scholarly journals The scaffold protein Nde1 safeguards the brain genome during S phase of early neural progenitor differentiation

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Shauna L Houlihan ◽  
Yuanyi Feng

Successfully completing the S phase of each cell cycle ensures genome integrity. Impediment of DNA replication can lead to DNA damage and genomic disorders. In this study, we show a novel function for NDE1, whose mutations cause brain developmental disorders, in safeguarding the genome through S phase during early steps of neural progenitor fate restrictive differentiation. Nde1 mutant neural progenitors showed catastrophic DNA double strand breaks concurrent with the DNA replication. This evoked DNA damage responses, led to the activation of p53-dependent apoptosis, and resulted in the reduction of neurons in cortical layer II/III. We discovered a nuclear pool of Nde1, identified the interaction of Nde1 with cohesin and its associated chromatin remodeler, and showed that stalled DNA replication in Nde1 mutants specifically occurred in mid-late S phase at heterochromatin domains. These findings suggest that NDE1-mediated heterochromatin replication is indispensible for neuronal differentiation, and that the loss of NDE1 function may lead to genomic neurological disorders.

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5624-5624
Author(s):  
Dhyani Anamika ◽  
Patricia Favaro ◽  
Sara Teresinha Olalla Saad

Abstract Ankyrin repeat and KH domain-containing protein 1, ANKHD1, is highly expressed in myeloma cells and plays an important role in multiple myeloma (MM) progression and growth. ANKHD1 is found to be overexpressed in S phase of cell cycle in MM cells and silencing of ANKHD1 expression leads to accumulation of cells in S phase, suggesting a role in S phase progression (1). Earlier studies by our group reported that ANKHD1 silencing downregulates all replication dependent histones and that this downregulation may be associated with replication stress and DNA damage (2). We observed increased expression of γH2AX protein (phosphorylated histone H2A variant, H2AX, at Serine 139), a marker for DNA double strand breaks (DSBs) and an early sign of DNA damage induced by replication stress, in ANKHD1 silenced MM cells. In the present study we further sought to investigate the mechanisms underlying the induction of DNA damage on ANKHD1 silencing. We first confirmed the increased expression of γH2AX by flow cytometry analysis and observed that both the mean fluorescence intensity as well as percentage of γH2AX positive cells were higher in ANKHD1 silenced MM cells as compared to control cells. Phosphorylation of histone 2AX requires activation of the phosphatidylinositol-3-OH-kinase-like family of protein kinases, DNA-PKcs (DNA-dependent protein kinase), ATM (ataxia telangiectasia mutated)andATR (ATM-Rad3-related) that serves as central components of the signaling cascade initiated by DSBs. Hence, we checked for the expression of these kinases and observed increased phosphorylation of both ATM and ATR kinases in ANKHD1 silenced MM cells. There was no difference in the expressions of DNA-PKcs in control and ANKHD1 silenced cells by western blot. We next checked for the expression of CHK1 (checkpoint kinase 1) and CHK2 (checkpoint kinase 2), essential serine threonine kinases downstream of ATM and ATR. We observed a decrease in pCHK2 (phosphorylated CHK2 at Thr 68), with no change in expression of pCHK1 (phosphorylated CHK1 at Ser 345) total CHK1 or total CHK2. We also checked for expression of CDC25a (a member of the CDC25 family of dual-specificity phosphatases), that is specifically degraded in response to DNA damage (DSBs) and delays S phase progression via activation of ATM /ATR-CHK2 signaling pathway. Expression of CDC25a was significantly decreased in ANKHD1 silencing cells, confirming the induction of DSBs, and probably accounting for S phase delay on ANKHD1 silencing. Since there was decrease in active CHK2 (pCHK2) and no change in CHK1 required for degradation of CDC25a, we assume that decrease in CDC25a in ANKHD1 silenced MM cells may be via activation of ATM/ ATR pathway independent of CHK2/CHK1. Expression of several other downstream factors of DSBs induced DNA damage response and repair such as BRCA1, PTEN, DNMT1, SP1, HDAC2 were also found to be modulated in ANKHD1 silenced MM cells. In conclusion, ANKHD1 silencing in MM cells leads to DNA damage and modulates expression of several genes implicated in DNA damage and repair. DNA damage induced after ANKHD1 silencing in MM cells activates ATM/ ATR-CDC25a pathway which may lead to the activation of S phase checkpoint in MM cells. Results however are preliminary and further studies are required to understand the role of ANKHD1 in intra S phase check point. References: 1) ANKHD1 regulates cell cycle progression and proliferation in multiple myeloma cells. Dhyani et al. FEBS letters 2012; 586: 4311-18. 2) ANKHD1 is essential for repair of DNA double strand breaks in multiple myeloma. Dhyani et al. ASH Abstract, Blood 2015; 126:1762. Disclosures No relevant conflicts of interest to declare.


Mutagenesis ◽  
2019 ◽  
Vol 35 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Alan E Tomkinson ◽  
Tasmin Naila ◽  
Seema Khattri Bhandari

Abstract The joining of interruptions in the phosphodiester backbone of DNA is critical to maintain genome stability. These breaks, which are generated as part of normal DNA transactions, such as DNA replication, V(D)J recombination and meiotic recombination as well as directly by DNA damage or due to DNA damage removal, are ultimately sealed by one of three human DNA ligases. DNA ligases I, III and IV each function in the nucleus whereas DNA ligase III is the sole enzyme in mitochondria. While the identification of specific protein partners and the phenotypes caused either by genetic or chemical inactivation have provided insights into the cellular functions of the DNA ligases and evidence for significant functional overlap in nuclear DNA replication and repair, different results have been obtained with mouse and human cells, indicating species-specific differences in the relative contributions of the DNA ligases. Inherited mutations in the human LIG1 and LIG4 genes that result in the generation of polypeptides with partial activity have been identified as the causative factors in rare DNA ligase deficiency syndromes that share a common clinical symptom, immunodeficiency. In the case of DNA ligase IV, the immunodeficiency is due to a defect in V(D)J recombination whereas the cause of the immunodeficiency due to DNA ligase I deficiency is not known. Overexpression of each of the DNA ligases has been observed in cancers. For DNA ligase I, this reflects increased proliferation. Elevated levels of DNA ligase III indicate an increased dependence on an alternative non-homologous end-joining pathway for the repair of DNA double-strand breaks whereas elevated level of DNA ligase IV confer radioresistance due to increased repair of DNA double-strand breaks by the major non-homologous end-joining pathway. Efforts to determine the potential of DNA ligase inhibitors as cancer therapeutics are on-going in preclinical cancer models.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3114-3114
Author(s):  
Francesca Cottini ◽  
Teru Hideshima ◽  
Giovanni Tonon ◽  
Kenneth C. Anderson

Abstract Multiple myeloma (MM) is a clonal proliferation of malignant plasma cells, carrying abnormal karyotypes, chromosomal translocations, and innumerous DNA copy-number variations. We and others have previously shown that MM cells have constitutive DNA damage and DNA damage response (DDR), while normal plasma cells (NPCs) are negative for these DDR markers. Moreover, we recently observed that markers of replicative stress, such as p-ATR and p-CHK1 together with RPA foci, are also present in MM cells. The MYC (or c-MYC) oncogene is pervasively altered in MM. Since MYC is associated with DNA replication stress, oxidative stress, and DDR, we explored whether MYC is implicated in these pathways in MM. Indeed, by analyzing various DNA damage gene expression signatures, we found a positive correlation between MYC levels and ongoing DNA damage. We next examined whether MYC modulation could alter replicative stress markers, and induce DNA double-strand breaks. In a gain-of-function model, c-MYC was expressed in U266 MM cell line, which has low c-MYC levels and importantly shows low levels of ongoing DNA damage. In parallel, the H929 and MM.1S MM cell lines were used to knock-down c-MYC expression. Re-expression of a functional MYC-EGFP in U266 cells induced replicative stress markers, such as RAD51, RPA, and phospho-CHK1 foci, as well as increased RAD51, RPA and phospho-CHK1 protein levels. To determine whether this phenotype was linked to concomitant oxidative stress, we incubated MM cells with an antioxidant reagent N-Acetylcysteine (NAC). We observed a modest reduction in replicative markers after NAC treatment, which was more evident by MYC overexpression. Taken together, these results suggest that the replicative stress induced by MYC is, at least in part, associated with oxidative stress. Additionally, MYC-EGFP positive U266 cells also show DNA damage, evidenced by appearance of phospho-H2A.X foci (which detect DNA double strand breaks), that in turn triggers an intense DNA damage response, assessed by phospho-ATM/phospho CHK2 positivity. In contrast, all these DDR markers were downregulated by MYC silencing, prior to cell death, in MM.1S and H929 MM cell lines. Finally, we examined whether targeting the replicative stress response may represent a novel therapeutic strategy in MM cells with high expression of MYC. Specifically, we treated U266 cells transduced with MYC or control LACZ cells, as well as MM.1S and H929 transfected with a specific MYC-shRNA or their scrambled shRNA controls, with a small molecule ATR inhibitor VE-821 which prevents proper DNA repair after DNA damage. Cells overexpressing MYC were significantly more sensitive to VE-821 treatment compared to controls; conversely MYC-silenced cells were more resistant to VE-821. These results suggest the potential utility of VE-821 as a novel therapeutic agent in cells with high expression of MYC. In conclusion, our data show that MYC may exert its oncogenic activity partly through its ability to trigger DNA replication stress, leading to DNA damage and genomic instability in MM cells. Given the pervasive deregulation of MYC present in MM cells, its role in DNA replication and DNA damage may correlate with the extensive genomic rearrangements observed in MM cells. Therefore, treatment strategies targeting this Achilles' heel may improve patient outcome in MM. Disclosures: Hideshima: Acetylon Pharmaceuticals: Consultancy. Anderson:Acetylon, Oncopep: Scientific Founder, Scientific Founder Other; Celgene, Millennium, BMS, Onyx: Membership on an entity's Board of Directors or advisory committees.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1762-1762
Author(s):  
Anamika Dhyani ◽  
Patricia Favaro ◽  
Sara T. Olalla Saad

Abstract ANKHD1, Ankyrin repeat and KH domain-containing protein is highly expressed and plays an important role in the proliferation and cell cycle progression of multiple myeloma (MM) cells. Inhibition of ANKHD1 expression upregulates p21 (CDKN1A, Cyclin Dependent Kinase Inhibitor), a potent cell cycle regulator, and its expression represses p21 promoter. Upregulation of p21 was found to be irrespective of the TP53 mutational status of MM cell lines. A study by our group has shown that ANKHD1 is highly expressed in S phase and that the inhibition of ANKHD1 expression downregulates replication dependent histones suggesting that it might be required for histone transcription (1). Assuming that ANKHD1 might be involved in the transcripitional activation of histones, we studied the effect of ANKHD1 silencing on nuclear protein of the ataxia telangiectasia mutated locus (NPAT), a component of the cell-cycle-dependent histone gene transcription machinery. NPAT associates with histone gene promoters in S phase and suppression of NPAT expression impedes expression of all histone subtypes. In present study, there was a decreased expression of NPAT in ANKHD1 silenced MM cells. Despite the fact that both ANKHD1 and NPAT were localized in the nucleus of MM cells, they did not appear to associate, as observed by confocal microscopy, suggesting at present that ANKHD1 does not modulate histones via NPAT. Since DNA replication is coupled with histone synthesis and downregulation of histones is associated with replication stress and DNA damage, we checked for expression of PCNA (Proliferating Cell Nuclear Antigen), protein involved in DNA replication and repair. PCNA expression was found to be significantly decreased in ANKHD1 inhibited MM cells, suggesting its role in PCNA mediated DNA replication and repair (Fig. 1). To confirm this, we studied the effect of ANKHD1 silencing on some of the components of DNA damage repair (DDR) pathway. We observed increased expression of gamma- H2AX (γ-H2AX i.e Phosphorylated Histone H2AX), marker for DNA double-strand breaks (DSBs) and an early sign of DNA damage induced by replication stress (Fig. 1). We also observed a decrease in phosphorylated CHK2 (Check Point Kinase 2), an essential serine threonine kinase involved in DDR. Accumulation of γ-H2AX on ANKHD1 silencing confirms DNA damage and suggests the possible mechanism of ANKHD1 mediated histones downregulation. In summary, ANKHD1 silencing in MM cells leads to DNA damage (DSBs), suggesting that ANKHD1 is essential for DNA replication and repair. Furthermore, as ANKHD1 negatively regulates p21, and p21 controls DNA replication and repair by interacting with PCNA, we hypothesize that ANKHD1 might be playing role in DNA repair via modulation of the p21-PCNA pathway. Results of the role of ANKHD1 in DNA repair are however preliminary and need to be explored. References: 1) ANKHD1 Is Required for S Phase Progression and Histone Gene Transcription in Multiple Myeloma. Dhyani et al. ASH Abstract; Blood 2014. Figure 1. Western blot analysis of proteins: a) PCNA and b) γ-H2AX, in control and ANKHD1 silenced U266 MM cell line. Tubulin and GAPDH were used as endogenous controls. Figure 1. Western blot analysis of proteins: a) PCNA and b) γ-H2AX, in control and ANKHD1 silenced U266 MM cell line. Tubulin and GAPDH were used as endogenous controls. Disclosures No relevant conflicts of interest to declare.


2019 ◽  
Vol 30 (21) ◽  
pp. 2620-2625 ◽  
Author(s):  
Michael J. Smith ◽  
Eric E. Bryant ◽  
Fraulin J. Joseph ◽  
Rodney Rothstein

During S phase in Saccharomyces cerevisiae, chromosomal loci become mobile in response to DNA double-strand breaks both at the break site (local mobility) and throughout the nucleus (global mobility). Increased nuclear exploration is regulated by the recombination machinery and the DNA damage checkpoint and is likely an important aspect of homology search. While mobility in response to DNA damage has been studied extensively in S phase, the response in interphase has not, and the question of whether homologous recombination proceeds to completion in G1 phase remains controversial. Here, we find that global mobility is triggered in G1 phase. As in S phase, global mobility in G1 phase is controlled by the DNA damage checkpoint and the Rad51 recombinase. Interestingly, despite the restriction of Rad52 mediator foci to S phase, Rad51 foci form at high levels in G1 phase. Together, these observations indicate that the recombination and checkpoint machineries promote global mobility in G1 phase, supporting the notion that recombination can occur in interphase diploids.


2019 ◽  
Author(s):  
Shivnarayan Dhuppar ◽  
Sitara Roy ◽  
Aprotim Mazumder

AbstractUltraviolet (UV) radiation is a major environmental mutagen. Exposure to UV leads to a sharp peak of γH2AX – the phosphorylated form of a histone variant H2AX – in the S phase within an asynchronous population of cells. γH2AX is often considered as a definitive marker of DNA damage inside a cell. In this report we show that γH2AX in the S phase cells after UV irradiation does not report on the extent of primary DNA damage in the form of cyclobutane pyrimidine dimers or on the extent of its secondary manifestations as DNA double strand breaks or in the inhibition of global transcription. Instead γH2AX in the S phase corresponds to the sites of active replication at the time of UV irradiation – despite which, the cells complete the replication of their genomes and arrest within the G2 phase. Moreover, cells in all the phases of the cell cycle develop similar levels of DNA damage. Our study suggests that it is not DNA damage but the response elicited, which peaks in the S phase upon UV damage.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Deepti Sharma ◽  
Louis De Falco ◽  
Sivaraman Padavattan ◽  
Chang Rao ◽  
Susana Geifman-Shochat ◽  
...  

AbstractThe poly(ADP-ribose) polymerase, PARP1, plays a key role in maintaining genomic integrity by detecting DNA damage and mediating repair. γH2A.X is the primary histone marker for DNA double-strand breaks and PARP1 localizes to H2A.X-enriched chromatin damage sites, but the basis for this association is not clear. We characterize the kinetics of PARP1 binding to a variety of nucleosomes harbouring DNA double-strand breaks, which reveal that PARP1 associates faster with (γ)H2A.X- versus H2A-nucleosomes, resulting in a higher affinity for the former, which is maximal for γH2A.X-nucleosome that is also the activator eliciting the greatest poly-ADP-ribosylation catalytic efficiency. The enhanced activities with γH2A.X-nucleosome coincide with increased accessibility of the DNA termini resulting from the H2A.X-Ser139 phosphorylation. Indeed, H2A- and (γ)H2A.X-nucleosomes have distinct stability characteristics, which are rationalized by mutational analysis and (γ)H2A.X-nucleosome core crystal structures. This suggests that the γH2A.X epigenetic marker directly facilitates DNA repair by stabilizing PARP1 association and promoting catalysis.


Author(s):  
Sang-Min Jang ◽  
Christophe E. Redon ◽  
Haiqing Fu ◽  
Fred E. Indig ◽  
Mirit I. Aladjem

Abstract Background The p97/valosin-containing protein (VCP) complex is a crucial factor for the segregation of ubiquitinated proteins in the DNA damage response and repair pathway. Objective We investigated whether blocking the p97/VCP function can inhibit the proliferation of RepID-deficient cancer cells using immunofluorescence, clonogenic survival assay, fluorescence-activated cell sorting, and immunoblotting. Result p97/VCP was recruited to chromatin and colocalized with DNA double-strand breaks in RepID-deficient cancer cells that undergo spontaneous DNA damage. Inhibition of p97/VCP induced death of RepID-depleted cancer cells. This study highlights the potential of targeting p97/VCP complex as an anticancer therapeutic approach. Conclusion Our results show that RepID is required to prevent excessive DNA damage at the endogenous levels. Localization of p97/VCP to DSB sites was induced based on spontaneous DNA damage in RepID-depleted cancer cells. Anticancer drugs targeting p97/VCP may be highly potent in RepID-deficient cells. Therefore, we suggest that p97/VCP inhibitors synergize with RepID depletion to kill cancer cells.


2021 ◽  
Vol 22 (14) ◽  
pp. 7638
Author(s):  
Yvonne Lorat ◽  
Judith Reindl ◽  
Anna Isermann ◽  
Christian Rübe ◽  
Anna A. Friedl ◽  
...  

Background: Charged-particle radiotherapy is an emerging treatment modality for radioresistant tumors. The enhanced effectiveness of high-energy particles (such as heavy ions) has been related to the spatial clustering of DNA lesions due to highly localized energy deposition. Here, DNA damage patterns induced by single and multiple carbon ions were analyzed in the nuclear chromatin environment by different high-resolution microscopy approaches. Material and Methods: Using the heavy-ion microbeam SNAKE, fibroblast monolayers were irradiated with defined numbers of carbon ions (1/10/100 ions per pulse, ipp) focused to micrometer-sized stripes or spots. Radiation-induced lesions were visualized as DNA damage foci (γH2AX, 53BP1) by conventional fluorescence and stimulated emission depletion (STED) microscopy. At micro- and nanoscale level, DNA double-strand breaks (DSBs) were visualized within their chromatin context by labeling the Ku heterodimer. Single and clustered pKu70-labeled DSBs were quantified in euchromatic and heterochromatic regions at 0.1 h, 5 h and 24 h post-IR by transmission electron microscopy (TEM). Results: Increasing numbers of carbon ions per beam spot enhanced spatial clustering of DNA lesions and increased damage complexity with two or more DSBs in close proximity. This effect was detectable in euchromatin, but was much more pronounced in heterochromatin. Analyzing the dynamics of damage processing, our findings indicate that euchromatic DSBs were processed efficiently and repaired in a timely manner. In heterochromatin, by contrast, the number of clustered DSBs continuously increased further over the first hours following IR exposure, indicating the challenging task for the cell to process highly clustered DSBs appropriately. Conclusion: Increasing numbers of carbon ions applied to sub-nuclear chromatin regions enhanced the spatial clustering of DSBs and increased damage complexity, this being more pronounced in heterochromatic regions. Inefficient processing of clustered DSBs may explain the enhanced therapeutic efficacy of particle-based radiotherapy in cancer treatment.


2019 ◽  
Vol 116 (39) ◽  
pp. 19552-19562 ◽  
Author(s):  
Justine Sitz ◽  
Sophie Anne Blanchet ◽  
Steven F. Gameiro ◽  
Elise Biquand ◽  
Tia M. Morgan ◽  
...  

High-risk human papillomaviruses (HR-HPVs) promote cervical cancer as well as a subset of anogenital and head and neck cancers. Due to their limited coding capacity, HPVs hijack the host cell’s DNA replication and repair machineries to replicate their own genomes. How this host–pathogen interaction contributes to genomic instability is unknown. Here, we report that HPV-infected cancer cells express high levels of RNF168, an E3 ubiquitin ligase that is critical for proper DNA repair following DNA double-strand breaks, and accumulate high numbers of 53BP1 nuclear bodies, a marker of genomic instability induced by replication stress. We describe a mechanism by which HPV E7 subverts the function of RNF168 at DNA double-strand breaks, providing a rationale for increased homology-directed recombination in E6/E7-expressing cervical cancer cells. By targeting a new regulatory domain of RNF168, E7 binds directly to the E3 ligase without affecting its enzymatic activity. As RNF168 knockdown impairs viral genome amplification in differentiated keratinocytes, we propose that E7 hijacks the E3 ligase to promote the viral replicative cycle. This study reveals a mechanism by which tumor viruses reshape the cellular response to DNA damage by manipulating RNF168-dependent ubiquitin signaling. Importantly, our findings reveal a pathway by which HPV may promote the genomic instability that drives oncogenesis.


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