Regulation Of Genome Stability Research Articles

Long non-coding RNAs correlate with genomic stability in prostate cancer: A clinical outcome and survival analysis

BackgroundLong non-coding RNAs (lncRNAs) participate in the regulation of genomic stability. Understanding their biological functions can help us identify the mechanisms of the occurrence and progression of cancers and can provide theoretical guidance and the basis for treatment. ResultsBased on the mutation hypothesis, we proposed a computational framework to identify genomic instability-related lncRNAs. Based on the differentially-expressed lncRNAs (DElncRNAs), we constructed a genomic instability-derived lncRNA signature (GILncSig) to calculate and stratify outcomes in patients with prostate cancer. It is an independent predictor of overall survival. The area under the curve = 0.805. This value may be more significant than the classic prognostic markers TP53 and Speckle-type POZ protein (SPOP) in terms of outcome prediction. ConclusionsIn summary, we conducted a computation approach and resource for mining genome instability-related lncRNAs. It may turn out to be highly significant for genomic instability and customized decision-making for patients with prostate cancer. It also may lead to effective methods and resources to study the molecular mechanism of genomic instability-related lncRNAs.

Epigenetic Regulation of Genomic Stability by Vitamin C.

DNA methylation plays an important role in the maintenance of genomic stability. Ten-eleven translocation proteins (TETs) are a family of iron (Fe2+) and α-KG -dependent dioxygenases that regulate DNA methylation levels by oxidizing 5-methylcystosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). These oxidized methylcytosines promote passive demethylation upon DNA replication, or active DNA demethylation, by triggering base excision repair and replacement of 5fC and 5caC with an unmethylated cytosine. Several studies over the last decade have shown that loss of TET function leads to DNA hypermethylation and increased genomic instability. Vitamin C, a cofactor of TET enzymes, increases 5hmC formation and promotes DNA demethylation, suggesting that this essential vitamin, in addition to its antioxidant properties, can also directly influence genomic stability. This review will highlight the functional role of DNA methylation, TET activity and vitamin C, in the crosstalk between DNA methylation and DNA repair.

The coordination between DNA polymerase β and ligase governs the formation of mutagenic repair intermediates as an important determinant of faithful base excision repair

Base excision repair (BER) is a critical process for preventing the mutagenic and lethal consequences of DNA damage that arises from endogenous and environmental agents and underlies disease and aging. BER pathway involves a series of sequential enzymatic steps that are tightly coordinated in a process known as the substrate-product channeling between repair proteins so that release of cytotoxic BER intermediates is minimized. DNA ligase I and III catalyze the ultimate ligation step following DNA polymerase (pol) β nucleotide insertion at downstream steps of BER pathway. DNA ligases and DNA polymerases that play roles in DNA replication and repair transactions have long been prime candidates for key regulators of genome stability. However, the ligation efficiency of pol β-promoted mutagenesis products with 3′-DNA mismatches or 8-oxo-2'-deoxyguanosine (8-oxodG) at the downstream steps of BER pathway remains undefined. We show that pol β 8-oxo-2'-deoxyribonucleoside 5'-triphosphate (8-oxodGTP) insertion confounds DNA ligases leading to the formation of ligation failure products with a 5'-adenylate (AMP) block. However, pol β Watson-Crick-like dGTP mismatch insertion opposite T can be efficiently ligated by the BER DNA ligases in vitro. Moreover, we report the mutagenic ligation of pol β 8-oxodGTP insertion products by the LIG1 MgHiFimutant with a perturbed fidelity and enhanced ligation failure by the variants of LIG1 deficiency disease that exhibits the symptoms of developmental abnormalities, immunodeficiency, lymphoma, and predisposition to cancer. Our results also demonstrate that the BER DNA ligases are compromised by subtle changes in all 12 possible noncanonical base pairs at the 3′-end of the nicked repair intermediate. Finally, we found that Aprataxin and Flap Endonuclease 1, as compensatory DNA-end processing enzymes, can remove the 5'-AMP block from the abortive ligation products harboring 3′-8-oxodG or all possible mispairs. These findings contribute to understanding of how the identity of the damaged or mismatch affects the substrate channeling of the repair pathway, importance of mechanism underlying the interplay between pol β and DNA ligases for faithful BER, and how a multi-protein complex can coordinate to maintain the repair efficiency.

Caspase-2 as a master regulator of genomic stability.

Genomic instability underlies genesis and the development of various types of cancer. During tumorigenesis, cancer initiating cells assume a set of features, which allow them to survive and proliferate. Different mutations and chromosomal alterations promote a selection of the most aggressive cancer clones that worsen the prognosis of the disease. Despite that caspase-2 was described as a protease fulfilling an initiator and an effector function in apoptosis, it has recently been discovered to play an important role in the maintenance of genomic integrity and normal chromosome configuration. This protein is able to stabilize p53 and affect the level of transcription factors, which activates cell response to oxidative stress. Here we focus on the discussion on the mechanism(s) of how caspase-2 regulates genomic stability and decreases tumorigenesis.

Sustained CHK2 activity, but not ATM activity, is critical to maintain a G1 arrest after DNA damage in untransformed cells

BackgroundThe G1 checkpoint is a critical regulator of genomic stability in untransformed cells, preventing cell cycle progression after DNA damage. DNA double-strand breaks (DSBs) recruit and activate ATM, a kinase which in turn activates the CHK2 kinase to establish G1 arrest. While the onset of G1 arrest is well understood, the specific role that ATM and CHK2 play in regulating G1 checkpoint maintenance remains poorly characterized.ResultsHere we examine the impact of ATM and CHK2 activities on G1 checkpoint maintenance in untransformed cells after DNA damage caused by DSBs. We show that ATM becomes dispensable for G1 checkpoint maintenance as early as 1 h after DSB induction. In contrast, CHK2 kinase activity is necessary to maintain the G1 arrest, independently of ATM, ATR, and DNA-PKcs, implying that the G1 arrest is maintained in a lesion-independent manner. Sustained CHK2 activity is achieved through auto-activation and its acute inhibition enables cells to abrogate the G1-checkpoint and enter into S-phase. Accordingly, we show that CHK2 activity is lost in cells that recover from the G1 arrest, pointing to the involvement of a phosphatase with fast turnover.ConclusionOur data indicate that G1 checkpoint maintenance relies on CHK2 and that its negative regulation is crucial for G1 checkpoint recovery after DSB induction.

Autophagy restricts mitochondrial DNA damage-induced release of ENDOG (endonuclease G) to regulate genome stability

ABSTRACT Genotoxic insult causes nuclear and mitochondrial DNA damages with macroautophagy/autophagy induction. The role of mitochondrial DNA (mtDNA) damage in the requirement of autophagy for nuclear DNA (nDNA) stability is unclear. Using site-specific DNA damage approaches, we show that specific nDNA damage alone does not require autophagy for repair unless in the presence of mtDNA damage. We provide evidence that after IR exposure-induced mtDNA and nDNA damages, autophagy suppression causes non-apoptotic mitochondrial permeability, by which mitochondrial ENDOG (endonuclease G) is released and translocated to nuclei to sustain nDNA damage in a TET (tet methylcytosine dioxygenase)-dependent manner. Furthermore, blocking lysosome function is sufficient to increase the amount of mtDNA leakage to the cytosol, accompanied by ENDOG-free mitochondrial puncta formation with concurrent ENDOG nuclear accumulation. We proposed that autophagy eliminates the mitochondria specified by mtDNA damage-driven mitochondrial permeability to prevent ENDOG-mediated genome instability. Finally, we showed that HBx, a hepatitis B viral protein capable of suppressing autophagy, also causes mitochondrial permeability-dependent ENDOG mis-localization in nuclei and is linked to hepatitis B virus (HBV)-mediated hepatocellular carcinoma development. Abbreviations: 3-MA: 3-methyladenine; 5-hmC: 5-hydroxymethylcytosine; ACTB: actin beta; ATG5: autophagy related 5; ATM: ATM serine/threonine kinase; DFFB/CAD: DNA fragmentation factor subunit beta; cmtDNA: cytosolic mitochondrial DNA; ConA: concanamycin A; CQ: chloroquine; CsA: cyclosporin A; Dox: doxycycline; DSB: double-strand break; ENDOG: endonuclease G; GFP: green fluorescent protein; Gy: gray; H2AX: H2A.X variant histone; HBV: hepatitis B virus; HBx: hepatitis B virus X protein; HCC: hepatocellular carcinoma; I-PpoI: intron-encoded endonuclease; IR: ionizing radiation; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOMP: mitochondrial outer membrane permeability; mPTP: mitochondrial permeability transition pore; mtDNA: mitochondrial DNA; nDNA: nuclear DNA; 4-OHT: 4-hydroxytamoxifen; rDNA: ribosomal DNA; ROS: reactive oxygen species; SQSTM1/p62: sequestosome 1; TET: tet methylcytosine dioxygenase; TFAM: transcription factor A, mitochondrial; TOMM20: translocase of outer mitochondrial membrane 20; VDAC: voltage dependent anion channel.

H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation.

Epigenetic mechanisms play diverse roles in the regulation of genome stability in eukaryotes. In Arabidopsis thaliana, genome stability is maintained during DNA replication by the H3.1K27 methyltransferases ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) and ATXR6, which catalyze the deposition of K27me1 on replication-dependent H3.1 variants. The loss of H3.1K27me1 in atxr5 atxr6 double mutants leads to heterochromatin defects, including transcriptional de-repression and genomic instability, but the molecular mechanisms involved remain largely unknown. In this study, we identified the transcriptional co-activator and conserved histone acetyltransferase GCN5 as a mediator of transcriptional de-repression and genomic instability in the absence of H3.1K27me1. GCN5 is part of a SAGA-like complex in plants that requires the GCN5-interacting protein ADA2b and the chromatin remodeler CHR6 to mediate the heterochromatic defects in atxr5 atxr6 mutants. Our results also indicate that Arabidopsis GCN5 acetylates multiple lysine residues on H3.1 variants, but H3.1K27 and H3.1K36 play essential functions in inducing genomic instability in the absence of H3.1K27me1. Finally, we show that H3.1K36 acetylation by GCN5 is negatively regulated by H3.1K27me1 in vitro. Overall, this work reveals a key molecular role for H3.1K27me1 in maintaining transcriptional silencing and genome stability in heterochromatin by restricting GCN5-mediated histone acetylation in plants.

Chromatin Regulation and Genome Maintenance by Mammalian SIRT7

Members of the Sirtuin family of enzymes are important regulators of genomic stability, stress responses, and metabolic programs that impact on human physiology, aging, and age-related disease processes. We previously showed that the mammalian Sirtuins SIRT6 and SIRT7 have high-selectivity histone deacetylase activities at chromatin, and inactivation of SIRT6 or SIRT7 results in dysregulated histone acetylation states and gene expression programs, with pathological consequences at the cellular and whole organism levels. Recently, we have been exploring novel functions of SIRT6 and SIRT7 in silencing of heterochromatic regions of the genome, the deregulation of which has been linked to aging and cancer biology. We found that pericentric heterochromatin silencing by SIRT6 prevents acute cellular senescence that is triggered by pathologic pericentric transcripts. We also uncovered a second novel trigger of human cellular senescence, ribosomal DNA instability in nucleoli, and we showed that SIRT7 guards against senescence induced by this instability. In our studies, a long-term focus has been identifying substrates of SIRT6 and SIRT7 and their roles in aging and disease pathways. In new work, are studying a novel physiologic substrate of SIRT7 at chromatin, H3K36Ac, and we are characterizing the genomic landscape of this SIRT7-dependent deacetylation target, and its downstream chromatin and nuclear signaling mechanisms. We will also discuss mechanistic insights into the functions of SIRT6 and SIRT7 from new proteomic, cellular, and mouse model studies.

A Noncanonical DNA Damage Checkpoint Response in a Major Fungal Pathogen.

DNA damage checkpoints are key guardians of genome integrity. Eukaryotic cells respond to DNA damage by triggering extensive phosphorylation of Rad53/CHK2 effector kinase, whereupon activated Rad53/CHK2 mediates further aspects of checkpoint activation, including cell cycle arrest and transcriptional changes. Budding yeast Candida glabrata, closely related to model eukaryote Saccharomyces cerevisiae, is an opportunistic pathogen characterized by high genetic diversity and rapid emergence of drug-resistant mutants. However, the mechanisms underlying this genetic variability are unclear. We used Western blotting and mass spectrometry to show that, unlike S. cerevisiae, C. glabrata cells exposed to DNA damage did not induce C. glabrata Rad53 (CgRad53) phosphorylation. Furthermore, flow cytometry analysis showed that, unlike S. cerevisiae, C. glabrata cells did not accumulate in S phase upon DNA damage. Consistent with these observations, time-lapse microscopy showed C. glabrata cells continuing to divide in the presence of DNA damage, resulting in mitotic errors and cell death. Finally, transcriptome sequencing (RNAseq) analysis revealed transcriptional rewiring of the DNA damage response in C. glabrata and identified several key protectors of genome stability upregulated by DNA damage in S. cerevisiae but downregulated in C. glabrata, including proliferating cell nuclear antigen (PCNA). Together, our results reveal a noncanonical fungal DNA damage response in C. glabrata, which may contribute to rapidly generating genetic change and drug resistance.IMPORTANCE In order to preserve genome integrity, all cells must mount appropriate responses to DNA damage, including slowing down or arresting the cell cycle to give the cells time to repair the damage and changing gene expression, for example to induce genes involved in DNA repair. The Rad53 protein kinase is a conserved central mediator of these responses in eukaryotic cells, and its extensive phosphorylation upon DNA damage is necessary for its activation and subsequent activity. Interestingly, here we show that in the opportunistic fungal pathogen Candida glabrata, Rad53 phosphorylation is not induced by DNA damage, nor do these cells arrest in S phase under these conditions, in contrast to the closely related yeast Saccharomyces cerevisiae Instead, C. glabrata cells continue to divide in the presence of DNA damage, resulting in significant cell lethality. Finally, we show that a number of genes involved in DNA repair are strongly induced by DNA damage in S. cerevisiae but repressed in C. glabrata Together, these findings shed new light on mechanisms regulating genome stability in fungal pathogens.

More than Meets the ISG15: Emerging Roles in the DNA Damage Response and Beyond.

Maintenance of genome stability is a crucial priority for any organism. To meet this priority, robust signalling networks exist to facilitate error-free DNA replication and repair. These signalling cascades are subject to various regulatory post-translational modifications that range from simple additions of chemical moieties to the conjugation of ubiquitin-like proteins (UBLs). Interferon Stimulated Gene 15 (ISG15) is one such UBL. While classically thought of as a component of antiviral immunity, ISG15 has recently emerged as a regulator of genome stability, with key roles in the DNA damage response (DDR) to modulate p53 signalling and error-free DNA replication. Additional proteomic analyses and cancer-focused studies hint at wider-reaching, uncharacterised functions for ISG15 in genome stability. We review these recent discoveries and highlight future perspectives to increase our understanding of this multifaceted UBL in health and disease.

An E3 ubiquitin ligase, cullin-4 regulates retinal differentiation in Drosophila eye.

During organogenesis, cell proliferation is followed by the differentiation of specific cell types to form an organ. Any aberration in differentiation can result in developmental defects, which can result in a partial to a near-complete loss of an organ. We employ the Drosophila eye model to understand the genetic and molecular mechanisms involved in the process of differentiation. In a forward genetic screen, we identified, cullin-4 (cul-4), which encodes an E3 ubiquitin ligase, to play an important role in retinal differentiation. During development, cul-4 is known to be involved in protein degradation, regulation of genomic stability, and regulation of cell cycle. Previously, we have reported that cul-4 regulates cell death during eye development by downregulating Wingless (Wg)/Wnt signaling pathway. We found that loss-of-function of cul-4 results in a reduced eye phenotype, which can be due to onset of cell death. However, we found that loss-of-function of cul-4 also affects retinal development by downregulating retinal determination (RD) gene expression. Early markers of retinal differentiation are dysregulated in cul-4 loss of function conditions, indicating that cul-4 is necessary for differentiation. Furthermore, loss-of-function of cul-4 ectopically induces expression of negative regulators of eye development like Wg and Homothorax (Hth). During eye development, Wg is known to block the progression of a synchronous wave of differentiation referred to as Morphogenetic furrow (MF). In cul-4 loss-of-function background, expression of dpp-lacZ, a MF marker, is significantly downregulated. Our data suggest a new role of cul-4 in retinal differentiation. These studies may have significant bearings on our understanding of early eye development.

Genome-wide identification and expression profiling of cytosine-5 DNA methyltransferases during drought and heat stress in wheat (Triticum aestivum)

DNA methylation is a potential epigenetic mechanism that regulates genome stability, development, and stress mitigation in plants. It is mediated by cytosine-5 DNA methyltransferases (C5-MTases). We identified 52 wheat C5-MTases; and based on domain structure and phylogenetics, these 52 C5-MTases were classified into four sub-families including MET, CMT, DRM and DNMT2; and were distributed on 18 chromosomes. Cis-acting regulatory elements analysis identified abiotic stress-responsive, phytohormone-responsive, development-related and light-related elements in the promoters of TaC5-MTases. We also examined the transcript abundance of TaC5-MTases in different tissues, developmental stages and under abiotic stresses. Notably, most of the TaC5-MTases (TaCMT2, TaCMT3b, TaCMT3c, TaMET1, TaDRM10, TaDNMT2) showed differential regulation of their transcript abundance during drought and heat stress. Overall, the above results provide significant insights into the expression and the probable functions of TaC5-MTases and will also expedite future research programs to explore the mechanisms of epigenetic regulation in wheat.

Abstract 3537: Evaluation of genomic instability using microsatellite instability, ploidy status, and p53 expression in archival paraffin embedded tissue from primary ovarian cancer specimens

Abstract A retrospective study of a subset of ovarian cancer cases was evaluated to assess the role of microsatellite instability (MSI) and ploidy status. P53 function is important in the regulation of genomic stability and its expression was examined by immuno-histochemical staining. Genomic instability is also considered a possible indicator of immuno-therapy responsive tumors. Ovarian cancer patients diagnosed between 1983 to 1987 at Saskatoon Cancer Center, Canada, were evaluated for genomic stability. Nearly 400 Epithelial Ovarian Cancer (EOC) cases were reviewed, and Paraffin Embedded Tissue (PET) blocks from 112 cases were retrieved from hospitals in the region. PET blocks containing over 70% neoplastic tissue were chosen for the study. P53 expression was determined in eighteen cases using the mouse monoclonal antibody D07. An assessment of MSI and LOH was performed using the PCR mixes from Perkin Elmer (PE) AB. The replication error repair (RER)/Loss of Heterozygosity (LOH) assays were performed at nine loci using the primers obtained from PE. Fourteen out of eighteen cases were evaluated for ploidy status using a method described in literature[1]. Statistical analyses were performed to determine the significance of MSI/LOH, ploidy status, and p53 expression. In this study, 34 (30%) of 112 EOC cases were found to be aneuploid. Fourteen EOC cases had ploidy status that could be evaluated. Of the eighteen patients analyzed for MSI, at least nine patients showed instability at one or more loci. Of these nine, there were two RER positive phenotypes with aneuploid DNA content which were also p53 immuno-negative. Of the seven (78%) RER negative tumors, 57% (4/7) p53 negative, and the remaining three cases overexpressed p53. In five EOC cases, with an RER negative phenotype, 60% (3/5) were aneuploid and 40% (2/5) were diploid. Furthermore, LOH was a common event at the nine loci. The three events: MSI, lack of p53 overexpression, and aneuploidy, may be characteristics of a subset of ovarian cancer cases. Secondly, the study suggests that RER positivity occurs in ovarian cancer pathogenesis. We conclude that the data indicates general genomic instability due to MSI and DNA ploidy status. [1] A. Geissel and J. L. Griffin, “Preparation of nuclei for flow cytometry,” in AFIP Advances in Laboratory Methods in histology and Pathology, ed. Mikel UV (Washington DC: American Registry of Pathology, 1994), 111-121. Citation Format: Kavitha Advikolanu Rao, Anthony M. Magliocco, Andrew W. Maksymiuk. Evaluation of genomic instability using microsatellite instability, ploidy status, and p53 expression in archival paraffin embedded tissue from primary ovarian cancer specimens [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3537.

Abstract 2372: DUSP3-NPM-P53 axis: a new regulator of genomic stability of cells under genotoxic stress

Abstract The dual-specificity phosphatase 3 (DUSP3) is an atypical tyrosine phosphatase that dephosphorylates residues of p-Tyrosine and p-Threonine in protein substrates. DUSP3 is overexpressed in some human tumors, where it regulates cell cycle progression and has preferably nuclear localization. DUSP3 contributes to cellular genomic stability through mechanisms that begin to be clarified here. Our group used biochemical, bioinformatics, proteomics and interactome approaches to identify and validate nuclear proteins interacting with DUSP3 under cellular conditions of genotoxic stress promoted by UV-radiation. One of these targets is the nucleophosmin (NPM) protein, which plays key roles in nucleotide excision repair (NER) pathway. Surface Plasmon Resonance analyses showed a very strong physical bimolecular interaction between NPM-DUSP3. In order to verify the involvement of this phosphatase in DNA repair, DUSP3 knockdown was carried out in MRC-5 (normal fibroblasts) or XPA (NER-deficient cell line lacking the XPA protein) cell lines. By alkaline comet assays we found DUSP3 knockdown caused delay in DNA repair even in XPA cells, which is not to repair UV-radiation induced damage. This effect was supported by immuno-slot-blot assays specifically measuring the distortions of CPD and 6,4-photoproducts (6-4-PP) caused by UV-radiation on cells genome. Once again, MRC-5 cells DUSP3 silenced exhibited delay in the repair of these lesions, whereas XPA cells were not able to repair them even after 72h of the UVC exposure, but the accumulation of CPD and 6-4-PP lesions was even higher under DUSP3 silencing. Next we verify that NPM is a substrate of DUSP3 by immunoprecipitating tyrosine-phosphorylated NPM, and which levels are increased in both cells under DUSP3 knockdown. Using phospho-specific antibodies designed against the four tyrosine residues of NPM, immunoblotings revealed that DUSP3 specifically dephosphorylates tyrosine 29, 67 and 271 residues of NPM after UV radiation altering its subnuclear localization. Furthermore immunoblotting and imunofluorescence assays revealed an unexpected increase in phospho-p53-Ser15 and p53 transcriptional activity in DUSP3 deficient cells after exposure to UV radiation, which can be correlated to nuclear NPM functions in the repair of UV-promoted DNA lesions. Even so, we observed that DUSP3 knockdown also causes an earlier nucleolus-nucleoplasm translocation of NPM after genotoxic stress that is followed by an earlier ARF translocation and co-localization of both proteins with HDM2 and p53 at nucleoplasm. This leads to disruption of HDM2-p53 interaction, to non-degradation and earlier phosphorylation of p53-Ser15. Interestingly, using cycloheximide to inhibit protein synthesis, we confirmed that the half-life of p53 and NPM is longer in the DUSP3-deficient cells. Altogether our data highlight DUSP3 unknown roles in different signaling modules regulating biological processes involved in genomic stability through an unusual target, the NPM-p53 axis. Citation Format: Fábio L. Forti, Lilian C. Russo. DUSP3-NPM-P53 axis: a new regulator of genomic stability of cells under genotoxic stress [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2372.

USP7 Is a Master Regulator of Genome Stability.

Genetic alterations, including DNA mutations and chromosomal abnormalities, are primary drivers of tumor formation and cancer progression. These alterations can endow cells with a selective growth advantage, enabling cancers to evade cell death, proliferation limits, and immune checkpoints, to metastasize throughout the body. Genetic alterations occur due to failures of the genome stability pathways. In many cancers, the rate of alteration is further accelerated by the deregulation of these processes. The deubiquitinating enzyme ubiquitin specific protease 7 (USP7) has recently emerged as a key regulator of ubiquitination in the genome stability pathways. USP7 is also deregulated in many cancer types, where deviances in USP7 protein levels are correlated with cancer progression. In this work, we review the increasingly evident role of USP7 in maintaining genome stability, the links between USP7 deregulation and cancer progression, as well as the rationale of targeting USP7 in cancer therapy.

SIRT1 Promotes Neuronal Fortification in Neurodegenerative Diseases through Attenuation of Pathological Hallmarks and Enhancement of Cellular Lifespan.

Neurodegeneration is a complex neurological phenomenon characterized by disturbed coherence in neuronal efflux. Progressive neuronal loss and brain damage due to various age-related pathological hallmarks perturb the behavioral balance and quality of life. Sirtuins have been widely investigated for their neuroprotective role, with SIRT1 being the most contemplated member of the family. SIRT1 exhibits significant capabilities to enhance neurogenesis and cellular lifespan by regulating various pathways, which makes it an exciting therapeutic target to inhibit neurodegenerative disease progression. SIRT1 mediated neuronal fortification involves modulation of molecular co-factors and biochemical pathways responsible for the induction and sustenance of pro-inflammatory and pro-oxidative environment in the cellular milieu. In this review, we present the major role played by SIRT1 in maintaining cellular strength through the regulation of genomic stability, neuronal growth, energy metabolism, oxidative stress, inhibiting mechanisms and anti-inflammatory responses. The therapeutic significance of SIRT1 has been put into perspective through a comprehensive discussion about its ameliorating potential against neurodegenerative stimuli in a variety of diseases that characteristically impair cognition, memory and motor coordination. This review enhances the acquaintance concerned with the neuroprotective potential of SIRT1 and thus promotes the development of novel SIRT1 regulating therapeutic agents and strategies.

Sumoylation on its 25th anniversary: mechanisms, pathology, and emerging concepts.

Sumoylation is an essential post-translational modification intimately involved in a diverse range of eukaryotic cellular mechanisms. Small ubiquitin-like modifier (SUMO) protein isoforms can be reversibly linked to lysine residues that reside within specific motifs on thousands of target substrates, leading to modulations in stability, solubility, localization, and interactor profile. Since its initial discovery almost 25years ago, SUMO has been described as a key regulator of genomic stability, cell proliferation, and infection among other processes. In this review, we trace the exciting developments in the history of this critical modifier, highlighting SUMO's roles in pathogenesis as well as its potential for the development of targeted therapies for numerous diseases.

BGL3 lncRNA mediates retention of the BRCA1/BARD1 complex at DNA damage sites.

Long non-coding RNAs (lncRNAs) are emerging regulators of genomic stability and human disease. However, the molecular mechanisms by which nuclear lncRNAs directly contribute to DNA damage responses remain largely unknown. Using RNA antisense purification coupled with quantitative mass spectrometry (RAP-qMS), we found that the lncRNA BGL3 binds to PARP1 and BARD1, exhibiting unexpected roles in homologous recombination. Mechanistically, BGL3 is recruited to DNA double-strand breaks (DSBs) by PARP1 at an early time point, which requires its interaction with the DNA-binding domain of PARP1. BGL3 also binds the C-terminal BRCT domain and an internal region (amino acids 127-424) of BARD1, which mediates interaction of the BRCA1/BARD1 complex with its binding partners such as HP1γ and RAD51, resulting in BRCA1/BARD1 retention at DSBs. Cells depleted for BGL3 displayed genomic instability and were sensitive to DNA-damaging reagents. Overall, our findings underscore the biochemical versatility of RNA as a mediator molecule in the DNA damage response pathway, which affects the accumulation of BRCA1/BARD1 at DSBs.

Chromatin Regulation and Genome Maintenance by Mammalian SIRT6 and SIRT7

Members of the Sirtuin family of enzymes are important regulators of genomic stability, stress responses, and metabolic programs that impact on human physiology, aging, and age‐related disease processes. We previously showed that the mammalian Sirtuins SIRT6 and SIRT7 have high‐selectivity histone deacetylase activities at chromatin, and inactivation of SIRT6 or SIRT7 results in dysregulated histone acetylation states and gene expression programs, with pathological consequences at the cellular and whole organism levels. Recently, we have been exploring novel functions of SIRT6 and SIRT7 in silencing of heterochromatic regions of the genome, the deregulation of which has been linked to aging and cancer biology. We found that pericentric heterochromatin silencing by SIRT6 prevents acute cellular senescence that is triggered by pathologic pericentric transcripts. We also uncovered a second novel trigger of human cellular senescence, ribosomal DNA instability in nucleoli, and we showed that SIRT7 guards against senescence induced by this instability. In our studies, a long‐term focus has been identifying substrates of SIRT6 and SIRT7 and their roles in aging and disease pathways. In new work, we have identified a novel physiologic substrate of SIRT7 at chromatin, and we are characterizing the genomic landscape of this SIRT7‐dependent deacetylation target, and its downstream chromatin and nuclear signaling mechanisms. We will also discuss mechanistic insights into the functions of SIRT6 and SIRT7 from new proteomic, cellular, and mouse model studies.Support or Funding InformationVA Merit Review NIH/NIA

The Deubiquitinase USP38 Promotes NHEJ Repair through Regulation of HDAC1 Activity and Regulates Cancer Cell Response to Genotoxic Insults.

The DNA damage response (DDR) is essential for maintaining genome integrity. Mounting evidence reveals that protein modifications play vital roles in the DDR. Here, we show that USP38 is involved in the DDR by regulating the activity of HDAC1. In response to DNA damage, USP38 interacted with HDAC1 and specifically removed the K63-linked ubiquitin chain promoting the deacetylase activity of HDAC1. As a result, HDAC1 was able to deacetylate H3K56. USP38 deletion resulted in persistent focal accumulation of nonhomologous end joining (NHEJ) factors at DNA damage sites and impaired NHEJ efficiency, causing genome instability and sensitizing cancer cells to genotoxic insults. Knockout of USP38 rendered mice hypersensitive to irradiation and shortened survival. In addition, USP38 was expressed at low levels in certain types of cancers including renal cell carcinoma, indicating dysregulation of USP38 expression contributes to genomic instability and may lead to tumorigenesis. In summary, this study identifies a critical role of USP38 in modulating genome integrity and cancer cell resistance to genotoxic insults by deubiquitinating HDAC1 and regulating its deacetylation activity. SIGNIFICANCE: This study demonstrates that USP38 regulates genome stability and mediates cancer cell resistance to DNA-damaging therapy, providing insight into tumorigenesis and implicating USP38 as a potential target for cancer diagnosis.