrine therapy. This study aimed to elucidate the molecular mechanisms underlying delayed recurrence and identify biomarkers. When miRNA expression was assessed in luminal breast cancer tissues with and without delayed recurrence using NanoString, a significant increase in the expression of miR483-3p was observed in samples from patients with delayed recurrence compared with those without. miR483-3p expression was elevated in tamoxifen resistant (TAMR) EFM19 cells than in non-resistant EFM19 cells. Notably, genes associated with cancer metastasis (AMOTL2, ANKRD1, CTGF, and VEGF) were upregulated in TAMR EFM19 cells, although cell motility and proliferation were reduced. Transfection of miR483-3p mimics into both non-resistant EFM19 and MCF7 cells resulted in increased expression of cancer metastasis-related genes, but decreased proliferation and migration. Given that miR483-3p can bind to the 3'UTR region of O-GlcNAc transferase (OGT) and potentially affect its protein expression, we examined OGT protein levels and found that transfection with miR483-3p mimics selectively reduced OGT expression. Overall, breast cancer cells subjected to long-term hormone therapy displayed elevated miR483-3p expression, reducing motility and dormancy induction via decreased OGT expression. These findings suggest that miR483-3p is a potential biomarker for long-term endocrine therapy.

Disease terms identified:
Neoplasm Metastasis Breast Neoplasms Disease Resistance Neoplasms Carcinoma, Hepatocellular

Cell lines identified:
EFM19 MCF7 MDA-MB-415

Protein

Abstract:
Extracellular O-GlcNAc is a unique post-translational modification that occurs in the epidermal growth factor-like (EGF) domain of the endoplasmic reticulum (ER) lumen. The EGF domain-specific O-GlcNAc transferase (EOGT), catalyzes the transfer of O-GlcNAc to serine/threonine residues of the C-terminal EGF domain. Thus, EOGT-dependent O-GlcNAc modifications are mainly found in selective proteins that are localized in the extracellular spaces or extracellular regions of membrane proteins. In mammals, O-GlcNAc glycans can be extended to oligosaccharide structures similar to other types of EGF domain-specific O-glycans. The in vivo importance of O-GlcNAc glycans in mammals has been demonstrated in a human congenital disease caused by EOGT mutations and is extensively supported by genetic deletion in mice. This article reviews the findings on the structure and biochemical mechanism of EOGT-catalyzed O-GlcNAc biosynthesis, modified proteins, and in vivo functions elucidated by recent research in mammals.

Disease terms identified:

Cell lines identified:

Protein

Abstract:
The reversible glycosylation of nuclear and cytoplasmic proteins (O-GlcNAcylation) is catalyzed by a single enzyme, namely O-GlcNAc transferase (OGT). The mammalian Ogt gene is X-linked, and it is essential for embryonic development and for the viability of proliferating cells. We perturbed OGT's function in vivo by creating a murine allelic series of four single amino acid substitutions, reducing OGT's catalytic activity to a range of degrees. The severity of the embryonic lethality was proportional to the extent of impairment of OGT's catalysis, demonstrating that the O-GlcNAc modification itself is required for early development. We identified hypomorphic Ogt alleles that perturb O-GlcNAc homeostasis while being compatible with embryogenesis. The analysis of the transcriptomes of the mutant embryos at different developmental stages suggested a sexually-dimorphic developmental delay caused by the decrease in O-GlcNAc. Furthermore, a mild reduction of OGT's enzymatic activity was sufficient to loosen the silencing of endogenous retroviruses in vivo.

Disease terms identified:
Diabetes Mellitus Intellectual Disability Placenta Diseases Developmental Disabilities Carcinoma, Embryonal Embryo Loss Hypersensitivity, Immediate

Cell lines identified:
S2 ROSA26 mouse embryonic fibroblasts A9 ESCs FVB LSL 2F MEFs

Protein

Abstract:
Our previous study revealed a link between O-GlcNAc transferase (OGT) localization and protein phosphatase 2A (PP2A) activity in osteoblast. Given the association of PP2A downregulation with osteoblast differentiation, we hypothesized that OGT localization changes during this process. We examined OGT localization in MC3T3-E1 cells undergoing differentiation under normal and high glucose conditions. Changes in PP2A activity were followed by alterations in OGT localization. Organ culture of calvaria revealed similar OGT localization changes in bone-surrounding osteoblasts near the suture area. Furthermore, the levels of O-GlcNAc modification in various proteins including Runt-related transcription factor 2, Osterix, and ATP synthase subunit alpha (ATP5A) were shifted in parallel with OGT translocation. These findings suggest a regulatory role of OGT, under the influence of PP2A, during osteoblast differentiation.

Disease terms identified:

Cell lines identified:

Protein
RUNX2 SP7 SP7

Abstract:
Enhancing protein O-GlcNAcylation by pharmacological inhibition of the enzyme O-GlcNAcase (OGA) has been considered as a strategy to decrease tau and amyloid-beta phosphorylation, aggregation, and pathology in Alzheimer's disease (AD). There is still more to be learned about the impact of enhancing global protein O-GlcNAcylation, which is important for understanding the potential of using OGA inhibition to treat neurodegenerative diseases. In this study, we investigated the acute effect of pharmacologically increasing O-GlcNAc levels, using the OGA inhibitor Thiamet G (TG), in normal mouse brains. We hypothesized that the transcriptome signature in response to a 3 h TG treatment (50 mg/kg) provides a comprehensive view of the effect of OGA inhibition. We then performed mRNA sequencing of the brain using NovaSeq PE 150 (n = 5 each group). We identified 1234 significant differentially expressed genes with TG versus saline treatment. Functional enrichment analysis of the upregulated genes identified several upregulated pathways, including genes normally down in AD. Among the downregulated pathways were the cell adhesion pathway as well as genes normally up in AD and aging. When comparing acute to chronic TG treatment, protein autophosphorylation and kinase activity pathways were upregulated, whereas cell adhesion and astrocyte markers were downregulated in both datasets. AMPK subunit Prkab2 was one gene in the kinase activity pathway, and the increase after acute and chronic treatment was confirmed using qPCR. Interestingly, mitochondrial genes and genes normally down in AD were up in acute treatment and down in chronic treatment. Data from this analysis will enable the evaluation of the mechanisms underlying the impact of OGA inhibition in the treatment of AD. In particular, OGA inhibitors appear to have downstream effects related to bioenergetics which may limit their therapeutic benefits.

Disease terms identified:
Diffuse Neurofibrillary Tangles with Calcification Neurodegenerative Diseases Down Syndrome Alzheimer Disease Memory Disorders Cognition Disorders

Cell lines identified:
S2

Protein

Abstract:
The aim of this study was to investigate the potential molecular mechanisms by which taurine protects against cartilage degeneration.

Disease terms identified:
Inflammation Cartilage Diseases Osteoarthritis Anterior Cruciate Ligament Injuries

Cell lines identified:

Protein
GPX4

Abstract:
Tris (2-chloroethyl) phosphate (TCEP), recognized as an emerging pollutant, has been frequently detected in human blood. Maintenance of blood homeostasis is indispensable for regulating various physiological states and overall health, yet hematological toxicology of TCEP has not been extensively investigated. Platelets, a vital component of blood, are fundamental in the processes of hemostasis and thrombosis through their activation; thus, this study was designed to elucidate the effects and underlying mechanisms of TCEP on platelet activation. Utilizing an in vivo model, we conducted a proteomic analysis of platelets and found that TCEP exposure inhibited platelet activation. An ex vivo platelet evaluation system was employed to further dissect the processes of platelet activation, revealing that TCEP predominantly suppressed platelet aggregation, degranulation and clot retraction. These processes were highly dependent on energy metabolism, and TCEP was found to decrease ATP levels, primarily by impairing glycolysis and pentose phosphate pathways. Subsequent investigation into the molecular mechanisms revealed that TCEP decreased the activity of phosphofructokinase platelet (PFKP) by enhancing O-linked N-acetylglucosamine (O-GlcNAc) transferase interaction with PFKP. This study is the first to uncover the disruptive effects of TCEP on platelet activation process, providing valuable insights into the assessment of hematologic health risks associated with TCEP-like emerging pollutants exposure.

Disease terms identified:

Cell lines identified:

Protein

Abstract:
Glycosylation is a critical post-translational modification that influences protein folding, stability and function. While extensively studied in extracellular and intracellular regions, glycosylation within transmembrane (TM) regions and at membrane interfaces remains poorly understood. This study aimed to map O- and N-glycosylation sites in these regions using a comprehensive database search and structural validation where possible. Extensive database searches revealed glycosylation sites in a range of membrane proteins. Only the sites falling in the TM regions and at the membrane interface (according to Uniprot annotations) were retained. The location of these sites was confirmed based on available 3D structures. We identified 32 O-glycosylation sites and 7 N-glycosylation sites in the TM domains of 29 proteins. O-GlcNAc sites validated as located within TM regions presented side chains either oriented toward the lipid bilayer or buried within the protein. N-glycosylation sites predicted in protein TM regions were largely confined to interface or extracellular domains. The results obtained here highlight the occurrence of glycosylation in TM regions of proteins and at membrane interfaces. This dataset provides a valuable foundation for the further exploration of structural and functional roles of glycosylation in membrane-associated regions.

Disease terms identified:

Cell lines identified:

Protein

Abstract:
Renal cell carcinoma (RCC) is one of the most common urological malignancies worldwide, and advanced patients often face challenges with chemotherapy resistance and poor prognosis. Ferroptosis, a novel form of cell death, offers potential therapeutic prospects. In this study, we found that DJ-1 was elevated in kidney renal clear cell carcinoma (KIRC), and this abnormal expression pattern was closely associated with clinical pathological characteristics and worse prognosis. Our experiments both in vivo and in vitro revealed that DJ-1 enhanced the malignant characteristics of KIRC, leading to increased tumor growth. Additionally, DJ-1 inhibited ferroptosis through promoting homocysteine (Hcy) synthesis in the transsulfuration pathway in KIRC cells. Mechanistic studies revealed that O-GlcNAc transferase (OGT) mediated O-GlcNAcylation of DJ-1 was crucial for maintaining its homodimeric structure. Importantly, O-GlcNAcylation-deficient mutation of DJ-1 at T19 residue enhanced the interaction between S-adenosyl homocysteine hydrolase (SAHH) and the negative regulatory factor S-adenosyl homocysteine hydrolase-like-1 (AHCYL1), thereby inhibited the activities of SAHH and transsulfuration pathway. In summary, the oncogenic role of DJ-1 in KIRC was closely related to the reduction of ferroptosis, and the O-GlcNAcylation of DJ-1 exerted an antioxidant effect by activating the transsulfuration pathway. Therefore, DJ-1, specifically O-GlcNAcylation of DJ-1 could represent an important target for ferroptosis-based anti-tumor therapy.

Disease terms identified:
Neoplasms Carcinoma, Renal Cell

Cell lines identified:

Protein
PARK7

Abstract:
Fat mass and obesity-associated protein (FTO) was the first m6A demethylase identified, which is responsible for eliminating m6A modifications in target RNAs. While it is well-established that numerous cytosolic and nuclear proteins undergo O-GlcNAcylation, the possibility of FTO being O-GlcNAcylated and its functional implications remain unclear. This study found that a negative correlation between FTO expression and O-GlcNAcylation in patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). The decreased O-GlcNAcylation on FTO can result in diminished m6A modification of SRY-related high mobility group box 4 (SOX4). This led to the promotion of cell apoptosis and inhibition of cell proliferation in MDS/AML. The O-GlcNAcylation of FTO stabilized SOX4 transcripts in an m6A-dependent manner, resulting in increased AKT and MAPK phosphorylation and decreased cell apoptosis. Inhibiting FTO O-GlcNAcylation significantly slowed AML progression in vitro, a finding supported by clinical data in MDS/AML patients. In conclusion, our study highlights the crucial role of FTO O-GlcNAcylation in RNA m6A methylation and the progression of MDS/AML, thereby providing a potential therapeutic avenue for these formidable diseases.

Disease terms identified:
Carcinogenesis Leukemia Leukemia, Myeloid, Acute Hematologic Neoplasms Myelodysplastic Syndromes Neoplasms

Cell lines identified:
KG1a-FTO-S173-HA SKM1 HA KG1a-FTO-S173A KG1a-FTO-HA KG1a FTO- KG1a-FTO

Protein
FTO

Abstract:
O-GlcNAcylation is a post-translational modification characterized by the covalent attachment of a single moiety of GlcNAc on serine/threonine residues in proteins. Tyrosine hydroxylase (TH), the rate-limiting step enzyme in the catecholamine synthesis pathway and responsible for production of the dopamine precursor, L-DOPA, has its activity regulated by phosphorylation. Here, we show an inverse feedback mechanism between O-GlcNAcylation and phosphorylation of TH at serine 40 (TH pSer40). First, we showed that, during PC12 cells neuritogenesis, TH O-GlcNAcylation decreases concurrently with the increase of pSer40. In addition, an increase in O-GlcNAcylation induces a decrease in TH pSer40 only in undifferentiated PC12 cells, while the decrease in O-GlcNAcylation leads to an increase in TH pSer40 levels in both undifferentiated and differentiated PC12 cells. We further show that this feedback culminates on the regulation of L-DOPA intracellular levels. Interestingly, it is noteworthy that decreasing O-GlcNAcylation is much more effective on TH pSer40 regulation than increasing its levels. Finally, ex vivo analysis confirmed the upregulation of TH pSer40 when O-GlcNAcylation levels are reduced in dopaminergic neurons from C57Bl/6 mice. Taken together, these findings demonstrate a dynamic control of L-DOPA production by a molecular crosstalk between O-GlcNAcylation and phosphorylation at Ser40 in tyrosine hydroxylase.

Disease terms identified:

Cell lines identified:
PC12

Protein
TY3H

Abstract:
O-GlcNAcylation is an important biological process in regulating the function of many nucleocytoplasmic proteins in cells.  Enhancement of O-GlcNAcylation was associated with cancer development and progression.  Here, we demonstrated the involvement of O-GlcNAcylation in melanoma metastasis.  Using the data from GEO database, we found that O-GlcNAcylation and its related enzymes, including glutamine fructose-6-phosphate amidotransferase (GFAT), O-GlcNAc transferase (OGT), and O-GlcNAcase (OGA); were elevated in metastatic melanoma compared with primary tumors and normal tissues.  Functional analyses in melanoma cell lines--MNT-1, SK-MEL-28, and A-375 showed that suppression of O-GlcNAcylation by siRNA against OGT significantly reduces the migration and invasion abilities of the cells.  Phosphorylation of Akt and NFkB was drastically suppressed after knockdown of OGT, suggesting the role of O-GlcNAcylation in regulating the Akt-NFkB signaling pathway.  In addition, we found that the NFkB target genes, such as ZEB-2 and MCT-1, were significantly upregulated in metastatic tumors compared with primary tumors.  MCT-1 expression in melanoma tissues was also correlated with O-GlcNAcylation level.  Taken together, we have demonstrated in this study the possible role of O-GlcNAcylation in controlling melanoma metastasis via upregulating MCT-1 expression through activation of Akt-NFkB signaling pathway.

Disease terms identified:
Neoplasm Metastasis Neoplasms Melanoma

Cell lines identified:

Protein

Abstract:
The accurate prediction of O-GlcNAcylation sites is crucial for understanding disease mechanisms and developing effective treatments. Previous machine learning models primarily relied on primary or secondary protein structural and related properties, which have limitations in capturing the spatial interactions of neighboring amino acids. This study introduces local environmental features as a novel approach that incorporates three-dimensional spatial information, significantly improving model performance by considering the spatial context around the target site. Additionally, we utilize sparse recurrent neural networks to effectively capture sequential nature of the proteins and to identify key factors influencing O-GlcNAcylation as an explainable machine learning model.

Disease terms identified:

Cell lines identified:

Protein

Abstract:
Autophagy is a "self-eating" biological process that degrades cytoplasmic contents to ensure cellular homeostasis. Its response to stimuli occurs in two stages: Within a few to several hours of exposure to a stress condition, autophagic flow rapidly increases, which is mediated by post-translational modification (PTM). Subsequently, the transcriptional program is activated and mediates the persistent autophagic response. O-linked β-N-acetylglucosamine (O-GlcNAc) modification is an inducible and dynamically cycling PTM; mounting evidence suggests that O-GlcNAc modification participates in the total autophagic process, including autophagy initiation, autophagosome formation, autophagosome-lysosome fusion, and transcriptional process. In this review, we summarize the current knowledge on the emerging role of O-GlcNAc modification in regulating autophagy-associated proteins and explain the different regulatory effects on autophagy exerted by O-GlcNAc modification.

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Protein

Abstract:
Aging changes the protein activity status to affect the body's functions. However, how aging regulates protein posttranslational modifications (PTMs) to modulate the antiviral defense ability of the body remains unclear. Here, we found that aging promotes STAT1 β-hydroxybutyrylation (Kbhb) at Lys592, which inhibits the interaction between STAT1 and type-I interferon (IFN-I) receptor 2 (IFNAR2), thereby attenuating IFN-I-mediated antiviral defense activity. Additionally, we discovered that a small molecule from a plant source, hydroxy camptothecine, can effectively reduce the level of STAT1 Kbhb, thus increasing antiviral defense ability in vivo. Further studies revealed that STAT1 O-GlcNAc modifications at Thr699 block CBP-induced STAT1 Kbhb. Importantly, fructose can improve IFN-I antiviral defense activity by orchestrating STAT1 O-GlcNAc and Kbhb modifications. This study reveals the significance of the switch between STAT1 Kbhb and O-GlcNAc modifications in regulating IFN-I antiviral immunity during aging and provides potential strategies to improve the body's antiviral defense ability in elderly individuals.

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Protein
STAT1

Abstract:
A key nutrient sensing process in all animal tissues is the dynamic attachment of O-linked N-acetylglucosamine (O-GlcNAc). Determining the targets and roles of O-GlcNAc glycoproteins has the potential to reveal insights into healthy and diseased metabolic states. In cell studies, thousands of proteins are known to be O-GlcNAcylated, but reference datasets for most tissue types in animals are lacking. Here, we apply a chemoenzymatic labeling study to compile a high coverage dataset of quadriceps skeletal muscle O-GlcNAc glycoproteins from mice. Our dataset contains over 550 proteins, and > 80% of the dataset matched known O-GlcNAc proteins. This dataset was further annotated via bioinformatics, revealing the distribution, protein interactions, and gene ontology (GO) functions of these skeletal muscle proteins. We compared these quadriceps glycoproteins with a high-coverage O-GlcNAc enrichment profile from mouse hearts and describe the key overlap and differences between these tissue types. Quadriceps muscles can be used for biopsies, so we envision this dataset to have potential biomedical relevance in detecting aberrant glycoproteins in metabolic diseases and physiological studies. This new knowledge adds to the growing collection of tissues with high-coverage O-GlcNAc profiles, which we anticipate will further the systems biology of O-GlcNAc mechanisms, functions, and roles in disease.

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Protein
A0A087WS16 A0A0N4SUN5 A0A286YCS6 A0A5F8MPM4 A0A5F8MPQ4 A0A668KL51 A0A7N9VR94 A2A6J0 A2A6Q8 OBSCN A2AEX6 A2AI87 A2AKD7 TITIN KLH41 ARMT1 OSBL8 SHAN1 D3Z0V7 D3Z2B4 CD054 E0CZE0 E9PYG6 E9PYI8 E9PZD8 RYR1 E9Q1W3 NU153 E9Q3P4 RN213 E9Q616 TRDN E9QL12 E9QN70 E9QND8 F6QYF8 F6VY18 F6YT88 F8VPN4 F8WGD9 MYH2 G3UYC5 RGS22 G3X972 AT2B1 G5E895 G5E8L1 G5E8R7 H7BWZ9 J3QN31 M0QW57 HXK2 CA2D1 PRDX6 DLDH HCD2 MK12 SYPL1 CASQ1 PHB2 CAN1 CALU CAVN1 IMPA1 NIPS2 AT2A2 PDLI3 PGAM2 PDLI1 RTN2 NTR1 WDR1 PLIN4 ZFR SEM3F ACTN3 SYPL2 CAH2 CO3 LAMC1 NU5M ATP8 FABP4 MYG ALDOA KAPCA AATC AATM TBA3 LDHA MAOX KCRM ANXA2 A1AT1 SPA3K HS90A PHKG1 SODC MDHM ITB1 PDIA1 PGK1 MYL3 SODM UBB CALM3 ANXA1 EF1A1 CATB TAU GSTM1 H2B1F H10 FINC FABPH DMD COX5A TNNI2 MYH3 MYH8 CAH1 GPDA RL7 MDHC HSPB1 ANXA6 GLNA B4GT1 H12 CAH3 LEG1 LDHB HS71L G3P ENOA PPIA TPIS CATD COF1 FAS GSTP1 SERPH COX5B COX41 BIP VIME TNNC2 PLMN ENOB VTDB CLK1 EST1C RS2 TLN1 RADI DHE3 FKB1A MAP4 PLAP PDIA3 ADHX KCC2B PGS2 MUG1 PABP1 DESM AIMP1 PRVA UBP4 ODPA FAAA PRDX1 RL12 HSPA9 CAP1 ACSL1 ECI1 STA5B H14 H11 H15 H13 ALDR COF2 ACADM MYO1B ALDH2 CAZA2 PFKAM CACP RL5 CBR1 ADT1 SAHH CSRP3 ACADV FMOD ACADL CAV3 ADT2 EAA3 AAAT KPYM CPT2 ODB2 MOT1 IDHP STMN1 RD23B PUR8 ADK ACYP2 CX6B1 UBP5 ATPB UCP3 EF2 TPM1 IRPL1 ACTB CDC42 RAB5B RAB10 UB2D1 1433G RS7 PP1B 1433E RS11 EF1A2 H4 RAB1A RAN RL23 CYC RS3 YBOX1 RAC1 LIS1 HSP7C CH60 1433Z HMGB1 IF5A1 ACTS TBA4A TBB4B MP2K6 PEBP1 STIM1 HINT1 MYBPH NACAM TCPH TCPB TCPD TCPE TCPZ SGCB WNK1 ARF5 ISC2A CSRP1 RS3A SPSY MYL11 FUMH LYPA1 ARVC PRDX5 XDH NDKB TERA UBA1 CAC1S ATPA CO6A1 PGBM PYC ACADS KCMA1 PADI2 CD36 Q14BI5 FAT4 CNNM3 Q3TCF3 PDLI7 PRC2C SCRN3 DDB1 K0930 Q3UER8 LIMC1 PRRC1 EID3 AMPD1 Q561M1 MYPN Q5F247 MLIP Q5MJ56 CLU MYH4 MYH1 UBR3 MYPC2 ODO1 LAMA2 COCA1 STIP1 REEP5 VDAC2 VDAC3 VDAC1 COQ8A PRDX2 HCFC1 LAMB2 HSP74 HCDH FBN1 GDIB PZP NNTM DDX3X MYOM1 SPEG NDUA4 NUP62 AT2A3 GPDM VINC PUR2 CLH1 MYOF HECD1 F120A HELZ Q6NVF7 IF4G1 Q6P1B9 Q6P6L5 KCRS LPPRC KMT2D AT1A2 Q6S9I0 CAND1 CAND2 CMYA5 VWA2 TLN2 2AAA MIC27 PICAL Q7TPG0 MBB1A SRCA ATX2L Q7TQS8 KPBB Q80T54 NU214 UBP2L PANK4 Q810Q0 EFTU H2A3 LPP PSD11 S2512 ECHM EIF2A ODPX MAON ODP2 ECHA Q8BPI2 Q8BUY2 DHPR SYP2L THIM STAC3 ASGL1 TLK1 PRR33 STBD1 MIC60 SYNPO CPLN1 SYEP UN45B PGP DRS7C EI2BE PDLI5 AGO3 EFGM FIBB COQ9 SDHA VRK3 NNRE HIBCH THIL AIMP2 BLMH CMBL UBQL1 TSN8 SLF1 CACB1 AT2A1 CLYBL PRAF3 LSM1 MAVS MYLK2 EST1D MYH9 PSMD2 HNRL1 LMCD1 HNRPU S25A3 FLNC NDUS1 RINI ATPG DDX1 UBAP2 NDUS2 CISD1 SH319 HEMO SYNP2 NDUV1 MYH7 PCCA UGPA ETFD MACD1 C1TC CLIP1 MPI CPT1B TALDO THTM GORS2 ECHB ACON NAMPT 3HIDH DHRS4 NDUAA ETFA PARK7 ASPN MCCA PPR3A GDIR1 LGUL NDUC2 DECR NDUA2 SDHB TMED6 GLRX3 AT5F1 ACO13 RL14 NDUB7 M2OM UCRI CHSP1 SFT2C PUR9 SGT1 CENPV SERB1 SPCS2 QCR1 NSF1C CISY ODPB PGM1 SCOT1 GAL3A RAB1B ODO2 NDUV2 FUND2 IDH3A RL4 EF1G CA074 ATPO PXL2B QCR2 ACDSB MYPT1 Q9DBT6 DCAF6 OCTC NDUA9 NDUA8 PUR6 NDUBA NDUS3 ETFB ATP5H MIC26 MMSA RB27A JPH2 JPH1 IVD DYHC1 NIT2 ACTN2 MYOTI PROF2 MYOZ1 PRELP YBOX3 MBNL1 LDB3 HIG1A TRXR1 B4GT5 PPCE PLEC S2513 NDRG2 DNJA2 UBQL2 FHL3 GLYG ESTD KAD1 PDC6I PYGM SUCA ECI2 SH3BG ARC1B ABEC2 VAPA AIFM1 GYS1 STRAP LETM1 SUCB1 S4R1W1

Abstract:
How reversible glycosylation of DNA-bound proteins acts on transcription remains scarcely understood. O-linked β-N-acetylglucosamine (O-GlcNAc) is the only known form of glycosylation modifying nuclear proteins, including RNA polymerase II (RNA Pol II) and many transcription factors. Yet, the regulatory function of the O-GlcNAc modification in mammalian chromatin remains unclear.

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Protein
YTDC1 MYC PO5F1 PO2F1 TBP SOX2 TYY1 TET1 TET2 SIN3A KLF4 CTCF HCFC1 NF2L1 SMAD3 ZN281 RAF1 BRD4 NRF1

Abstract:
O-linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation) is a monosaccharide modification on proteins predominantly inside cells. It is widely appreciated that spatiotemporal protein O-GlcNAcylation regulates a plethora of biological processes. High-throughput analytical techniques, particularly site-specific O-GlcNAc proteomics, have tremendously advanced the profiling of O-GlcNAc proteomes. Recently we established O-GlcNAcAtlas, a highly curated database of O-GlcNAc proteins/peptides/sites from experiments reported in the past forty years. However, a resource for O-GlcNAcylation quantification information is not available yet. Herein, we provide an updated database O-GlcNAcAtlas 4.0 by incorporating information of O-GlcNAcylation quantification. Exhaustive curation of published literature yielded a total of about 5,400 quantification events for 3,130 unique O-GlcNAc sites. The quantification vales were then systematically integrated with the specific O-GlcNAc sites and catalogued in O-GlcNAcAtlas, with key experimental details (including sample sources, conditions and methods) presented. Taken together, we present O-GlcNAcAtlas 4.0, a unique database hosting qualitative and quantitative data of O-GlcNAcylation on proteins. As a comprehensive repository supplemented with protein O-GlcNAcylation dynamics, the updated database will further facilitate related functional investigations by the biomedical community. O-GlcNAcAtlas 4.0 is freely accessible at https://oglcnac.org/atlas/.

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Protein

Abstract:
Protein O-GlcNAcylation is a prevalent and dynamic post-translational modification that targets a multitude of nuclear and cytoplasmic proteins. Through the modification of diverse substrates, O-GlcNAcylation plays a pivotal role in essential cellular processes, including transcription, translation, and protein homeostasis. Dysregulation of O-GlcNAc homeostasis has been implicated in a variety of diseases, including cardiovascular diseases, cancer, and neurodegenerative diseases. Studying O-GlcNAcylated proteins in different tissues is crucial to understanding the pathogenesis of these diseases. However, identifying phenotype-relevant candidate substrates in a tissue-specific manner remains unfeasible. We developed a novel tool for the analysis of O-GlcNAcylated proteins, combining a catalytically inactive CpOGA mutant CpOGA^CD and TurboID proximity labeling technology. This tool converts O-GlcNAc modifications into biotin labeling, enabling the enrichment and mass spectrometry (MS) identification of O-GlcNAcylated proteins in specific tissues. Meanwhile, TurboID-CpOGA^DM, which carries two point mutations that inactivate both its catalytic and binding activities toward O-GlcNAc modification, was used as a control to differentiate O-GlcNAc-independent protein-protein interactions. We have successfully used TurboID-CpOGA^CD/DM (TurboID-CpOGA^M) to enrich O-GlcNAc proteins in Drosophila combining the UAS/Gal4 system. Our protocol provides a comprehensive workflow for tissue-specific enrichment of candidate O-GlcNAcylated substrates and offers a valuable tool for dissecting tissue-specific O-GlcNAcylation functions in Drosophila. Key features • Innovative approach to studying O-GlcNAcylation: Combines a catalytically inactive CpOGA mutant (CpOGA^CD), TurboID proximity labeling technology, and the UAS/Gal4 system for tissue-specific analysis. • Tissue-specific focus: Enables enrichment and mass spectrometry (MS) identification of O-GlcNAcylated proteins in specific tissues of Drosophila. • Biotin labeling conversion: Converts O-GlcNAc modifications into biotin tags, facilitating downstream enrichment and analysis. • Powerful tool for understanding the role of O-GlcNAcylation in cellular processes and its involvement in diseases such as cardiovascular diseases, cancer, and neurodegenerative disorders.

Disease terms identified:
Neurodegenerative Diseases Neoplasms Cardiovascular Diseases

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Protein