Apoptotic DNA fragmentation

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Apoptotic DNA fragmentation, visualised by the DNA laddering assay (left). A 1 kb marker (middle) and control DNA (right) are included for comparison. Apoptotic DNA Laddering.png
Apoptotic DNA fragmentation, visualised by the DNA laddering assay (left). A 1 kb marker (middle) and control DNA (right) are included for comparison.

Apoptotic DNA fragmentation is a key feature of apoptosis, a type of programmed cell death. Apoptosis is characterized by the activation of endogenous endonucleases, particularly the caspase-3 activated DNase (CAD), [1] with subsequent cleavage of nuclear DNA into internucleosomal fragments of roughly 180 base pairs  (bp) and multiples thereof (360, 540 etc.). The apoptotic DNA fragmentation is being used as a marker of apoptosis and for identification of apoptotic cells either via the DNA laddering assay, [2] the TUNEL assay, [3] [4] or the by detection of cells with fractional DNA content ("sub G1 cells") on DNA content frequency histograms e.g. as in the Nicoletti assay. [5] [6]

Contents

Mechanism

The enzyme responsible for apoptotic DNA fragmentation is the Caspase-Activated DNase (CAD). CAD is normally inhibited by another protein, the Inhibitor of Caspase Activated DNase (ICAD). During apoptosis, the apoptotic effector caspase, caspase-3, cleaves ICAD and thus causes CAD to become activated. [7]

A nucleosome, consisting of DNA (grey) wrapped around a histone tetramer (coloured). In apoptotic DNA fragmentation, the DNA is cleaved in the internucleosomal linker region, which is the part of the DNA not wrapped around the histones. Complete Histone with DNA.png
A nucleosome, consisting of DNA (grey) wrapped around a histone tetramer (coloured). In apoptotic DNA fragmentation, the DNA is cleaved in the internucleosomal linker region, which is the part of the DNA not wrapped around the histones.

CAD cleaves DNA at internucleosomal linker sites between nucleosomes, protein-containing structures that occur in chromatin at ~180-bp intervals. This is because the DNA is normally tightly wrapped around histones, the core proteins of the nucleosomes. The linker sites are the only parts of the DNA strand that are exposed and thus accessible to CAD.

Degradation of nuclear DNA into nucleosomal units is one of the hallmarks of apoptotic cell death. It occurs in response to various apoptotic stimuli in a wide variety of cell types. Molecular characterization of this process identified a specific DNase (CAD, caspase-activated DNase) that cleaves chromosomal DNA in a caspase-dependent manner. CAD is synthesized with the help of ICAD (inhibitor of CAD), which works as a specific chaperone for CAD and is found complexed with ICAD in proliferating cells. When cells are induced to undergo apoptosis, caspase 3 cleaves ICAD to dissociate the CAD:ICAD complex, allowing CAD to cleave chromosomal DNA. Cells that lack ICAD or that express caspase-resistant mutant ICAD thus do not show DNA fragmentation during apoptosis, although they do exhibit some other features of apoptosis and die.

Even though much work has been performed on the analysis of apoptotic events, little information is available to link the timing of morphological features at the cell surface and in the nucleus to the biochemical degradation of DNA in the same cells. Apoptosis can be initiated by a myriad of different mechanisms in different cell types, and the kinetics of these events vary widely, from only a few minutes to several days depending on the cell system. The presence or absence of particular apoptotic event(s), including DNA fragmentation, depends on the "time window" at which the kinetic process of apoptosis is being investigated. Often this may complicate identification of apoptotic cells if cell populations are analyzed only at a single time point e.g. after induction of apoptosis.

Historical background

The discovery of the internucleosomal fragmentation of genomic DNA to regular repeating oligonucleosomal fragments generated by Ca/Mg-dependent endonuclease is accepted as one of the best-characterized biochemical markers of apoptosis (programmed cell death).

In 1970, Williamson described that cytoplasmic DNA isolated from mouse liver cells after culture was characterized by DNA fragments with a molecular weight consisting of multiples of 135 kDa. This finding was consistent with the hypothesis that these DNA fragments were a specific degradation product of nuclear DNA. [8] In 1972, Kerr, Wyllie , and Currie coined the term apoptosis and distinguished this type of cell death from necrosis based on morphological features. [9] In 1973, Hewish and Burgoyne , during the study of subchromatin structure, found that chromatin is accessible to the Ca++/Mg++ endonuclease, resulting in the formation of a digestion product with a regular series of molecular weight similar to the one previously described by Williamson (1970). [10] In 1974, Williams, Little, and Shipley, using cells exposed to widely differing types of trauma, found that during cell death, degraded DNA in "every case had a modal value of between 10(x6) and 10(x7) Dalton and cellular metabolism is required to produce degradation of DNA". However, this observation was without indication of "whether the incision attack on the DNA molecule was a random or rather at a particular site, that have structural or functional meaning". [11] In 1976, Scalka, Matyasova, and Cejkova described internucleosomal fragmentation of irradiated lymphoid chromatin DNA in vivo. [12]

Six years passed from 1972 to 1978/1980 until the discovery and evaluation of internucleosomal fragmentation of DNA during apoptotic cell death as a hallmark of apoptosis. Since 1972 (Kerr, Wyllie, and Currie [9] ), it is accepted that glucocorticoid-induced death of lymphocytes is a form of apoptosis. In 1978, Zakharyan and Pogosyan presented a paper revealing that glucocorticoid-induced DNA degradation in rat lymphoid tissue, thymus, and spleen occurred in a specific pattern producing fragments of DNA that were electrophoretically similar to those observed after treatment of chromatin with microccoccal nuclease, which indicated internucleosomal cleavage pattern of DNA degradation occurred during apoptosis. [13] [14] Thus, the first link between programmed cell death/apoptosis and internucleosomal fragmentation of chromatin DNA was discovered and soon became as a specific feature of apoptosis.

In 1980, Wyllie reported additional evidence for an internucleosomal DNA cleavage pattern as a specific feature of glucocorticoid-treated thymocytes undergoing apoptosis. [2] The internucleosomal DNA cleavage pattern was observed as a specific feature of apoptosis in 1978/1980 and has become a recognised hallmark of programmed cell death since then. In 1992 Gorczyca et al. [3] and Gavrieli et al.[4] independently described the DNA fragmentation assay based on the use of the terminal deoxynucleotidyl transferase (TUNEL) which become one of the standard methods to detect and identify apoptotic cells.

Detection assays

Flow cytometry is most frequently used to detect apoptotic DNA fragmentation. [15] Analysis of DNA content by flow cytometry can identify apoptotic cells with fragmented DNA as the cells with fractional DNA content, often called the sub-G1 cells. The flow-cytometric assay utilizing the fluorochrome acridine orange shows that DNA fragmentation within individual cells is discontinuous likely reflecting different levels of restriction in accessibility of DNA to DNase, by the supranucleosomal and nucleosomal levels of chromatin structure. [16] The presence of apoptotic "sub-G1cells" can also be detected in cells pre-fixed in ethanol but not after fixation in the crosslinking fixatives such as formaldehyde. The late-S and G2 apoptotic cells may not be detected with this approach because their fractional DNA content may overlap with that of the non-apoptotic G1 cells. [17] Treatment of cells with detergent, prior or concurrently with DNA fluorochrome, also reveals DNA fragmentation by virtue of the presence of the sub-G1 cells or cell fragments, as defined by Nicoletti et al.[5]

Apoptotic DNA fragmentation can also be detected by the TUNEL assay. The fluorochrome-based TUNEL assay applicable for flow cytometry, correlates the detection of DNA strand breaks with the cellular DNA content and thus with cell cycle-phase position. The avidin-peroxidase labeling TUNEL assay is applicable for light absorption microscopy. Many TUNEL-related kits are commercially available. Apoptotic DNA fragmentation is also analyzed using agarose gel electrophoresis to demonstrate a "ladder" pattern at ~180-BP intervals.[1] Necrosis, on the other hand, is usually characterized by random DNA fragmentation which forms a "smear" on agarose gels.

See also

Related Research Articles

<span class="mw-page-title-main">Apoptosis</span> Type of programmed cell death in multicellular organisms

Apoptosis is a form of programmed cell death that occurs in multicellular organisms and in some eukaryotic, single-celled microorganisms such as yeast. Biochemical events lead to characteristic cell changes (morphology) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, DNA fragmentation, and mRNA decay. The average adult human loses 50 to 70 billion cells each day due to apoptosis. For the average human child between 8 and 14 years old, each day the approximate loss is 20 to 30 billion cells.

Programmed cell death is the death of a cell as a result of events inside of a cell, such as apoptosis or autophagy. PCD is carried out in a biological process, which usually confers advantage during an organism's lifecycle. For example, the differentiation of fingers and toes in a developing human embryo occurs because cells between the fingers apoptose; the result is that the digits are separate. PCD serves fundamental functions during both plant and animal tissue development.

Deoxyribonuclease refers to a group of glycoprotein endonucleases which are enzymes that catalyze the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, thus degrading DNA. The role of the DNase enzyme in cells includes breaking down extracellular DNA (ecDNA) excreted by apoptosis, necrosis, and neutrophil extracellular traps (NET) of cells to help reduce inflammatory responses that otherwise are elicited. A wide variety of deoxyribonucleases are known and fall into one of two families, which differ in their substrate specificities, chemical mechanisms, and biological functions. Laboratory applications of DNase include purifying proteins when extracted from prokaryotic organisms. Additionally, DNase has been applied as a treatment for diseases that are caused by ecDNA in the blood plasma. Assays of DNase are emerging in the research field as well.

<span class="mw-page-title-main">Karyorrhexis</span> Destructive fragmentation of the nucleus of a dying cell

Karyorrhexis is the destructive fragmentation of the nucleus of a dying cell whereby its chromatin is distributed irregularly throughout the cytoplasm. It is usually preceded by pyknosis and can occur as a result of either programmed cell death (apoptosis), cellular senescence, or necrosis.

<span class="mw-page-title-main">Cell death</span> Biological cell ceasing to carry out its functions

Cell death is the event of a biological cell ceasing to carry out its functions. This may be the result of the natural process of old cells dying and being replaced by new ones, as in programmed cell death, or may result from factors such as diseases, localized injury, or the death of the organism of which the cells are part. Apoptosis or Type I cell-death, and autophagy or Type II cell-death are both forms of programmed cell death, while necrosis is a non-physiological process that occurs as a result of infection or injury.

DNA fragmentation is the separation or breaking of DNA strands into pieces. It can be done intentionally by laboratory personnel or by cells, or can occur spontaneously. Spontaneous or accidental DNA fragmentation is fragmentation that gradually accumulates in a cell. It can be measured by e.g. the Comet assay or by the TUNEL assay.

<span class="mw-page-title-main">TUNEL assay</span> Molecular biology method used to detect DNA fragmentation

Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) is a method for detecting DNA fragmentation by labeling the 3′- hydroxyl termini in the double-strand DNA breaks generated during apoptosis.

<span class="mw-page-title-main">DNA laddering</span>

DNA laddering is a feature that can be observed when DNA fragments, resulting from Apoptosis DNA fragmentation are visualized after separation by gel electrophoresis the first described in 1980 by Andrew Wyllie at the University Edinburgh medical school DNA fragments can also be detected in cells that underwent necrosis, but when these DNA fragments after separation are subjected to gel electrophoresis no clear "ladder" pattern is apparent.

<span class="mw-page-title-main">Deoxyribonuclease I</span> Protein-coding gene in the species Homo sapiens

Deoxyribonuclease I, is an endonuclease of the DNase family coded by the human gene DNASE1. DNase I is a nuclease that cleaves DNA preferentially at phosphodiester linkages adjacent to a pyrimidine nucleotide, yielding 5'-phosphate-terminated polynucleotides with a free hydroxyl group on position 3', on average producing tetranucleotides. It acts on single-stranded DNA, double-stranded DNA, and chromatin. In addition to its role as a waste-management endonuclease, it has been suggested to be one of the deoxyribonucleases responsible for DNA fragmentation during apoptosis.

<span class="mw-page-title-main">Apoptosis-inducing factor</span> Protein family

Apoptosis inducing factor is involved in initiating a caspase-independent pathway of apoptosis by causing DNA fragmentation and chromatin condensation. Apoptosis inducing factor is a flavoprotein. It also acts as an NADH oxidase. Another AIF function is to regulate the permeability of the mitochondrial membrane upon apoptosis. Normally it is found behind the outer membrane of the mitochondrion and is therefore secluded from the nucleus. However, when the mitochondrion is damaged, it moves to the cytosol and to the nucleus. Inactivation of AIF leads to resistance of embryonic stem cells to death following the withdrawal of growth factors indicating that it is involved in apoptosis.

Fragmentation describes the process of splitting into several pieces or fragments. In cell biology, fragmentation is useful for a cell during both DNA cloning and apoptosis. DNA cloning is important in asexual reproduction or creation of identical DNA molecules, and can be performed spontaneously by the cell or intentionally by laboratory researchers. Apoptosis is the programmed destruction of cells, and the DNA molecules within them, and is a highly regulated process. These two ways in which fragmentation is used in cellular processes describe normal cellular functions and common laboratory procedures performed with cells. However, problems within a cell can sometimes cause fragmentation that results in irregularities such as red blood cell fragmentation and sperm cell DNA fragmentation.

<span class="mw-page-title-main">Caspase 3</span> Protein found in humans

Caspase-3 is a caspase protein that interacts with caspase-8 and caspase-9. It is encoded by the CASP3 gene. CASP3 orthologs have been identified in numerous mammals for which complete genome data are available. Unique orthologs are also present in birds, lizards, lissamphibians, and teleosts.

<span class="mw-page-title-main">DFFA</span> Protein-coding gene in the species Homo sapiens

DNA fragmentation factor subunit alpha (DFFA), also known as Inhibitor of caspase-activated DNase (ICAD), is a protein that in humans is encoded by the DFFA gene.

<span class="mw-page-title-main">ENDOG</span> Protein-coding gene in the species Homo sapiens

Endonuclease G, mitochondrial is an enzyme that in humans is encoded by the ENDOG gene. This protein primarily participates in caspase-independent apoptosis via DNA degradation when translocating from the mitochondrion to nucleus under oxidative stress. As a result, EndoG has been implicated in cancer, aging, and neurodegenerative diseases such as Parkinson's disease (PD). Regulation of its expression levels thus holds potential to treat or ameliorate those conditions.

<span class="mw-page-title-main">Caspase-activated DNase</span> Protein found in humans

Caspase-activated DNase (CAD) or DNA fragmentation factor subunit beta is a protein that in humans is encoded by the DFFB gene. It breaks up the DNA during apoptosis and promotes cell differentiation. It is usually an inactive monomer inhibited by ICAD. This is cleaved before dimerization.

Cell cycle analysis by DNA content measurement is a method that most frequently employs flow cytometry to distinguish cells in different phases of the cell cycle. Before analysis, the cells are usually permeabilised and treated with a fluorescent dye that stains DNA quantitatively, such as propidium iodide (PI) or 4,6-diamidino-2-phenylindole (DAPI). The fluorescence intensity of the stained cells correlates with the amount of DNA they contain. As the DNA content doubles during the S phase, the DNA content (and thereby intensity of fluorescence) of cells in the G0 phase and G1 phase (before S), in the S phase, and in the G2 phase and M phase (after S) identifies the cell cycle phase position in the major phases (G0/G1 versus S versus G2/M phase) of the cell cycle. The cellular DNA content of individual cells is often plotted as their frequency histogram to provide information about relative frequency (percentage) of cells in the major phases of the cell cycle.

Ischemic cell death, or oncosis, is a form of accidental cell death. The process is characterized by an ATP depletion within the cell leading to impairment of ionic pumps, cell swelling, clearing of the cytosol, dilation of the endoplasmic reticulum and golgi apparatus, mitochondrial condensation, chromatin clumping, and cytoplasmic bleb formation. Oncosis refers to a series of cellular reactions following injury that precedes cell death. The process of oncosis is divided into three stages. First, the cell becomes committed to oncosis as a result of damage incurred to the plasma membrane through toxicity or ischemia, resulting in the leak of ions and water due to ATP depletion. The ionic imbalance that occurs subsequently causes the cell to swell without a concurrent change in membrane permeability to reverse the swelling. In stage two, the reversibility threshold for the cell is passed and the cell becomes committed to cell death. During this stage the membrane becomes abnormally permeable to trypan blue and propidium iodide, indicating membrane compromise. The final stage is cell death and removal of the cell via phagocytosis mediated by an inflammatory response.

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<span class="mw-page-title-main">Zbyszek Darzynkiewicz</span> Polish-American cell biologist (1936–2021)

ZbigniewDarzynkiewicz was a Polish-American cell biologist active in cancer research and in developing new methods in histochemistry for flow cytometry.

<span class="mw-page-title-main">Sperm Chromatin Structure Assay</span>

Sperm Chromatin Structure Assay (SCSA) is a diagnostic approach that detects sperm abnormality with a large extent of DNA fragmentation. First described by Evenson in 1980, the assay is a flow cytometric test that detects the vulnerability of sperm DNA to acid-induced denaturation DNA in situ. SCSA measures sperm DNA fragmentation attributed to intrinsic and extrinsic factors and reports the degree of fragmentation in terms of DNA Fragmentation Index (DFI). The use of SCSA expands from evaluation of male infertility and subfertility, toxicology studies and evaluation of quality of laboratory semen samples. Notably, SCSA outcompetes other convention sperm DNA fragmentation (sDF) assays such as TUNEL and COMET in terms of efficiency, objectivity, and repeatability.

References

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  9. 1 2 Kerr, John F. R.; Wyllie, Andrew; Currie, Alastair (August 1972). "Apoptosis: A Basic Biological Phenomenon with Wide-ranging Implications in Tissue Kinetics". British Journal of Cancer . 26 (4): 239–257. doi:10.1038/bjc.1972.33. ISSN   0007-0920. PMC   2008650 . PMID   4561027.
  10. ↑ Hewish, Dean R.; Burgoyne, Leigh A. (1973-05-15). "Chromatin sub-structure. The digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease". Biochemical and Biophysical Research Communications . 52 (2): 504–510. doi:10.1016/0006-291X(73)90740-7. ISSN   0006-291X. PMID   4711166.
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  15. ↑ Gavanji S, Bakhtari A, Famurewa AC, Othman EM (January 2023). "Cytotoxic Activity of Herbal Medicines as Assessed in Vitro: A Review". Chemistry & Biodiversity. 20 (2): 3–27. doi: 10.1002/cbdv.202201098 . PMID   36595710. S2CID   255473013.
  16. ↑ Kajstura, M; Halicka, HD; Pryjma, J; Darzynkiewicz, Z (2007). "Discontinuous fragmentation of nuclear DNA during apoptosis revealed by discrete "sub-G1" peaks on DNA content histograms". Cytometry A. 71 (3): 125–31. doi: 10.1002/cyto.a.20357 . PMID   17252584.
  17. ↑ Wlodkowic, D; Telford, W; Skommer, J; Darzynkiewicz, Z (2011). "Apoptosis and Beyond: Cytometry in Studies of Programmed Cell Death". Recent Advances in Cytometry, Part B - Advances in Applications. Methods in Cell Biology. Vol. 103. Elsevier. pp. 55–98. doi:10.1016/B978-0-12-385493-3.00004-8. ISBN   9780123854933. PMC   3263828 . PMID   21722800.{{cite book}}: |journal= ignored (help)

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