Individual capacity for repair of DNA damage and potential uses of stem cell lines for clinical applications:a matter of (genomic) integrity

Public and private human stem cell banking institutions are currently hosting hundreds of thousands partially characterized cell populations, including a significant number of human pluripotentstem cell lines. To be considered for use in clinical applications, stem cell preparations must undergo rigorous testing in order to ensure safety for the recipient. With development of the methodologies for in vitro derivation, ex vivo maintenance and expansion of stem cells and targeted differentiation of multipotent and pluripotent stem cells, many novel issues were added to the list of safety concerns of cell and tissue preparations. These issues are related to the potential changes that may occur in the course of in vitro propagation of stem cells and cell-derived products, how these changes may affect the quality of the preparation; and the potential effects on the recipient. Only a limited number of studies about the role of subtle variations of individual capacity for repair of genotoxic damage in maintenance in vitro of human stem cells are currently available. Nevertheless, the assessment of individual repair capacity may play a crucial role in the safety of use of human stem cells, as it constitutes a major factor in the risk of occurrence of genomic alterations that may seriously compromise the quality of the product. This article reviews the available data about the role of individual capacity for DNA damage repair in different human stem cell types and the potential adverse effects that may occur with the use of cell preparations with inferior repair capacity

Targeting ATM pathway for therapeutic intervention in cancer

The Ataxia Telangiectasia Mutated gene encodes the ATM protein, a key element in the DNA damage response (DDR) signalling pathway responsible for maintaining genomic integrity within the cell. The ATM protein belongs to a family of large protein kinases containing the phosphatidylinositol-3 catalytic domain, including ATM, ATR and PI3K. ATM provides the crucial link between DNA damage, cell cycle progression and cell death by first sensing double stranded DNA breaks and subsequently phosphorylating and activating other downstream proteins functioning in DNA damage repair, cell cycle arrest and apoptotic pathways,. Mammalian cells are constantly challenged by genotoxic agents from a variety of sources and therefore require a robust sensing and repair mechanism to maintain DNA integrity or activate alternative cell fate pathways. This review covers the role of ATM in DDR signalling and describes the interaction of the ATM kinase with other proteins in order to fulfil its various functions. Special emphasis is given to how the growing knowledge of the DDR can help identify drug targets for cancer therapy, thus providing a rationale for exploiting the ATM pathway in anticancer drug development. Moreover, we discuss how a network modelling approach can be used to identify and characterise ATM inhibitors and predict their therapeutic potential

MMP2 -1306C>T polymorphism in patients with COPD

The remodeling of the bronchial walls is an important process of the pathophysiology of COPD as the matrix metalloproteinase-2 (MMP-2) is shown to play an important role in this process. The aim of the current study was to elucidate the possible role of MMP2 -1306C>T promoter polymorphism as risk factor of COPD. We genotyped by PCR-RFLP 84 patients with COPD and 71 control individuals. The genotype, but not allele distribution, differed between COPD patients and controls (p=0.021 and 0.602, respectively). Carriers of the variant T allele (CT+TT) tended to have 1.64-fold higher risk for COPD (95% CI: 0.82-3.26, p=0.164) than those with CC genotype, as that risk was significant in the subset of older than 65 years individuals (OR=4.24, 95% CI:1.31-13.57, p=0.019). The risk for COPD of T carriers (CT+TT) was significant and even higher in the subset of older individuals (more than 65 years) and in those without diabetes as a co-morbidity. Patients with T genotypes had later onset of the disease (64.1±7.1 years) than those with CC genotype (59.7±9.5 years, p=0.045). In conclusion, our results suggest that the T genotypes of MMP2 -1306C>T SNP may determine a risk for COPD especially in advanced age

Unravelling the sex-specific diversity and functions of adrenal gland macrophages

Despite the ubiquitous function of macrophages across the body, the diversity, origin, and function of adrenal gland macrophages remain largely unknown. We define the heterogeneity of adrenal gland immune cells using single-cell RNA sequencing and use genetic models to explore the developmental mechanisms yielding macrophage diversity. We define populations of monocyte-derived and embryonically seeded adrenal gland macrophages and identify a female-specific subset with low major histocompatibility complex (MHC) class II expression. In adulthood, monocyte recruitment dominates adrenal gland macrophage maintenance in female mice. Adrenal gland macrophage sub-tissular distribution follows a sex-dimorphic pattern, with MHC class IIlow macrophages located at the cortico-medullary junction. Macrophage sex dimorphism depends on the presence of the cortical X-zone. Adrenal gland macrophage depletion results in altered tissue homeostasis, modulated lipid metabolism, and decreased local aldosterone production during stress exposure. Overall, these data reveal the heterogeneity of adrenal gland macrophages and point toward sex-restricted distribution and functions of these cells.</p

The final checkpoint. Cancer as an adaptive evolutionary mechanism

The mechanisms for identification of DNA damage and repair usually manage DNA damage very efficiently. If damaged cells manage to bypass the checkpoints where the integrity of the genome is assessed and the decisions whether to proceed with the cell cycle are made, they may evade the imperative to stop dividing and to die. As a result, cancer may develop. Warding off the potential sequence-altering effects of DNA damage during the life of the individual or the existence span of the species is controlled by a set of larger checkpoints acting on a progressively increasing scale, from systematic removal of damaged cells from the proliferative pool by means of repair of DNA damage/programmed cell death through ageing to, finally, cancer. They serve different purposes and act at different levels of the life cycle, safeguarding the integrity of the genetic backup of the individual, the genetic diversity of the population, and, finally, the survival of the species and of life on Earth. In the light of the theory that cancer is the final checkpoint or the nature's manner to prevent complex organisms from living forever at the expense of genetic stagnation, the eventual failure of modern anti-cancer treatments is only to be expected. Nevertheless, the medicine of today and the near future has enough potential to slow down the progression to terminal cancer so that the life expectancy and the quality of life of cancer-affected individuals may be comparable to those of healthy aged individuals

Individual capacity for detoxification of genotoxic compounds and repair of DNA damage. Commonly used methods for assessment of capacity for DNA repair

The first part of this paper reviews the major achievements in the rapidly expanding field of research of individual capacity for repair of genotoxic damage. The issues of individual repair capacity are addressed from multiple sides, analyzing the impact of the heritable components of the capacity for detoxification of genotoxic compounds, on the one hand (determining the risk for occurrence of DNA damage) and of the capacity for repair of DNA damage (when it has already occurred), on the other hand. The role of the capacity for repair of damage to DNA is discussed in the constitution of the risk for development of disease (mainly cancer, but also other common diseases and conditions, such as diabetes, atherosclerosis and cardiovascular disease) and as a major factor in the outcomes of genotoxic therapies (eligibility for therapy with specific agents, risk for severe adverse effects, post-therapeutic survival rates, etc.). The paper contains an extensive list of biomarkers (mainly DNA polymorphisms, but also enzymes and other phenotypic markers, such as markers of the capacity for self-renewal of cell populations) that may be potentially applicable in the assessment of the risk for carcinogenesis or for development other types of human disease.The second part of the paper provides a brief glimpse of the basic methodology used to obtain experimental results in assessment of the efficiency of DNA repair in living cells for research and diagnostic purposes

DNA repair systems

This paper provides detailed insight into the mechanisms of repair of different types of DNA damage and the direct molecular players (enzymes repairing the damage or tagging the damaged site for further processing; damage sensor molecules; other signalling and effector molecules). The genetic bases of diseases and conditions associated with defective DNA repair are comprehensively reviewed, from the ''classic'' severe diseases such as xeroderma pigmentosum and Cockayne syndrome to the much more subtle UV sensitivity syndromes. The review analyses the basic molecular mechanisms underlying the relatively rare monogenic diseases of DNA repair and management of genome integrity as well as the common multifactorial diseases and conditions with late onset that are associated with increased levels of oxidative stress (metabolic syndrome, diabetes type 2, cardiovascular disease) and with accumulation of ''errors'' in DNA (normal and pathological ageing phenotypes, various cancers). The role of cell cycle checkpoints in dividing cells and the mechanisms of decision-making for the fate of a damaged cell are discussed with regards to the cell homeostasis in normal and cancerous tissues. The role of major DNA damage-associated signalling and effector molecules (p53, ATM, poly-(ADP-ribose)-polymerase, DNA-dependent protein kinase, BRCA proteins, retinoblastoma protein, and others) is discussed and illustrated with examples in the context of health and disease. DNA repair and programmed cell death are viewed together as a unified mechanism for limiting the presence of damaged cells and cells with potentially oncogenic transformation in multicellular organisms. Special attention is paid to ageing as a natural phenomenon and an adaptive evolutionary mechanism, with a brief outline of ''successful ageing''. The differential rates of repair of DNA in transcribed and nontranscribed regions of the genome and the specificities of DNA repair profile in some types of cells (terminally differentiated cells, pluripotent stem cells, etc.) and in certain taxonomic groups (e.g. ''the rodent repairadox'') are discussed with regards to replicative ageing and the evolutionary processes on micro- and macroscale. The role of mutagenesis as a ''hit and miss'' mechanism and the ''leakiness'' of DNA repair for increasing genetic diversity in the course of individual life and on evolutionary scale and the phenomenology of ongoing molecular evolution are extensively reviewed

An old wives' tale. Reproductive outcomes in pregnant women aged 35 or older: the role of individual repair capacity

At present, childbirth is being progressively postponed until later age. Women aged 35 or older may have to wait longer to conceive than younger women and are more likely to be referred to fertility evaluations, but in a significant proportion a spontaneous conception would be achieved in the timeframe typical of younger women. Pregnancies where mothers are ≥ 35 are associated with more risks for pregnancy loss, chromosomal disease, pregnancy-associated complications, prematurity and low birthweight. These concerns, however, are not uncommon in younger women as well. This puts forward the question whether advanced age per se is the underlying cause for the increased risk for adverse outcomes in older pregnant women, or whether there might be other factors that account for it but do not radically worsen the prospects for favourable outcomes. The individual risks associated with childbirth late in life may stem from maternal genetic background rather than being a simple function of age. There is plenty of preliminary evidence that individual capacity for identification and repair of DNA damage may constitute a major factor in female fertility and fecundity. Subtle deficiencies in the repair capacity may have little to no importance in younger pregnant women but may make a significant difference in older women. The outcomes of pregnancies in women &amp;gt;35 are largely dependent on the pre-pregnancy health status and the quality of antenatal care, and may not be dramatically different from outcomes in younger women

The minus of a plus is a minus. Mass death of selected neuron populations in sporadic late-onset neurodegenerative disease may be due to a combination of subtly decreased capacity to repair oxidative DNA damage and increased propensity for damage-related apoptosis

Neurons in the adult central nervous system (CNS) are subjected to high levels of oxidative damage that is usually promptly repaired. Transcribed genomic regions are repaired with priority over untranscribed regions. The prioritization of DNA repair in neurons results in modification of the input into the assessment of genomic integrity in order to delay or avoid damage-related apoptosis unless the damage interferes directly with the functioning of the neuron. CNS neurons may be replaced, albeit rarely. Over-stimulation of adult neural progenitor niche caused by accelerated neuronal loss may result in its premature depletion. The combination of the two pathologic mechanisms (increased rates of neuronal death and depletion of the progenitor niche) may eventually result in irreversible loss of specific cell populations in the CNS and/or generalized neuronal loss. Here we propose that the risk of developing sporadic late-onset neurodegenerative disease (LONDD) may be modulated by the individual capacity for detection and repair of DNA damage and the genetic propensity to repair moderate-degree damage or to assess it as irreparable and route the cell towards apoptosis. Thus, subtly deficient DNA damage repair coupled with a tendency to repair the damage rather than kill the damaged cell may be associated with increased risk of cancer, whereas deficient DNA repair coupled with a propensity to destroy damaged cells may increase the risk of LONDD. Extensive studies of individual repair capacity may be needed to test this hypothesis and, potentially, use the results in the assessment of the risk of common late-onset disease