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Patients with chronic kidney disease (CKD) exhibit an increased cancer risk compared to a healthy control population. To be able to estimate the cancer risk of the patients and to assess the impact of interventional therapies thereon, it is of particular interest to measure the patients’ burden of genomic damage. Chromosomal abnormalities, reduced DNA repair, and DNA lesions were found indeed in cells of patients with CKD. Biomarkers for DNA damage measurable in easily accessible cells like peripheral blood lymphocytes are chromosomal aberrations, structural DNA lesions, and oxidatively modified DNA bases. In this review the most common methods quantifying the three parameters mentioned above, the cytokinesis-block micronucleus assay, the comet assay, and the quantification of 8-oxo-7,8-dihydro-2′-deoxyguanosine, are evaluated concerning the feasibility of the analysis and regarding the marker’s potential to predict clinical outcomes.
Cellular stress can induce DNA lesions that threaten the stability of genes. The DNA damage response (DDR) recognises and repairs broken DNA to maintain genome stability. Intriguingly, components of nuclear paraspeckles like the non-POU domain containing octamer-binding protein (NONO) participate in the repair of DNA double-strand breaks (DSBs). NONO is a multifunctional RNA-binding protein (RBP) that facilitates the retention and editing of messenger (m)RNA as well as pre-mRNA processing. However, the role of NONO in the DDR is poorly understood. Here, we establish a novel human U2OS cell line that expresses NONO fused to the engineered ascorbate peroxidase 2 (U2OS:NONO-APEX2-HA). We show that NONO-APEX2-HA accumulates in the nucleolus in response to DNA damage. Combining viability assays, subcellular localisation studies, coimmunoprecipitation experiments and in vivo proximity labeling, we demonstrate that NONO-APEX2-HA is a stably expressed fusion protein that mimics endogenous NONO in terms of expression, localisation and bona fide interactors. We propose that in vivo proximity labeling in U2OS:NONO-APEX2-HA cells is capable for the assessment of NONO interactomes by downstream assays. U2OS:NONO-APEX2-HA cells will likely be a valuable resource for the investigation of NONO interactome dynamics in response to DNA damage and other stimuli.
Mechanisms of apoptosis modulation and their contribution to genomic instability in tumor cells
(2004)
The concept of programmed cell death has been increasingly considered from various aspects since early 1970’s. Primarily, knowledge of apoptosis referred to morphological changes in which chromatin is condensed and increasingly fragmented, revealed as small structure in the nucleus. The membrane shrinks and the cell becomes dense as can be seen by flow cytometry. Interestingly, similar modes of cell deletion were observed in nematodes indicating that apoptosis is a highly conserved machinery. Three Caeonorhabditis elegans gene products are found to have high homology with mammalian apoptotic genes: CED-9 inhibits apoptosis and is related to bcl-2; CED-3 and CED-4 promote apoptosis and are related to caspase 9 and APAF-1. Apoptosis is not accidental death, but a highly controlled and medically important molecular process. More general terms such as ‘physiological’ or ‘regulated’ cell death cover different morphologies and sequences. Programmed suicide of cells that were subjected to toxic exogenous and endogenous stimuli plays a key role in understanding cancer development and its treatment. Apoptosis involves sequences of events that may overlap and play contradictory or antagonistic roles in cell death. Generally, the ability to trigger apoptotic processes in cancer cells would benefit an organism by keeping homeostasis intact. Programmed cell death is a regularly present mechanism, for instance, in lymphocyte recruitment in the thymus where immature lymphocytes may recognize host antigens. Therefore, such lymphocytes become apoptotic and are removed by macrophages. Removal prevents possible autoimmune diseases. Unlike apoptosis, necrosis is a passive process of cell death recognizable by membrane morphological changes and accompanied by leakage of intracellular material into intercellular space that may cause inflammation in the organism. Signals that may initiate apoptosis are generally classified into two groups: signals that launch extrinsic apoptotic pathways starting with aggregation of death receptors and intrinsic apoptotic pathways starting with disruption of intracellular homeostasis such as the release of mitochondrial factors or DNA degradation. Early in the process, apoptotic signals may lead to a broad range of signaling mechanisms such as DNA repair and assessment of DNA damage (check points). Thus, failure in any of these steps can cause a defective apoptotic response that plays a decisive role in both tumorigenesis and drug resistance in tumor treatment. More distinctly, the capability of cancer cells to go into apoptosis prevents further neoplastic changes. Generally, the purpose of this study is to investigate the balance between formation of genomic damage and induction of apoptosis under genotoxic stress. After genotoxic insult there are different possibilities for the fate of a cell (Figure 1). The genomic integrity is analyzed at cellular checkpoints, usually leading to a delay in cell cycle progression if DNA was damaged. Mutations in genes such as p53 and p21 change the cellular response to genotoxic stress and may alter the balance between apoptosis and genomic damage. However, p53 is usually mutated or not expressed in 70% of human tumors. Alterations in p53 states that reflect distinct apoptotic response upon induction of DNA damage were examined. In this study, three cell lines with distinct p53 states were used: TK6 harboring wild-type p53, WTK1 with mutated p53 and NH32 with knocked out p53. In the present work we applied different approaches to investigate the correlation between DNA damage and apoptotic responsiveness in cancer cell lines with different p53 states or in hormone responsive cell lines with over expressed bcl-2 gene. We were focused on effects caused by temporary down regulation of the p53 and Bcl-2 activity in human lymphoblastoid cell lines. In addition, we investigated the impact of estradiol-induced proliferation on apoptosis and DNA damage in stably transfected cells with bcl-2gene.
Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2'-deoxyguanosine (8-oxodG), 5-hydroxy-2'-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.
DNA damage occurs frequently during normal cellular progresses or by environmental factors. To preserve the genome integrity, DNA damage response (DDR) has evolved to repair DNA and the non-properly repaired DNA induces human diseases like immune deficiency and cancer. Since a large number of proteins involved in DDR are enzymes of ubiquitin system, it is critical to investigate how the ubiquitin system regulates cellular response to DNA damage. Hereby, we reveal a novel mechanism for DDR regulation via activation of SCF ubiquitin ligase upon DNA damage.
As an essential step for DNA damage-induced inhibition of DNA replication, Cdc25A degradation by the E3 ligase β-TrCP upon DNA damage requires the deubiquitinase Usp28. Usp28 deubiquitinates β-TrCP in response to DNA damage, thereby promotes its dimerization, which is required for its activity in substrate ubiquitination and degradation. Particularly, ubiquitination at a specific lysine on β-TrCP suppresses dimerization.
The key mediator protein of DDR, 53BP1, forms oligomers and associates with β-TrCP to inhibit its activity in unstressed cells. Upon DNA damage, 53BP1 is degraded in the nucleoplasm, which requires oligomerization and is promoted by Usp28 in a β-TrCP-dependent manner. Consequently, 53BP1 destruction releases and activates β-TrCP during DNA damage response.
Moreover, 53BP1 deletion and DNA damage promote β-TrCP dimerization and recruitment to chromatin sites that locate in the vicinity of putative replication origins. Subsequently, the chromatin-associated Cdc25A is degraded by β-TrCP at the origins. The stimulation of β-TrCP binding to the origins upon DNA damage is accompanied by unloading of Cdc45, a crucial component of pre-initiation complexes for replication. Loading of Cdc45 to origins is a key Cdk2-dependent step for DNA replication initiation, indicating that localized Cdc25A degradation by β-TrCP at origins inactivates Cdk2, thereby inhibits the initiation of DNA replication.
Collectively, this study suggests a novel mechanism for the regulation of DNA replication upon DNA damage, which involves 53BP1- and Usp28-dependent activation of the SCF(β-TrCP) ligase in Cdc25A degradation.