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  1. Article ; Online: The Intertwined Role of 8-oxodG and G4 in Transcription Regulation.

    Gorini, Francesca / Ambrosio, Susanna / Lania, Luigi / Majello, Barbara / Amente, Stefano

    International journal of molecular sciences

    2023  Volume 24, Issue 3

    Abstract: The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it ...

    Abstract The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it may cause a G > T (C > A) mutation; it is frequently referred to as a form of DNA damage and promptly corrected by DNA repair mechanisms. Moreover, 8-oxodG has recently been redefined as an epigenetic factor that impacts transcriptional regulatory elements and other epigenetic modifications. It has been proposed that 8-oxodG exerts epigenetic control through interplay with the G-quadruplex (G4), a non-canonical DNA structure, in transcription regulatory regions. In this review, we focused on the epigenetic roles of 8-oxodG and the G4 and explored their interplay at the genomic level.
    MeSH term(s) 8-Hydroxy-2'-Deoxyguanosine ; Deoxyguanosine ; DNA Damage ; DNA Repair ; DNA/chemistry
    Chemical Substances 8-Hydroxy-2'-Deoxyguanosine (88847-89-6) ; Deoxyguanosine (G9481N71RO) ; DNA (9007-49-2)
    Language English
    Publishing date 2023-01-19
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24032031
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Autophagy Roles in Genome Maintenance.

    Ambrosio, Susanna / Majello, Barbara

    Cancers

    2020  Volume 12, Issue 7

    Abstract: In recent years, a considerable correlation has emerged between autophagy and genome integrity. A range of mechanisms appear to be involved where autophagy participates in preventing genomic instability, as well as in DNA damage response and cell fate ... ...

    Abstract In recent years, a considerable correlation has emerged between autophagy and genome integrity. A range of mechanisms appear to be involved where autophagy participates in preventing genomic instability, as well as in DNA damage response and cell fate decision. These initial findings have attracted particular attention in the context of malignancy; however, the crosstalk between autophagy and DNA damage response is just beginning to be explored and key questions remain that need to be addressed, to move this area of research forward and illuminate the overall consequence of targeting this process in human therapies. Here we present current knowledge on the complex crosstalk between autophagy and genome integrity and discuss its implications for cancer cell survival and response to therapy.
    Language English
    Publishing date 2020-07-04
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers12071793
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: OxiDIP-Seq for Genome-wide Mapping of Damaged DNA Containing 8-Oxo-2'-Deoxyguanosine.

    Gorini, Francesca / Scala, Giovanni / Ambrosio, Susanna / Majello, Barbara / Amente, Stefano

    Bio-protocol

    2022  Volume 12, Issue 21

    Abstract: 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) is considered to be a premutagenic DNA lesion generated by 2'-deoxyguanosine (dG) oxidation due to reactive oxygen species (ROS). In recent years, the 8-oxodG distribution in human, mouse, and yeast genomes ... ...

    Abstract 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) is considered to be a premutagenic DNA lesion generated by 2'-deoxyguanosine (dG) oxidation due to reactive oxygen species (ROS). In recent years, the 8-oxodG distribution in human, mouse, and yeast genomes has been underlined using various next-generation sequencing (NGS)-based strategies. The present study reports the OxiDIP-Seq protocol, which combines specific 8-oxodG immuno-precipitation of single-stranded DNA with NGS, and the pipeline analysis that allows the genome-wide 8-oxodG distribution in mammalian cells. The development of this OxiDIP-Seq method increases knowledge on the oxidative DNA damage/repair field, providing a high-resolution map of 8-oxodG in human cells.
    Language English
    Publishing date 2022-11-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.4540
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Targeting Histone Demethylase LSD1/KDM1a in Neurodegenerative Diseases.

    Ambrosio, Susanna / Majello, Barbara

    Journal of experimental neuroscience

    2018  Volume 12, Page(s) 1179069518765743

    Abstract: The autophagy-lysosome pathway sustains cellular homeostasis and is a protective mechanism against neurodegenerative diseases. Recent findings highlight the role of the histone demethylases LSD1/LDM1A as a pivotal regulator of autophagy process, by ... ...

    Abstract The autophagy-lysosome pathway sustains cellular homeostasis and is a protective mechanism against neurodegenerative diseases. Recent findings highlight the role of the histone demethylases LSD1/LDM1A as a pivotal regulator of autophagy process, by controlling the mTORC1 cascade, in neuroblastoma cells. LSD1 binds to the promoter region of the
    Language English
    Publishing date 2018-03-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2659991-0
    ISSN 1179-0695
    ISSN 1179-0695
    DOI 10.1177/1179069518765743
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Accumulation of 8-oxodG within the human mitochondrial genome positively associates with transcription.

    Scala, Giovanni / Ambrosio, Susanna / Menna, Margherita / Gorini, Francesca / Caiazza, Carmen / Cooke, Marcus S / Majello, Barbara / Amente, Stefano

    NAR genomics and bioinformatics

    2023  Volume 5, Issue 4, Page(s) lqad100

    Abstract: Mitochondrial DNA (mtDNA) can be subject to internal and environmental stressors that lead to oxidatively generated damage and the formation of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxodG). The accumulation of 8-oxodG has been linked to degenerative ... ...

    Abstract Mitochondrial DNA (mtDNA) can be subject to internal and environmental stressors that lead to oxidatively generated damage and the formation of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxodG). The accumulation of 8-oxodG has been linked to degenerative diseases and aging, as well as cancer. Despite the well-described implications of 8-oxodG in mtDNA for mitochondrial function, there have been no reports of mapping of 8-oxodG across the mitochondrial genome. To address this, we used OxiDIP-Seq and mapped 8-oxodG levels in the mitochondrial genome of human MCF10A cells. Our findings indicated that, under steady-state conditions, 8-oxodG is non-uniformly distributed along the mitochondrial genome, and that the longer non-coding region appeared to be more protected from 8-oxodG accumulation compared with the coding region. However, when the cells have been exposed to oxidative stress, 8-oxodG preferentially accumulated in the coding region which is highly transcribed as H1 transcript. Our data suggest that 8-oxodG accumulation in the mitochondrial genome is positively associated with mitochondrial transcription.
    Language English
    Publishing date 2023-11-06
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqad100
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Histone methyl-transferases and demethylases in the autophagy regulatory network: the emerging role of KDM1A/LSD1 demethylase.

    Ambrosio, Susanna / Ballabio, Andrea / Majello, Barbara

    Autophagy

    2018  Volume 15, Issue 2, Page(s) 187–196

    Abstract: Macroautophagy/autophagy is a physiological mechanism that is essential for the maintenance of cellular homeostasis and stress adaptation. Defective autophagy is associated with many human diseases, including cancer and neurodegenerative disorders. The ... ...

    Abstract Macroautophagy/autophagy is a physiological mechanism that is essential for the maintenance of cellular homeostasis and stress adaptation. Defective autophagy is associated with many human diseases, including cancer and neurodegenerative disorders. The emerging implication of epigenetic events in the control of the autophagic process opens new avenues of investigation and offers the opportunity to develop novel therapeutic strategies in diseases associated with dysfunctional autophagy-lysosomal pathways. Accumulating evidence reveals that several methyltransferases and demethylases are essential regulators of autophagy, and recent studies have led to the identification of the lysine demethylase KDM1A/LSD1 as a promising drug target. KDM1A/LSD1 modulates autophagy at multiple levels, participating in the transcriptional control of several downstream effectors. This review summarizes our current understanding of the role of KDM1A/LSD1 in the autophagy regulatory network.
    MeSH term(s) Animals ; Autophagy/genetics ; Epigenesis, Genetic ; Histone Demethylases/metabolism ; Histone Methyltransferases/metabolism ; Humans ; Models, Biological ; Signal Transduction/genetics
    Chemical Substances Histone Demethylases (EC 1.14.11.-) ; Histone Methyltransferases (EC 2.1.1.-)
    Language English
    Publishing date 2018-09-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2454135-7
    ISSN 1554-8635 ; 1554-8627
    ISSN (online) 1554-8635
    ISSN 1554-8627
    DOI 10.1080/15548627.2018.1520546
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: 8-oxodG accumulation within super-enhancers marks fragile CTCF-mediated chromatin loops.

    Scala, Giovanni / Gorini, Francesca / Ambrosio, Susanna / Chiariello, Andrea M / Nicodemi, Mario / Lania, Luigi / Majello, Barbara / Amente, Stefano

    Nucleic acids research

    2022  Volume 50, Issue 6, Page(s) 3292–3306

    Abstract: 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a major product of the DNA oxidization process, has been proposed to have an epigenetic function in gene regulation and has been associated with genome instability. NGS-based methodologies are contributing ... ...

    Abstract 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a major product of the DNA oxidization process, has been proposed to have an epigenetic function in gene regulation and has been associated with genome instability. NGS-based methodologies are contributing to the characterization of the 8-oxodG function in the genome. However, the 8-oxodG epigenetic role at a genomic level and the mechanisms controlling the genomic 8-oxodG accumulation/maintenance have not yet been fully characterized. In this study, we report the identification and characterization of a set of enhancer regions accumulating 8-oxodG in human epithelial cells. We found that these oxidized enhancers are mainly super-enhancers and are associated with bidirectional-transcribed enhancer RNAs and DNA Damage Response activation. Moreover, using ChIA-PET and HiC data, we identified specific CTCF-mediated chromatin loops in which the oxidized enhancer and promoter regions physically associate. Oxidized enhancers and their associated chromatin loops accumulate endogenous double-strand breaks which are in turn repaired by NHEJ pathway through a transcription-dependent mechanism. Our work suggests that 8-oxodG accumulation in enhancers-promoters pairs occurs in a transcription-dependent manner and provides novel mechanistic insights on the intrinsic fragility of chromatin loops containing oxidized enhancers-promoters interactions.
    MeSH term(s) 8-Hydroxy-2'-Deoxyguanosine/metabolism ; CCCTC-Binding Factor/metabolism ; Chromatin/genetics ; DNA ; Enhancer Elements, Genetic ; Epigenesis, Genetic ; Genomic Instability ; Humans ; Promoter Regions, Genetic ; Transcription, Genetic
    Chemical Substances CCCTC-Binding Factor ; CTCF protein, human ; Chromatin ; 8-Hydroxy-2'-Deoxyguanosine (88847-89-6) ; DNA (9007-49-2)
    Language English
    Publishing date 2022-03-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac143
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: EGR1 drives cell proliferation by directly stimulating TFEB transcription in response to starvation.

    Cesana, Marcella / Tufano, Gennaro / Panariello, Francesco / Zampelli, Nicolina / Ambrosio, Susanna / De Cegli, Rossella / Mutarelli, Margherita / Vaccaro, Lorenzo / Ziller, Micheal J / Cacchiarelli, Davide / Medina, Diego L / Ballabio, Andrea

    PLoS biology

    2023  Volume 21, Issue 3, Page(s) e3002034

    Abstract: The stress-responsive transcription factor EB (TFEB) is a master controller of lysosomal biogenesis and autophagy and plays a major role in several cancer-associated diseases. TFEB is regulated at the posttranslational level by the nutrient-sensitive ... ...

    Abstract The stress-responsive transcription factor EB (TFEB) is a master controller of lysosomal biogenesis and autophagy and plays a major role in several cancer-associated diseases. TFEB is regulated at the posttranslational level by the nutrient-sensitive kinase complex mTORC1. However, little is known about the regulation of TFEB transcription. Here, through integrative genomic approaches, we identify the immediate-early gene EGR1 as a positive transcriptional regulator of TFEB expression in human cells and demonstrate that, in the absence of EGR1, TFEB-mediated transcriptional response to starvation is impaired. Remarkably, both genetic and pharmacological inhibition of EGR1, using the MEK1/2 inhibitor Trametinib, significantly reduced the proliferation of 2D and 3D cultures of cells displaying constitutive activation of TFEB, including those from a patient with Birt-Hogg-Dubé (BHD) syndrome, a TFEB-driven inherited cancer condition. Overall, we uncover an additional layer of TFEB regulation consisting in modulating its transcription via EGR1 and propose that interfering with the EGR1-TFEB axis may represent a therapeutic strategy to counteract constitutive TFEB activation in cancer-associated conditions.
    MeSH term(s) Humans ; Mechanistic Target of Rapamycin Complex 1/genetics ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Autophagy/genetics ; Lysosomes/metabolism ; Cell Proliferation/genetics ; Early Growth Response Protein 1/genetics ; Early Growth Response Protein 1/metabolism ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism
    Chemical Substances Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1) ; EGR1 protein, human ; Early Growth Response Protein 1 ; TFEB protein, human ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
    Language English
    Publishing date 2023-03-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3002034
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  9. Article: Epigenetic regulation of epithelial to mesenchymal transition by the Lysine-specific demethylase LSD1/KDM1A.

    Ambrosio, Susanna / Saccà, Carmen D / Majello, Barbara

    Biochimica et biophysica acta. Gene regulatory mechanisms

    2017  Volume 1860, Issue 9, Page(s) 905–910

    Abstract: The Lysine-specific demethylase 1, KDM1A/LSD1, plays a central role in the regulation of Pol II transcription through the removal of the activation mark (mono- and dimethyl lysine 4 of histone H3). LSD1 is often deregulated in human cancers, and it is ... ...

    Abstract The Lysine-specific demethylase 1, KDM1A/LSD1, plays a central role in the regulation of Pol II transcription through the removal of the activation mark (mono- and dimethyl lysine 4 of histone H3). LSD1 is often deregulated in human cancers, and it is frequently overexpressed in human solid cancers and leukemia. LSD1 regulates the epithelial mesenchymal transition (EMT) in epithelial cells, i.e., the ability to transition into mesenchymal cells, to lose homotypic adhesion and to acquire migratory capacity. From its initial discovery as a component of the Snail complex, multiple studies highlighted the causative role of LSD1 in cell invasiveness and EMT, describing its direct involvement in different molecular processes through the interaction with specific partners. Here we present an overview of the role of LSD1 in the EMT process, summarizing recent findings on its emerging functions in cell migration and invasion in cancer.
    MeSH term(s) Cell Movement/genetics ; Epigenesis, Genetic/genetics ; Epithelial-Mesenchymal Transition/genetics ; Epithelial-Mesenchymal Transition/physiology ; Gene Expression Regulation, Neoplastic/genetics ; Histone Demethylases/metabolism ; Humans ; Lysine/metabolism ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology
    Chemical Substances Histone Demethylases (EC 1.14.11.-) ; KDM1A protein, human (EC 1.5.-) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2017-07-15
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 60-7
    ISSN 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 1874-9399 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439
    ISSN (online) 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 1874-9399 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439
    DOI 10.1016/j.bbagrm.2017.07.001
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  10. Article ; Online: TFEB and TFE3 control glucose homeostasis by regulating insulin gene expression.

    Pasquier, Adrien / Pastore, Nunzia / D'Orsi, Luca / Colonna, Rita / Esposito, Alessandra / Maffia, Veronica / De Cegli, Rossella / Mutarelli, Margherita / Ambrosio, Susanna / Tufano, Gennaro / Grimaldi, Antonio / Cesana, Marcella / Cacchiarelli, Davide / Delalleau, Nathalie / Napolitano, Gennaro / Ballabio, Andrea

    The EMBO journal

    2023  Volume 42, Issue 21, Page(s) e113928

    Abstract: To fulfill their function, pancreatic beta cells require precise nutrient-sensing mechanisms that control insulin production. Transcription factor EB (TFEB) and its homolog TFE3 have emerged as crucial regulators of the adaptive response of cell ... ...

    Abstract To fulfill their function, pancreatic beta cells require precise nutrient-sensing mechanisms that control insulin production. Transcription factor EB (TFEB) and its homolog TFE3 have emerged as crucial regulators of the adaptive response of cell metabolism to environmental cues. Here, we show that TFEB and TFE3 regulate beta-cell function and insulin gene expression in response to variations in nutrient availability. We found that nutrient deprivation in beta cells promoted TFEB/TFE3 activation, which resulted in suppression of insulin gene expression. TFEB overexpression was sufficient to inhibit insulin transcription, whereas beta cells depleted of both TFEB and TFE3 failed to suppress insulin gene expression in response to amino acid deprivation. Interestingly, ChIP-seq analysis showed binding of TFEB to super-enhancer regions that regulate insulin transcription. Conditional, beta-cell-specific, Tfeb-overexpressing, and Tfeb/Tfe3 double-KO mice showed severe alteration of insulin transcription, secretion, and glucose tolerance, indicating that TFEB and TFE3 are important physiological mediators of pancreatic function. Our findings reveal a nutrient-controlled transcriptional mechanism that regulates insulin production, thus playing a key role in glucose homeostasis at both cellular and organismal levels.
    MeSH term(s) Animals ; Mice ; Autophagy/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Gene Expression ; Glucose ; Insulin ; Lysosomes/metabolism
    Chemical Substances Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Glucose (IY9XDZ35W2) ; Insulin ; Tcfe3 protein, mouse (136896-33-8) ; Tcfeb protein, mouse
    Language English
    Publishing date 2023-09-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 586044-1
    ISSN 1460-2075 ; 0261-4189
    ISSN (online) 1460-2075
    ISSN 0261-4189
    DOI 10.15252/embj.2023113928
    Database MEDical Literature Analysis and Retrieval System OnLINE

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