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Formichetti S, Serrano JB, Chitnavis U, Sadowska A, Liu N, Boskovic A, Boulard M. Perturbing nuclear glycosylation in the mouse preimplantation embryo slows down embryonic development. Proc Natl Acad Sci U S A 2025; 122:e2410520122. [PMID: 40203037 PMCID: PMC12012502 DOI: 10.1073/pnas.2410520122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 03/14/2025] [Indexed: 04/11/2025] Open
Abstract
The main form of intracellular protein glycosylation (O-GlcNAc) is reversible and has been mapped on thousands of cytoplasmic and nuclear proteins, including RNA polymerase II, transcription factors, and chromatin modifiers. The O-GlcNAc modification is catalyzed by a single enzyme known as O-GlcNAc Transferase, that is required for mammalian early development. Yet, neither the regulatory function of protein O-GlcNAcylation in the embryo nor the embryonic O-GlcNAc proteome have been documented. Here, we devised a strategy to enzymatically remove O-GlcNAc from preimplantation embryonic nuclei, where this modification accumulates coincidently with embryonic genome activation (EGA). Unexpectedly, the depletion of nuclear O-GlcNAc to undetectable levels has no impact on EGA, but dampens the transcriptional upregulation of the translational machinery, and triggers a spindle checkpoint response. These molecular alterations were phenotypically associated with a developmental delay starting from early cleavage stages and persisting after embryo implantation, establishing a link between nuclear glycosylation and the pace of embryonic development.
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Affiliation(s)
- Sara Formichetti
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL) Rome, Monterotondo00015, Italy
- Combined Faculty of Mathematics, Engineering and Natural Sciences, collaboration for Joint PhD Degree between European Molecular Biology Laboratory and Heidelberg University, Heidelberg69117, Germany
| | - Joana B. Serrano
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL) Rome, Monterotondo00015, Italy
| | - Urvashi Chitnavis
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL) Rome, Monterotondo00015, Italy
| | - Agnieszka Sadowska
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL) Rome, Monterotondo00015, Italy
| | - Na Liu
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL) Rome, Monterotondo00015, Italy
| | - Ana Boskovic
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL) Rome, Monterotondo00015, Italy
| | - Matthieu Boulard
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL) Rome, Monterotondo00015, Italy
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2
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Sepulveda H, Li X, Arteaga-Vazquez LJ, López-Moyado IF, Brunelli M, Hernández-Espinosa L, Yue X, Angel JC, Brown C, Dong Z, Jansz N, Puddu F, Modat A, Scotcher J, Creed P, Kennedy PH, Manriquez-Rodriguez C, Myers SA, Crawford R, Faulkner GJ, Rao A. OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide. Nat Struct Mol Biol 2025:10.1038/s41594-025-01505-9. [PMID: 40155743 DOI: 10.1038/s41594-025-01505-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/31/2025] [Indexed: 04/01/2025]
Abstract
O-GlcNAc transferase (OGT) interacts robustly with all three mammalian TET methylcytosine dioxygenases. Here we show that deletion of the Ogt gene in mouse embryonic stem (mES) cells results in a widespread increase in the TET product 5-hydroxymethylcytosine in both euchromatic and heterochromatic compartments, with a concomitant reduction in the TET substrate 5-methylcytosine at the same genomic regions. mES cells treated with an OGT inhibitor also displayed increased 5-hydroxymethylcytosine, and attenuating the TET1-OGT interaction in mES cells resulted in a genome-wide decrease of 5-methylcytosine, indicating that OGT restrains TET activity and limits inappropriate DNA demethylation in a manner that requires the TET-OGT interaction and the catalytic activity of OGT. DNA hypomethylation in OGT-deficient cells was accompanied by derepression of transposable elements predominantly located in heterochromatin. We suggest that OGT protects the genome against TET-mediated DNA demethylation and loss of heterochromatin integrity, preventing the aberrant increase in transposable element expression noted in cancer, autoimmune-inflammatory diseases, cellular senescence and aging.
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Affiliation(s)
- Hugo Sepulveda
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Laboratory of Transcription and Epigenetics, Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Xiang Li
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Leo J Arteaga-Vazquez
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Isaac F López-Moyado
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Melina Brunelli
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Lot Hernández-Espinosa
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Xiaojing Yue
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - J Carlos Angel
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Caitlin Brown
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Zhen Dong
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Natasha Jansz
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Fabio Puddu
- biomodal, Chesterford Research Park, Cambridge, UK
| | | | | | - Páidí Creed
- biomodal, Chesterford Research Park, Cambridge, UK
| | - Patrick H Kennedy
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Cindy Manriquez-Rodriguez
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Samuel A Myers
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | | | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia.
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
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3
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Rucli S, Descostes N, Ermakova Y, Chitnavis U, Couturier J, Boskovic A, Boulard M. Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II. Genome Biol 2025; 26:69. [PMID: 40128797 PMCID: PMC11931877 DOI: 10.1186/s13059-025-03537-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 03/11/2025] [Indexed: 03/26/2025] Open
Abstract
BACKGROUND 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. RESULTS Here, we combine genome-wide profiling of O-GlcNAc-modified proteins with perturbations of intracellular glycosylation, RNA Pol II-degron, and super-resolution microscopy. Genomic profiling of O-GlcNAc-modified proteins shows a non-random distribution across the genome, with high densities in heterochromatin regions as well as on actively transcribed gene promoters. Large-scale intersection of the O-GlcNAc signal at promoters with public ChIP-seq datasets identifies a high overlap with RNA Pol II and specific cofactors. Knockdown of O-GlcNAc Transferase (Ogt) shows that most direct target genes are downregulated, supporting a global positive role of O-GlcNAc on the transcription of cellular genes. Rapid degradation of RNA Pol II results in the decrease of the O-GlcNAc levels at promoters encoding transcription factors and DNA modifying enzymes. RNA Pol II depletion also unexpectedly causes an increase of O-GlcNAc levels at a set of promoters encoding for the transcription machinery. CONCLUSIONS This study provides a deconvoluted genomic profiling of O-GlcNAc-modified proteins in murine and human cells. Perturbations of O-GlcNAc or RNA Pol II uncover a context-specific reciprocal functional interplay between the transcription machinery and the O-GlcNAc modification.
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Affiliation(s)
- Sofia Rucli
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Rome, Italy
- Collaboration for a joint PhD degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Nicolas Descostes
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Rome, Italy
| | - Yulia Ermakova
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Rome, Italy
| | - Urvashi Chitnavis
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Rome, Italy
| | - Jeanne Couturier
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Rome, Italy
| | - Ana Boskovic
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Rome, Italy
| | - Matthieu Boulard
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Rome, Italy.
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4
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Formichetti S, Sadowska A, Ascolani M, Hansen J, Ganter K, Lancrin C, Humphreys N, Boulard M. Genetic gradual reduction of OGT activity unveils the essential role of O-GlcNAc in the mouse embryo. PLoS Genet 2025; 21:e1011507. [PMID: 39787076 PMCID: PMC11717234 DOI: 10.1371/journal.pgen.1011507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 11/18/2024] [Indexed: 01/12/2025] Open
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.
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Affiliation(s)
- Sara Formichetti
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Italy
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Germany
| | - Agnieszka Sadowska
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Italy
| | - Michela Ascolani
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Italy
| | - Julia Hansen
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Italy
| | - Kerstin Ganter
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Italy
| | - Christophe Lancrin
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Italy
| | - Neil Humphreys
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Italy
| | - Mathieu Boulard
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Italy
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5
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Jo S, Esch N, Nguyen A, Wong A, Mohan R, Kim C, Blandino-Rosano M, Bernal-Mizrachi E, Alejandro EU. Loss of O-GlcNAcylation modulates mTORC1 and autophagy in β cells, driving diabetes 2 progression. JCI Insight 2024; 9:e183033. [PMID: 39388284 PMCID: PMC11623944 DOI: 10.1172/jci.insight.183033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 10/08/2024] [Indexed: 10/12/2024] Open
Abstract
Type 2 diabetes (T2D) arises when pancreatic β cells fail to produce sufficient insulin to control blood glucose appropriately. Aberrant nutrient sensing by O-GlcNAcylation and mTORC1 is linked to T2D and the failure of insulin-producing β cells. However, the nature of their crosstalk in β cells remains unexplored. Recently, O-GlcNAcylation, a posttranslation modification controlled by enzymes O-GlcNAc transferase/O-GlcNAcase (OGT/OGA), emerged as a pivotal regulator for β cell health; deficiency in either enzyme causes β cell failure. The present study investigates the previously unidentified connection between nutrient sensor OGT and mTORC1 crosstalk to regulate β cell mass and function in vivo. We show reduced OGT and mTORC1 activity in islets of a preclinical β cell dysfunction model and islets from humans with obesity. Using loss or gain of function of OGT, we identified that O-GlcNAcylation positively regulated mTORC1 signaling in β cells. O-GlcNAcylation negatively modulated autophagy, as the removal of OGT increased autophagy, while the deletion of OGA decreased it. Increasing mTORC1 signaling, via deletion of TSC2, alleviated the diabetic phenotypes by increasing β cell mass but not β cell function in OGT-deficient mice. Downstream phospho-protein signaling analyses revealed diverging effects on MKK4 and calmodulin signaling between islets with OGT, TSC2, or combined deletion. These data provide evidence of OGT's significance as an upstream regulator of mTORC1 and autophagy, crucial for the regulation of β cell function and glucose homeostasis.
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Affiliation(s)
- Seokwon Jo
- Department of Integrative Biology & Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Nicholas Esch
- Department of Integrative Biology & Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Anh Nguyen
- Department of Integrative Biology & Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Alicia Wong
- Department of Integrative Biology & Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Ramkumar Mohan
- Department of Integrative Biology & Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Clara Kim
- Department of Integrative Biology & Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Manuel Blandino-Rosano
- Department of Internal Medicine, Division of Endocrinology, Metabolism and Diabetes, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Ernesto Bernal-Mizrachi
- Department of Internal Medicine, Division of Endocrinology, Metabolism and Diabetes, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Emilyn U. Alejandro
- Department of Integrative Biology & Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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6
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Cheng SS, Mody AC, Woo CM. Opportunities for Therapeutic Modulation of O-GlcNAc. Chem Rev 2024; 124:12918-13019. [PMID: 39509538 DOI: 10.1021/acs.chemrev.4c00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
O-Linked β-N-acetylglucosamine (O-GlcNAc) is an essential, dynamic monosaccharide post-translational modification (PTM) found on serine and threonine residues of thousands of nucleocytoplasmic proteins. The installation and removal of O-GlcNAc is controlled by a single pair of enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), respectively. Since its discovery four decades ago, O-GlcNAc has been found on diverse classes of proteins, playing important functional roles in many cellular processes. Dysregulation of O-GlcNAc homeostasis has been implicated in the pathogenesis of disease, including neurodegeneration, X-linked intellectual disability (XLID), cancer, diabetes, and immunological disorders. These foundational studies of O-GlcNAc in disease biology have motivated efforts to target O-GlcNAc therapeutically, with multiple clinical candidates under evaluation. In this review, we describe the characterization and biochemistry of OGT and OGA, cellular O-GlcNAc regulation, development of OGT and OGA inhibitors, O-GlcNAc in pathophysiology, clinical progress of O-GlcNAc modulators, and emerging opportunities for targeting O-GlcNAc. This comprehensive resource should motivate further study into O-GlcNAc function and inspire strategies for therapeutic modulation of O-GlcNAc.
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Affiliation(s)
- Steven S Cheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Alison C Mody
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Affiliate member of the Broad Institute, Cambridge, Massachusetts 02142, United States
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7
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Takemon Y, Pleasance ED, Gagliardi A, Hughes CS, Csizmok V, Wee K, Trinh DL, Huff RD, Mungall AJ, Moore RA, Chuah E, Mungall KL, Lewis E, Nelson J, Lim HJ, Renouf DJ, Jones SJ, Laskin J, Marra MA. Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities. Genome Med 2024; 16:136. [PMID: 39578878 PMCID: PMC11583415 DOI: 10.1186/s13073-024-01401-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 10/29/2024] [Indexed: 11/24/2024] Open
Abstract
BACKGROUND Loss-of-function (LOF) alterations in tumour suppressor genes cannot be directly targeted. Approaches characterising gene function and vulnerabilities conferred by such mutations are required. METHODS Here, we computationally map genetic networks of KMT2D, a tumour suppressor gene frequently mutated in several cancer types. Using KMT2D loss-of-function (KMT2DLOF) mutations as a model, we illustrate the utility of in silico genetic networks in uncovering novel functional associations and vulnerabilities in cancer cells with LOF alterations affecting tumour suppressor genes. RESULTS We revealed genetic interactors with functions in histone modification, metabolism, and immune response and synthetic lethal (SL) candidates, including some encoding existing therapeutic targets. Notably, we predicted WRN as a novel SL interactor and, using recently available WRN inhibitor (HRO761 and VVD-133214) treatment response data, we observed that KMT2D mutational status significantly distinguishes treatment-sensitive MSI cell lines from treatment-insensitive MSI cell lines. CONCLUSIONS Our study thus illustrates how tumour suppressor gene LOF alterations can be exploited to reveal potentially targetable cancer cell vulnerabilities.
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Affiliation(s)
- Yuka Takemon
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Erin D Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Alessia Gagliardi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | | | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Diane L Trinh
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Ryan D Huff
- Division of Respiratory Medicine, Department of Medicine, Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Eleanor Lewis
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Jessica Nelson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
- Pancreas Centre BC, Vancouver, BC, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
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8
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Wang Z, Zhang W, Yin X, Wu Q, Zhang Y, Qian Y, Bao Q, Liu F. Multi-omics analyses were combined to construct ubiquitination-related features in colon adenocarcinoma and identify ASNS as a novel biomarker. Front Immunol 2024; 15:1466286. [PMID: 39445026 PMCID: PMC11496147 DOI: 10.3389/fimmu.2024.1466286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 09/19/2024] [Indexed: 10/25/2024] Open
Abstract
Background As one of the malignant tumors with the highest incidence and fatality in the world, colon adenocarcinoma (COAD) has a very complex pathogenic mechanism, which has not yet been fully elucidated. Ubiquitin can regulate cell proliferation, cell cycle, apoptosis, DNA damage repair, and other processes by changing the activity of substrate proteins or causing ubiquitin-proteasome degradation. These are the key links in the pathogenesis of COAD, and ubiquitin plays an important role in the occurrence and development of COAD. Methods We integrated transcriptomics, single-cell and clinical omics, and TCGA and GEO databases of COAD patient data. Cox and Lasso regression was employed to assess ubiquitination genes in COAD for generating ubiquitination-related features. The aim was to evaluate the prognostic value of these features for tumors and their impact on the immune microenvironment. At the same time, the expression level of model genes was further analyzed using single-cell data. Finally, the expression and function of ASNS, a key gene for this trait, were detected in vitro. Results In our study, based on identifiable changes in the expression of marker genes, this feature can be used to classify patients with COAD. Kaplan-Meier survival analysis indicated that those with elevated risk scores in each cohort experienced inferior outcomes. There is good validation in both the training queue and the validation queue. The results of the immune infiltration analysis showed that the immune infiltration rate was significantly increased in the high-risk group. After the knockdown of ASNS, an important gene in the signature, the activity and migration capacity of SW620 and RKO cell lines and colony formation capacity were dramatically reduced in cell tests. Conclusion We screened ubiquitination-related genes and constructed ubiquitination-related features, which can be used as reliable prognostic indicators of COAD. ASNS was identified as a possible biomarker for COAD.
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Affiliation(s)
- Zhaohui Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of General Surgery, Anqing First People’s Hospital of Anhui Medical University, Anqing, China
| | - Wenbing Zhang
- Department of General Surgery, Anqing First People’s Hospital of Anhui Medical University, Anqing, China
| | - Xin Yin
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qinqing Wu
- Department of Preventive Medicine, Shantou University Medical College, Shantou, China
| | - Yongwei Zhang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of General Surgery, Anqing First People’s Hospital of Anhui Medical University, Anqing, China
| | - Yeben Qian
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of General Surgery, Anqing First People’s Hospital of Anhui Medical University, Anqing, China
| | - Qian Bao
- Department of Pediatric Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Fubao Liu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of General Surgery, Anqing First People’s Hospital of Anhui Medical University, Anqing, China
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9
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Liu X, Wang J, Xiang Y, Wang K, Yan D, Tong Y. The roles of OGT and its mechanisms in cancer. Cell Biosci 2024; 14:121. [PMID: 39285476 PMCID: PMC11406787 DOI: 10.1186/s13578-024-01301-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024] Open
Abstract
O-linked-N-acetylglucosaminylation (O-GlcNAcylation) is a common and important post-translational modification (PTM) linking O-linked β-N-acetylglucosamine (O-GlcNAc) to serine and threonine residues in proteins. Extensive research indicates its impact on target protein stability, activity, and interactions. O-linked N-acetylglucosamine transferase (OGT) is a critical enzyme that catalyzes O-GlcNAc modification, responsible for adding O-GlcNAc to proteins. OGT and O-GlcNAcylation are overexpressed in many tumors and closely associated with tumor growth, invasion, metabolism, drug resistance, and immune evasion. This review delineates the biochemical functions of OGT and summarizes its effects and mechanisms in tumors. Targeting OGT presents a promising novel approach for treating human malignancies.
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Affiliation(s)
- Xin Liu
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Jing Wang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Yaoxian Xiang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Kangjie Wang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Dong Yan
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Yingying Tong
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China.
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10
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Zhang L, Bai W, Peng Y, Lin Y, Tian M. Role of O-GlcNAcylation in Central Nervous System Development and Injuries: A Systematic Review. Mol Neurobiol 2024; 61:7075-7091. [PMID: 38367136 DOI: 10.1007/s12035-024-04045-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
The development of central nervous system (CNS) can form perceptual, memory, and cognitive functions, while injuries to CNS often lead to severe neurological dysfunction and even death. As one of the prevalent post-translational modifications (PTMs), O-GlcNAcylation has recently attracted great attentions due to its functions in regulating the activity, subcellular localization, and stability of target proteins. It has been indicated that O-GlcNAcylation could interact with phosphorylation, ubiquitination, and methylation to jointly regulate the function and activity of proteins. Furthermore, a growing number of studies have suggested that O-GlcNAcylation played an important role in the CNS. During development, O-GlcNAcylation participated in the neurogenesis, neuronal development, and neuronal function. In addition, O-GlcNAcylation was involved in the progress of CNS injuries including ischemic stroke, subarachnoid hemorrhage (SAH), and intracerebral hemorrhage (ICH) and played a crucial role in the improvement of brain damage such as attenuating cognitive impairment, inhibiting neuroinflammation, suppressing endoplasmic reticulum (ER) stress, and maintaining blood-brain barrier (BBB) integrity. Therefore, O-GlcNAcylation showed great promise as a potential target in CNS development and injuries. In this article, we presented a review highlighting the role of O-GlcNAcylation in CNS development and injuries. Hence, on the basis of these properties and effects, intervention with O-GlcNAcylation may be developed as therapeutic agents for CNS diseases.
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Affiliation(s)
- Li Zhang
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Jiangsu Province, Nanjing, People's Republic of China
| | - Wanshan Bai
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Jiangsu Province, Nanjing, People's Republic of China
| | - Yaonan Peng
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Jiangsu Province, Nanjing, People's Republic of China
| | - Yixing Lin
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Jiangsu Province, Nanjing, People's Republic of China
| | - Mi Tian
- Department of Anesthesiology, Affiliated Zhongda Hospital of Southeast University, Jiangsu Province, Nanjing, People's Republic of China.
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11
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Zhou H, Ye P, Xiong W, Duan X, Jing S, He Y, Zeng Z, Wei Y, Ye Q. Genome-scale CRISPR-Cas9 screening in stem cells: theories, applications and challenges. Stem Cell Res Ther 2024; 15:218. [PMID: 39026343 PMCID: PMC11264826 DOI: 10.1186/s13287-024-03831-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024] Open
Abstract
Due to the rapid development of stem cell technology, there have been tremendous advances in molecular biological and pathological research, cell therapy as well as organoid technologies over the past decades. Advances in genome editing technology, particularly the discovery of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-related protein 9 (Cas9), have further facilitated the rapid development of stem cell researches. The CRISPR-Cas9 technology now goes beyond creating single gene editing to enable the inhibition or activation of endogenous gene loci by fusing inhibitory (CRISPRi) or activating (CRISPRa) domains with deactivated Cas9 proteins (dCas9). These tools have been utilized in genome-scale CRISPRi/a screen to recognize hereditary modifiers that are synergistic or opposing to malady mutations in an orderly and fair manner, thereby identifying illness mechanisms and discovering novel restorative targets to accelerate medicinal discovery investigation. However, the application of this technique is still relatively rare in stem cell research. There are numerous specialized challenges in applying large-scale useful genomics approaches to differentiated stem cell populations. Here, we present the first comprehensive review on CRISPR-based functional genomics screening in the field of stem cells, as well as practical considerations implemented in a range of scenarios, and exploration of the insights of CRISPR-based screen into cell fates, disease mechanisms and cell treatments in stem cell models. This review will broadly benefit scientists, engineers and medical practitioners in the areas of stem cell research.
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Affiliation(s)
- Heng Zhou
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Peng Ye
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Wei Xiong
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Xingxiang Duan
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Shuili Jing
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Yan He
- Institute of Regenerative and Translational Medicine, Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, 430064, Hubei, People's Republic of China
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Zhi Zeng
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.
| | - Yen Wei
- The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, People's Republic of China.
| | - Qingsong Ye
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.
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12
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Leng Y, Tian T, Tang B, Ma Y, Li Z, Shi Q, Liu J, Zhou Y, Wang W, Huang C, Zhao X, Feng W, Liu Y, Liang J, Liu T, Liu S, Ren Q, Liu J, Zhang T, Zhou J, Huang Q, Zhang Y, Yin B, Xu Y, Liu L, Shen L, Zhao H. The oncogenic role and regulatory mechanism of ACAA2 in human ovarian cancer. Mol Carcinog 2024; 63:1362-1377. [PMID: 38656551 DOI: 10.1002/mc.23729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/29/2024] [Accepted: 04/06/2024] [Indexed: 04/26/2024]
Abstract
Acetyl-CoAacyltransferase2 (ACAA2) is a key enzyme in the fatty acid oxidation pathway that catalyzes the final step of mitochondrial β oxidation, which plays an important role in fatty acid metabolism. The expression of ACAA2 is closely related to the occurrence and malignant progression of tumors. However, the function of ACAA2 in ovarian cancer is unclear. The expression level and prognostic value of ACAA2 were analyzed by databases. Gain and loss of function were carried out to explore the function of ACAA2 in ovarian cancer. RNA-seq and bioinformatics methods were applied to illustrate the regulatory mechanism of ACAA2. ACAA2 overexpression promoted the growth, proliferation, migration, and invasion of ovarian cancer, and ACAA2 knockdown inhibited the malignant progression of ovarian cancer as well as the ability of subcutaneous tumor formation in nude mice. At the same time, we found that OGT can induce glycosylation modification of ACAA2 and regulate the karyoplasmic distribution of ACAA2. OGT plays a vital role in ovarian cancer as a function of oncogenes. In addition, through RNA-seq sequencing, we found that ACAA2 regulates the expression of DIXDC1. ACAA2 regulated the malignant progression of ovarian cancer through the WNT/β-Catenin signaling pathway probably. ACAA2 is an oncogene in ovarian cancer and has the potential to be a target for ovarian cancer therapy.
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Affiliation(s)
- Yahui Leng
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Tian Tian
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Bingbing Tang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yongqing Ma
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zihang Li
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Qin Shi
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jiaqi Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yang Zhou
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Wenlong Wang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chengyang Huang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Xuan Zhao
- The Second Clinical College, Xi'an Medical University, Xi'an, China
| | - Wenxiao Feng
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yanni Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jingyin Liang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Tianhui Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Song Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Qiulei Ren
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jiakun Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Te Zhang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Junsuo Zhou
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Qian Huang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yaling Zhang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Bin Yin
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yuewen Xu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Liaoyuan Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Li Shen
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Hongyan Zhao
- School of Basic Medicine, Hubei University of Medicine, Shiyan, China
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
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13
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Potter SC, Gibbs BE, Hammel FA, Joiner CM, Paulo JA, Janetzko J, Levine ZG, Fei GQ, Haggarty SJ, Walker S. Dissecting OGT's TPR domain to identify determinants of cellular function. Proc Natl Acad Sci U S A 2024; 121:e2401729121. [PMID: 38768345 PMCID: PMC11145291 DOI: 10.1073/pnas.2401729121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
O-GlcNAc transferase (OGT) is an essential mammalian enzyme that glycosylates myriad intracellular proteins and cleaves the transcriptional coregulator Host Cell Factor 1 to regulate cell cycle processes. Via these catalytic activities as well as noncatalytic protein-protein interactions, OGT maintains cell homeostasis. OGT's tetratricopeptide repeat (TPR) domain is important in substrate recognition, but there is little information on how changing the TPR domain impacts its cellular functions. Here, we investigate how altering OGT's TPR domain impacts cell growth after the endogenous enzyme is deleted. We find that disrupting the TPR residues required for OGT dimerization leads to faster cell growth, whereas truncating the TPR domain slows cell growth. We also find that OGT requires eight of its 13 TPRs to sustain cell viability. OGT-8, like the nonviable shorter OGT variants, is mislocalized and has reduced Ser/Thr glycosylation activity; moreover, its interactions with most of wild-type OGT's binding partners are broadly attenuated. Therefore, although OGT's five N-terminal TPRs are not essential for cell viability, they are required for proper subcellular localization and for mediating many of OGT's protein-protein interactions. Because the viable OGT truncation variant we have identified preserves OGT's essential functions, it may facilitate their identification.
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Affiliation(s)
- Sarah C Potter
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Bettine E Gibbs
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115
| | - Forrest A Hammel
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115
| | - Cassandra M Joiner
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115
| | - John Janetzko
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Zebulon G Levine
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115
| | - George Q Fei
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115
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14
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Qiu Z, Cui J, Huang Q, Qi B, Xia Z. Roles of O-GlcNAcylation in Mitochondrial Homeostasis and Cardiovascular Diseases. Antioxidants (Basel) 2024; 13:571. [PMID: 38790676 PMCID: PMC11117601 DOI: 10.3390/antiox13050571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/28/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Protein posttranslational modifications are important factors that mediate the fine regulation of signaling molecules. O-linked β-N-acetylglucosamine-modification (O-GlcNAcylation) is a monosaccharide modification on N-acetylglucosamine linked to the hydroxyl terminus of serine and threonine of proteins. O-GlcNAcylation is responsive to cellular stress as a reversible and posttranslational modification of nuclear, mitochondrial and cytoplasmic proteins. Mitochondrial proteins are the main targets of O-GlcNAcylation and O-GlcNAcylation is a key regulator of mitochondrial homeostasis by directly regulating the mitochondrial proteome or protein activity and function. Disruption of O-GlcNAcylation is closely related to mitochondrial dysfunction. More importantly, the O-GlcNAcylation of cardiac proteins has been proven to be protective or harmful to cardiac function. Mitochondrial homeostasis is crucial for cardiac contractile function and myocardial cell metabolism, and the imbalance of mitochondrial homeostasis plays a crucial role in the pathogenesis of cardiovascular diseases (CVDs). In this review, we will focus on the interactions between protein O-GlcNAcylation and mitochondrial homeostasis and provide insights on the role of mitochondrial protein O-GlcNAcylation in CVDs.
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Affiliation(s)
- Zhen Qiu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.Q.); (J.C.); (Q.H.)
| | - Jiahui Cui
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.Q.); (J.C.); (Q.H.)
| | - Qin Huang
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.Q.); (J.C.); (Q.H.)
| | - Biao Qi
- Department of Anesthesiology, Hubei 672 Orthopaedics Hospital of Integrated Chinese and Western Medicine, Wuhan Orthopaedics Hospital of Intergrated Traditional Medicine Chinese and Western Medicine, The Affiliated Hospital of Wuhan Sports University, Wuhan 430070, China
| | - Zhongyuan Xia
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.Q.); (J.C.); (Q.H.)
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15
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Boyd SS, Robarts DR, Nguyen K, Villar M, Alghusen I, Kotulkar M, Denson A, Fedosyuk H, Whelan SA, Lee NCY, Hanover J, Dias WB, Tan EP, McGreal SR, Artigues A, Swerdlow RH, Thompson JA, Apte U, Slawson C. Multi-Omics after O-GlcNAc Alteration Identifies Cellular Processes Working Synergistically to Promote Aneuploidy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589379. [PMID: 38659829 PMCID: PMC11042281 DOI: 10.1101/2024.04.16.589379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Pharmacologic or genetic manipulation of O-GlcNAcylation, an intracellular, single sugar post-translational modification, are difficult to interpret due to the pleotropic nature of O-GlcNAc and the vast signaling pathways it regulates. To address this issue, we employed either OGT (O-GlcNAc transferase), OGA (O-GlcNAcase) liver knockouts, or pharmacological inhibition of OGA coupled with multi-Omics analysis and bioinformatics. We identified numerous genes, proteins, phospho-proteins, or metabolites that were either inversely or equivalently changed between conditions. Moreover, we identified pathways in OGT knockout samples associated with increased aneuploidy. To test and validate these pathways, we induced liver growth in OGT knockouts by partial hepatectomy. OGT knockout livers showed a robust aneuploidy phenotype with disruptions in mitosis, nutrient sensing, protein metabolism/amino acid metabolism, stress response, and HIPPO signaling demonstrating how OGT is essential in controlling aneuploidy pathways. Moreover, these data show how a multi-Omics platform can discern how OGT can synergistically fine-tune multiple cellular pathways.
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16
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Zhu Z, Ren W, Li S, Gao L, Zhi K. Functional significance of O-linked N-acetylglucosamine protein modification in regulating autophagy. Pharmacol Res 2024; 202:107120. [PMID: 38417774 DOI: 10.1016/j.phrs.2024.107120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Autophagy is a core molecular pathway that preserves cellular and organismal homeostasis. Being susceptible to nutrient availability and stress, eukaryotic cells recycle or degrade internal components via membrane transport pathways to provide sustainable biological molecules and energy sources. The dysregulation of this highly conserved physiological process has been strongly linked to human disease. Post-translational modification, a mechanism that regulates protein function, plays a crucial role in autophagy regulation. O-linked N-acetylglucosamine protein modification (O-GlcNAcylation), a monosaccharide post-translational modification of intracellular proteins, is essential in nutritional and stress regulatory mechanisms. O-GlcNAcylation has emerged as an essential regulatory mechanism of autophagy. It regulates autophagy throughout its lifetime by targeting the core components of the autophagy regulatory network. This review provides an overview of the O-GlcNAcylation of autophagy-associated proteins and their regulation and function in the autophagy pathway. Therefore, this article may contribute to further understanding of the role of O-GlcNAc-regulated autophagy and provide new perspectives for the treatment of human diseases.
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Affiliation(s)
- Zhuang Zhu
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
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17
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Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. The 2023 Report on the Proteome from the HUPO Human Proteome Project. J Proteome Res 2024; 23:532-549. [PMID: 38232391 PMCID: PMC11026053 DOI: 10.1021/acs.jproteome.3c00591] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1-4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | - Christopher M. Overall
- University of British Columbia, Vancouver, BC V6T 1Z4, Canada, Yonsei University Republic of Korea
| | | | - Charles Pineau
- University Rennes, Inserm U1085, Irset, 35042 Rennes, France
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | | | - Michael H. A. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | | | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, 127 South San Vicente Boulevard, Pavilion, 9th Floor, Los Angeles, CA, 90048, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, CA, 92093, United States
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
- University of Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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18
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Sepulveda H, Li X, Yue X, Carlos Angel J, Arteaga-Vazquez LJ, Brown C, Brunelli M, Jansz N, Puddu F, Scotcher J, Creed P, Kennedy P, Manriquez C, Myers SA, Crawford R, Faulkner GJ, Rao A. OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578097. [PMID: 38352366 PMCID: PMC10862820 DOI: 10.1101/2024.01.31.578097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
Abstract
The O- GlcNAc transferase OGT interacts robustly with all three mammalian TET methylcytosine dioxygenases. We show here that deletion of the Ogt gene in mouse embryonic stem cells (mESC) results in a widespread increase in the TET product 5-hydroxymethylcytosine (5hmC) in both euchromatic and heterochromatic compartments, with concomitant reduction of the TET substrate 5-methylcytosine (5mC) at the same genomic regions. mESC engineered to abolish the TET1-OGT interaction likewise displayed a genome-wide decrease of 5mC. DNA hypomethylation in OGT-deficient cells was accompanied by de-repression of transposable elements (TEs) predominantly located in heterochromatin, and this increase in TE expression was sometimes accompanied by increased cis -expression of genes and exons located 3' of the expressed TE. Thus, the TET-OGT interaction prevents DNA demethylation and TE expression in heterochromatin by restraining TET activity genome-wide. We suggest that OGT protects the genome against DNA hypomethylation and impaired heterochromatin integrity, preventing the aberrant increase in TE expression observed in cancer, autoimmune-inflammatory diseases, cellular senescence and ageing.
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Ye L, Ding W, Xiao D, Jia Y, Zhao Z, Ao X, Wang J. O-GlcNAcylation: cellular physiology and therapeutic target for human diseases. MedComm (Beijing) 2023; 4:e456. [PMID: 38116061 PMCID: PMC10728774 DOI: 10.1002/mco2.456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
O-linked-β-N-acetylglucosamine (O-GlcNAcylation) is a distinctive posttranslational protein modification involving the coordinated action of O-GlcNAc transferase and O-GlcNAcase, primarily targeting serine or threonine residues in various proteins. This modification impacts protein functionality, influencing stability, protein-protein interactions, and localization. Its interaction with other modifications such as phosphorylation and ubiquitination is becoming increasingly evident. Dysregulation of O-GlcNAcylation is associated with numerous human diseases, including diabetes, nervous system degeneration, and cancers. This review extensively explores the regulatory mechanisms of O-GlcNAcylation, its effects on cellular physiology, and its role in the pathogenesis of diseases. It examines the implications of aberrant O-GlcNAcylation in diabetes and tumorigenesis, highlighting novel insights into its potential role in cardiovascular diseases. The review also discusses the interplay of O-GlcNAcylation with other protein modifications and its impact on cell growth and metabolism. By synthesizing current research, this review elucidates the multifaceted roles of O-GlcNAcylation, providing a comprehensive reference for future studies. It underscores the potential of targeting the O-GlcNAcylation cycle in developing novel therapeutic strategies for various pathologies.
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Affiliation(s)
- Lin Ye
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Wei Ding
- The Affiliated Hospital of Qingdao UniversityQingdao Medical CollegeQingdao UniversityQingdaoChina
| | - Dandan Xiao
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Yi Jia
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Zhonghao Zhao
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Xiang Ao
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Jianxun Wang
- School of Basic MedicineQingdao UniversityQingdaoChina
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