The effect of dexamethasone on the generation of plasma DNA from dead and dying cells

Moonlighting chromatin: when DNA escapes nuclear control

Extracellular chromatin, for example in the form of neutrophil extracellular traps (NETs), is an important element that propels the pathological progression of a plethora of diseases. DNA drives the interferon system, serves as autoantigen, and forms the extracellular scaffold for proteins of the innate immune system. An insufficient clearance of extruded chromatin after the release of DNA from the nucleus into the extracellular milieu can perform a secret task of moonlighting in immune-inflammatory and occlusive disorders. Here, we discuss (I) the cellular events involved in the extracellular release of chromatin and NET formation, (II) the devastating consequence of a dysregulated NET formation, and (III) the imbalance between NET formation and clearance. We include the role of NET formation in the occlusion of vessels and ducts, in lung disease, in autoimmune diseases, in chronic oral disorders, in cancer, in the formation of adhesions, and in traumatic spinal cord injury. To develop effective therapies, it is of utmost importance to target pathways that cause decondensation of chromatin during exaggerated NET formation and aggregation. Alternatively, therapies that support the clearance of extracellular chromatin are conceivable.

Prognostic value of the donor-derived cell-free DNA assay in acute renal rejection therapy: A prospective cohort study

Donor-derived cell-free DNA (dd-cfDNA) is a promising biomarker for monitoring allograft status. However, whether dd-cfDNA can reflect real-time anti-rejection treatment effects remains unclear. We prospectively recruited 28 patients with acute renal rejection, including 5 with ABMR, 12 with type IA or type IB rejection, and 11 with type IIA or IIB rejection. dd-cfDNA levels in peripheral blood were measured using human single nucleotide polymorphism (SNP) locus capture hybridization. The percentage of dd-cfDNA (dd-cfDNA%) declined significantly from 2.566 ± 0.549% to 0.773 ± 0.116% (P < .001) after anti-rejection therapy. The dd-cfDNA% decreased steadily over the course of 3 days with daily methylprednisolone injections, but no significant difference in the dd-cfDNA% was observed between the end of anti-rejection therapy and 2 weeks later. Changes in the dd-cfDNA% (∆dd-cfDNA%) demonstrated a positive correlation with estimated glomerular filtration rates at 1 month (ρ = 2.570, P = .022), 3 months (ρ = 3.210, P = .027), and 6 months (ρ = 2.860, P = .019) after therapy. Thus, the dd-cfDNA assay shows prognostic capabilities in therapy outcome and allograft recovery; however, its ability is inhibited by methylprednisolone regardless of the types of rejection. Additionally, a reassessment of frequency intervals for testing is required.

Postchemotherapy and tumor-selective targeting with the La-specific DAB4 monoclonal antibody relates to apoptotic cell clearance

Early identification of tumor responses to treatment is crucial for devising more effective and safer cancer treatments. No widely applicable, noninvasive method currently exists for specifically detecting tumor cell death after cytotoxic treatment and thus for predicting treatment outcomes.

METHODS

We have further characterized the targeting of the murine monoclonal antibody DAB4 specifically to dead tumor cells in vitro, in vivo, and in clinical samples. We found that sustained DAB4 binding to treated cells was closely associated with markers of intrinsic apoptosis and DNA double-strand break formation. In a competition binding assay, DAB4 bound EL4 murine thymic lymphoma cells in preference to the normal counterpart of murine thymocytes. Defective in vivo clearance of apoptotic cells augmented in vivo accumulation of DAB4 in tumors particularly after chemotherapy but was unchanged in normal tissues. Tumor targeting of DAB4 was selective for syngeneic murine tumors and for human tumor xenografts of prostate cancer (PC-3) and pancreatic cancer (Panc-1) before and more so after chemotherapy. Furthermore, DAB4 was shown to bind to dead primary acute lymphoblastic leukemic blasts cultured with cytotoxic drugs and dead epithelial cancer cells isolated from peripheral blood of small cell lung carcinoma patients given chemotherapy.

CONCLUSION

Collectively, these results further demonstrate the selectivity of DAB4 for chemotherapy-induced dead tumor cells. This postchemotherapy selectivity is related to a relative increase in the availability of DAB4-binding targets in tumor tissue rather than in normal tissues. The in vitro findings were translated in vivo to human xenograft models and to ex vivo analyses of clinical samples, providing further evidence of the potential of DAB4 as a marker of tumor cell death after DNA-damaging cytotoxic treatment that could be harnessed as a predictive marker of treatment responses.

The translocation of nuclear molecules during inflammation and cell death

SIGNIFICANCE

Inflammation is a complex biological process that represents the body's response to infection and/or injury. Endogenous molecules that induce inflammation are called death- or damage-associated molecular patterns (DAMPs). Among cellular constituents with DAMP activity, nuclear molecules can stimulate pattern recognition receptors, including toll-like receptors (TLRs). Current research is elucidating the translocation of nuclear molecules during cell death and identifying novel anti-inflammatory approaches to block their DAMP activity.

RECENT ADVANCES

High mobility group box protein 1 (HMGB1), a non-histone nuclear protein, can translocate from cells during immune cell activation and cell death. Depending on redox state, HMGB1 can interact with TLR4 although it can bind to molecules such as cytokines to trigger other receptors. DNA and histones, which are bound together in the nucleus, also have important immunological activity. For DNA, DAMP activity may vary depending upon the binding to molecules that affect cell entry and intracellular location. The role of nuclear molecules in disease has been established in animal models using antibodies as inhibitors.

CRITICAL ISSUES

Key issues about the DAMP activity of nuclear molecules relate to (i) the impact on function of biochemical modifications such as redox state and post-translational modification, and (ii) the composition and properties of complexes that nuclear molecules may form with other blood components to affect immunological activity.

FUTURE DIRECTIONS

With the recognition of the immunological activity of the products of dead cells, future studies will define the diversity and properties of nuclear molecules in the extracellular space and develop strategies to block their activity during inflammation.

The blood nucleome in the pathogenesis of SLE

Systemic lupus erythematosus (SLE) is prototypic autoimmune disease characterized by the production of autoantibodies to DNA among other nuclear molecules. These antibodies can form immune complexes that promote pathogenesis by stimulating cytokine production and depositing in the kidney to instigate nephritis. The antigens that form these complexes arise from the blood nucleome, a pool of circulating macromolecules comprised of DNA, RNA and nuclear proteins released from cells. Cell death is a major source of these molecules, releasing DNA in a process that can be modeled in mice by the administration of cells killed ex vivo. In the mouse model, the appearance of blood DNA requires macrophages and differs between males and females. This finding raises the possibility that augmented levels of extracellular DNA and other nuclear antigens can contribute to the increased frequency of SLE in females. Extracellular DNA can occur in both a soluble and particulate form, with microparticles generated in vitro displaying antigenically active DNA. Together, these findings suggest that cell death is an important event in lupus pathogenesis and can provide a supply of blood DNA essential for immune complex formation.

Cell-free DNA as a noninvasive acute rejection marker in renal transplantation

BACKGROUND

Acute rejection (AR) is a key conditioning factor for long-term graft function and survival in renal transplantation patients. The standard care with creatinine measurements and biopsy upon allograft dysfunction implies that AR is usually detected at advanced stages. Rapid noninvasive biomarkers of rejection are needed to improve the management of these patients. We assessed whether total cell-free DNA (tCF-DNA) and donor-derived cell-free DNA (ddCF-DNA) were useful markers for this purpose, both in plasma and in urine.

METHODS

Plasma and urine samples from 100 renal transplant recipients were obtained during the first 3 months after transplantation. tCF-DNA and ddCF-DNA were analyzed by quantitative PCR for the HBB (hemoglobin, beta) and the TSPY1 (testis specific protein, Y-linked 1) genes, respectively. We observed 19 episodes of AR, as well as other complications, such as acute tubular necrosis, nephrotoxicity, and infections.

RESULTS

Plasma tCF-DNA concentrations increased markedly during AR episodes, often before clinical diagnosis, and returned to reference values after antirejection treatment. A cutoff plasma tCF-DNA concentration of 12 000 genome equivalents/mL correctly classified AR and non-AR episodes in 86% of posttransplantation complications (diagnostic sensitivity, 89%; specificity, 85%). Although similar increases were observed during severe posttransplantation infections, use of the combination of plasma tCF-DNA and procalcitonin (PCT), a specific marker of sepsis, significantly improved the diagnostic specificity (to 98%; 95% CI, 92%-100%), with 97% of the episodes being correctly classified. Use of transrenal DNA and ddCF-DNA concentrations did not add relevant information.

CONCLUSIONS

Given that renal biopsy is the gold standard for detecting AR, analysis of both plasma tCF-DNA and PCT could permit a more selective use of this invasive procedure.

The origin of extracellular DNA during the clearance of dead and dying cells

DNA is a nuclear molecule that has both an intracellular and extracellular role. Inside the cell, it is the essential molecule of heredity while outside the cell it can have immunological activity, both alone and in the context of immune complexes. Furthermore, extracellular DNA has information content that can be mined by genomic techniques. Because of the association of extracellular DNA with clinical conditions marked by cell death, dead and dying cells have been considered the origin of this material. To investigate this process, in vitro and in vivo systems have been used to determine the release of DNA from cells, using Jurkat T cells as a model. Thus, in vitro, apoptotic Jurkat cells release DNA whereas necrotic cells do not. The presence of macrophages in these cultures, however, modifies the release process, causing release from necrotic cells as well. In in vivo experiments in which Jurkat cells are administered to normal mice, both apoptotic and necrotic cells give rise to DNA in the blood in a process that requires macrophages and can be modified by glucocorticoids. In this model, female and male mice differ in the extent of DNA release from the administered Jurkat cells. Together, these results indicate that, while apoptosis and necrosis can lead to a blood DNA response, this process requires macrophages and may be hormonally mediated.

The Generation of Extracellular DNA in SLE: the Role of Death and Sex

DNA is a large macromolecule that plays a central role in the pathogenesis of systemic lupus erythematosus (SLE), serving as a target antigen of autoantibodies as well as a major component of immune complexes. These complexes can both promote immune disturbances as well as deposit in the kidney to incite inflammation. While the origin of anti-DNA autoantibodies in SLE has received intense investigation, the mechanisms by which DNA exits cells to form immune complexes in the circulation is not well understood. To determine the origin of DNA circulating in the blood in SLE, our laboratory has been using a murine model system to track the in vivo fate of DNA from Jurkat T cells that have been made apoptotic or necrotic in vitro and then administered to mice. Results of these studies indicate that DNA from apoptotic and necrotic cells appears in the blood in a time- and dose-dependent manner. Irrespective of origin, this DNA has properties of nucleosomes as shown by its molecular weight. The process of release requires the presence of macrophages and can be modified by glucocorticoids as well as inflammation. In addition, sex may play a role in the generation of extracellular DNA from dead cells as male and female mice differ in their responses in this model. Together, these studies clarify the origin of extracellular DNA circulating in the blood in SLE and suggest steps in this process that can be interdicted by novel therapy.

The extracellular release of HMGB1 during apoptotic cell death

High mobility group box 1 protein (HMGB1) is a non-histone nuclear protein with dual function. Inside the cell, HMGB1 binds DNA and regulates transcription, whereas outside the cell, it serves as a cytokine and mediates the late effects of LPS. The movement of HMGB1 into the extracellular space has been demonstrated for macrophages stimulated with LPS as well as cells undergoing necrosis but not apoptosis. The differential release of HMGB1 during death processes could reflect the structure of chromatin in these settings as well as the mechanisms for HMGB1 translocation. Since apoptotic cells can release some nuclear molecules such as DNA to which HMGB1 can bind, we therefore investigated whether HMGB1 release can occur during apoptosis as well as necrosis. For this purpose, Jurkat cells were treated with chemical inducers of apoptosis (staurosporine, etoposide, or camptothecin), and HMGB1 release into the medium was assessed by Western blotting. Results of these experiments indicate that HMGB1 appears in the media of apoptotic Jurkat cells in a time-dependent manner and that this release can be reduced by Z-VAD-fmk. Panc-1 and U937 cells treated with these agents showed similar release. In addition, HeLa cells induced to undergo apoptosis showed HMGB1 release. Furthermore, we showed using confocal microscopy that HMGB1 and DNA change their nuclear location in Jurkat cells undergoing apoptosis. Together, these studies indicate that HMGB1 release can occur during the course of apoptosis as well as necrosis and suggest that the release process may vary with cell type.

The immune response to cell death in SLE

Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterized by the production of antinuclear antibodies (ANA). These antibodies target a wide variety of antigens whose presence in an immunologically active form may result from cell death processes that cause their translocation and release from cells. As indicated by in vivo model systems, the release of DNA from cells may not be a simple consequence of cell death but rather may require the intervention of other cell types including macrophages. Thus, in mice, administration of either apoptotic or necrotic cells produces a blood DNA response, whereas mice lacking macrophages fail to show blood DNA under the same conditions. Furthermore, the circulating DNA arising from apoptotic and necrotic cells displays a similar pattern with respect to size distribution, with both showing DNA laddering, a pattern indicating enzymatic cleavage. Since circulating DNA in the form of immune complexes can play a role in lupus pathogenesis, these findings suggest that the generation and clearance of dead cells are important events that may underlie autoimmunity in this disease and may be targeted for therapy.