Metabolic DNA and the problem of ageing

The diverse origins of circulating cell-free DNA in the human body: a critical re-evaluation of the literature

Since the detection of cell-free DNA (cfDNA) in human plasma in 1948, it has been investigated as a non-invasive screening tool for many diseases, especially solid tumours and foetal genetic abnormalities. However, to date our lack of knowledge regarding the origin and purpose of cfDNA in a physiological environment has limited its use to more obvious diagnostics, neglecting, for example, its potential utility in the identification of predisposition to disease, earlier detection of cancers, and lifestyle-induced epigenetic changes. Moreover, the concept or mechanism of cfDNA could also have potential therapeutic uses such as in immuno- or gene therapy. This review presents an extensive compilation of the putative origins of cfDNA and then contrasts the contributions of cellular breakdown processes with active mechanisms for the release of cfDNA into the extracellular environment. The involvement of cfDNA derived from both cellular breakdown and active release in lateral information transfer is also discussed. We hope to encourage researchers to adopt a more holistic view of cfDNA research, taking into account all the biological pathways in which cfDNA is involved, and to give serious consideration to the integration of in vitro and in vivo research. We also wish to encourage researchers not to limit their focus to the apoptotic or necrotic fraction of cfDNA, but to investigate the intercellular messaging capabilities of the actively released fraction of cfDNA and to study the role of cfDNA in pathogenesis.

A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles

The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.

Age changes of chromatin. A review

The age-related studies of chromatin and DNA has attracted significant interest in recent years. However, individual works describe only some and a few of the many changes of chromatin. It is often difficult to decide whether these changes have secondary or primary nature. The overview of these studies makes it possible to realize how many very complex and interdependent changes occur in chromatin during ageing. Chromatin is the most complex among self-reproducible parts of the cell. A very sophisticated structure of chromatin makes possible the differential transcription of a genetic programme which supports the accurate specialized functions of each cell in interphase and also provides a mechanism for perfect reproduction of this complex machinery of genetic information during cell division. It is known that chromatin proteins, more than chromatin DNA show tissue specificity and developmental changes. There are many theories of cellular ageing which select some special types of DNA, RNA or protein changes and to promote them as the main or primary causes of cellular senescence. However, if these changes are considered within the more comprehensive picture of functional structure of chromatin the results show the interdependence of individual alterations and their proper place in the complex, multichannel, species and tissue-specific character of actual ageing. An attempt to summarize the basic facts and theories about age changes of the two main parts of chromatin structure, proteins and DNA is being made in this review. At the same time the author tried to develop a concept of non-random distribution of the age changes in chromatin and a possible higher rate of accumulation of different alteration and lesions in the transcribed and functionally active parts of chromatin.

Decrease of learning capacity in offspring with increasing paternal age in the rat

The same 15 male Wistar rats at the ages of 2.5, 6, 10, 14, 18, and 22 months were successively randomly mated with 2.5-month-old females. In a separate experiment, 15 male Wistar rats at the age of 2.5 months and 15 at the age of 23 months were simultaneously randomly mated with 2.5-month-old females. Offspring were evaluated in regard to the mean number per litter, sex ratio, frequency of gross external malformations, growth pattern, and mortality in the first 13 weeks of life and reproductive capacity at 13 weeks of age. They were also evaluated for spontaneous activity and emotionality with an open field test and for learning capacity with an avoidance conditioning test, both carried out between 10 and 13 weeks of age. Only learning capacity of the offspring, expressed in percentage of success for male or female, decreased consistently and significantly as the father's age increased. But females did not seem to be affected in the same way as males. The genetic implications are briefly discussed.

Age dependency of DNA repair in rats after DNA damage by carcinogens

Damage to DNA seems to be an important cause of cancer and to play a role in aging. Much of this damage results from the action of chemical agents in the environment. These chemicals provide a chance to study DNA repair mechanisms and to construct a model for the investigation of changes in repair with aging. To damage the DNA of male Sprague-Dawley rats aged 6, 22-24 and 24-26 months, three carcinogens were used: N-methyl-N-nitrosourea (MNU), methyl methane sulfonate (MMS) and N,N-dimethyl-nitrosamine (DMN). DNA repair was measured as unscheduled DNA synthesis (UDS) in ten (MNU and DMN) and five (MMS) different organs. MNU and MMS react with DNA without being first metabolized and show a higher UDS in lower concentration than DMN which is metabolized enzymatically prior to the reaction. This result suggests that MNU and MMS produce more damage in the DNA. There are distinct differences in the spleen, lung, liver, kidney and heart in young animals as well as in the tissues of the kidney and the duodenum in old rats. Clearly we can see a reduction of UDS in the old as compared to the young animals after damage by MNU in the skin, lung, brain and heart, by MMS in the heart and liver, and by DMN in the kidney, duodenum, lung and liver, and by all three mutagens in the spleen and testes. These results confirm those obtained after damaging DNA by means of gamma- and UV-irradiation.

DNA synthesis in circulating erythroblasts of anemic duck. Isolation and properties of nuclear and cytoplasmic-nonmitochondrial DNA

In the circulating blood of anemic ducks, 5% of all erythroid cells synthesize DNA. Immature erythroblasts, at all stages of differentiation, synthesize DNA although to a varying degree, while reticulocytes and erythrocytes do not. In the erythroid cell population labeled in vitro 2 h with 32Pi, half of the labeled DNA sediments as small-molecular-weight molecules, suggesting that these molecules fail to integrate into the high-molecular-weight components. Labeled DNA is found in the cytoplasmic postmitochondrial fractions and it is in a form of deoxyribonucleoproteins which cosediment with ribosomes as well as subribosomal particles in sucrose gradients. However, fixation with HCHO and centrifugation to equilibrium in CsCl gradient of these particles shows that the deoxyribonucleoprotein bands at the density different than the ribosomes and, thus, not physically linked to them. In EDTA-dissociated ribosomes, the deoxyribonucleoprotein particles cosediment with ribosomes as well as subribosomal particles in sucorse gradients. However, fixation with HCHO and centrifugation to equilibrium in CsCl gradient of these particles shows that the deoxyribonucleoprotein bands at the density different than the ribosomes and, thus, not physically linked to them. In EDTA-dissociated ribosomes, the deoxyribonucleoprotein particles cosdeiment with ribosomal subunits in such a way that the larger the particle, the larger the molecular weight of the DNA cosedimenting with it. The specific radioactivity of the cytoplasmic ribosome-derived and postribosomal-particle-derived DNAs and the small molecular-weight nuclear DNA is similar and 10-20-fold higher than that of the bulk nuclear DNA. The former three DNA species sediment between 4-14 S. It is concluded that the cytoplasmic nonmitochondrial DNA species are of the nuclear origin. Less than 0.5% of the total cellular nonmitochondrial DNA can be purified from the nucleus and the cytoplasm as fast-labeled small-molecular-weight components. All of the cellular nonmitochondrial DNA species band at the same mean buoyand density in Cs2SO4/urea gradients. All behave as native structures in hydroxyapatite and contain less than 5% of their length as single-stranded regions.