Cell-Free DNA as a Biomarker in Autoimmune Rheumatic Diseases

Abstract

Endogenous DNA is primarily found intracellularly in nuclei and mitochondria. However, extracellular, cell-free (cf) DNA, has been observed in several pathological conditions, including autoimmune diseases, prompting the interest of developing cfDNA as a potential biomarker. There is an upsurge in studies considering cfDNA to stratify patients, monitor the treatment response and predict disease progression, thus evaluating the prognostic potential of cfDNA for autoimmune diseases. Since the discovery of elevated cfDNA levels in lupus patients in the 1960s, cfDNA research in autoimmune diseases has mainly focused on the overall quantification of cfDNA and the association with disease activity. However, with recent technological advancements, including genomic and methylomic sequencing, qualitative changes in cfDNA are being explored in autoimmune diseases, similar to the ones used in molecular profiling of cfDNA in cancer patients. Further, the intracellular origin, e.g., if derived from mitochondrial or nuclear source, as well as the complexing with carrier molecules, including LL-37 and HMGB1, has emerged as important factors to consider when analyzing the quality and inflammatory potential of cfDNA. The clinical relevance of cfDNA in autoimmune rheumatic diseases is strengthened by mechanistic insights into the biological processes that result in an enhanced release of DNA into the circulation during autoimmune and inflammatory conditions. Prior work have established an important role of accelerated apoptosis and impaired clearance in leakage of nucleic acids into the extracellular environment. Findings from more recent studies, including our own investigations, have demonstrated that NETosis, a neutrophil cell death process, can result in a selective extrusion of inflammatory mitochondrial DNA; a process which is enhanced in patients with lupus and rheumatoid arthritis. In this review, we will summarize the evolution of cfDNA, both nuclear and mitochondrial DNA, as biomarkers for autoimmune rheumatic diseases and discuss limitations, challenges and implications to establish cfDNA as a biomarker for clinical use. This review will also highlight recent advancements in mechanistic studies demonstrating mitochondrial DNA as a central component of cfDNA in autoimmune rheumatic diseases.

The Impact of Pre-transplant Cell-free DNA Levels on Leukemia Relapse and Transplant-related Complications in Allogeneic Hematopoietic Stem Cell Transplant Recipients

“…Aside from several physiological states such as pregnancy and physical activity, pathological conditions, including inflammation and autoimmune diseases, may present with elevated cfDNA levels. In cancer, cfDNA levels may be increased up to 1000 ng/mL, which draws attention to an association between cfDNA levels and tumor burden (1,4,8,(10)(11)(12)(13). A previously reported association between age and cfDNA was confirmed in our study.…”

“…Aside from the physiopathological diversity of underlying autoimmune disorders and distinct stages of disease activity at the time of sampling, the role of the heterogeneous methods that were used in sample collection/processing, cfDNA extraction, and quantification should be emphasized. This point of view, which is mainly based on the lack of uniformity and standardization of cfDNA analysis, may lead to a distinct perspective that may particularly elucidate the predictor impact of lower cfDNA levels in the present study (11)(12)(13). Several studies underlined the predictor role of cfDNA in endotheliopathies, which shows a significant association of cfDNA with endothelial markers, including syndecan-1 and thrombomodulin (19,20).…”

Post-mortem ventricular cerebrospinal fluid cell-free-mtDNA in neurodegenerative disease

“…Normality of vCSF-cfmtDNA distributions were assessed by Shapiro-Wilks and could not be rejected at the 0.05 level. Thus, all vCSF-cfmtDNA levels are expressed as log [10] copy-number per microliter. Data were analysed in R (v4.0) 90 using data appropriate tests (detailed in the text).…”

Cell-free DNA donor fraction analysis in pediatric and adult heart transplant patients by multiplexed allele-specific quantitative PCR: Validation of a rapid and highly sensitive clinical test for stratification of rejection probability

“…A smaller, but biologically impactful, component of DNA is released from living cells under metabolic control by processes including exocytosis and NETosis (neutrophil extracellular traps) [52,53]. The low level of DNA release into the circulation seen in good health becomes elevated in response to induced cellular injury in various pathologic states including sepsis and severe infections, trauma, ischemic injury, autoimmune disease, and cancer [54][55][56][57][58][59]. Transient non-pathologic cfDNA elevations also occur after intense or prolonged exercise [60], but rapidly return to baseline upon recovery, consistent with the short half-life of cfDNA fragments in plasma, which generally ranges from 4-30 min [61][62][63].…”