Circulating cell-free DNA is predominantly composed of retrotransposable elements and non-telomeric satellite DNA

Cell-Free DNA: Features and Attributes Shaping the Next Frontier in Liquid Biopsy

Cell-free DNA (cfDNA) is changing the face of liquid biopsy as a minimally invasive tool for disease detection and monitoring, with its main applications in oncology and prenatal testing, and rising roles in transplant patient monitoring. However, the processes of cfDNA biogenesis, fragmentation, and clearance are complex and require further investigation. Evidence suggests that cfDNA production relates to mechanisms of cell death and DNA repair, both of which further influence fragment size and its applicability as a biomarker. An emerging domain, cfDNA fragmentomics is being explored for advancing the field of diagnostics using non-mutational signatures such as fragment size ratios and methylation patterns. Thus, this review examines structural diversity in cfDNA with various fragment sizes. In examining these cfDNA subsets, we discuss their distinct biological origins and potential clinical utility. Development of sequencing methodologies has broadened the application of cfDNA in diagnosing cancers and organ-specific pathologies, as well as directing personalized therapies. This has been achieved by identifying and uncovering different subsets of cfDNA in biofluids using different methodologies and biofluids. Different cfDNA subsets provide important insights regarding genomic and epigenetic features, enhancing the understanding of gene regulation, tissue-specific functions, and disease progression. Advancement of these key areas further asserts increasing clinical relevance for the use of cfDNA as a biomarker. Continued exploration of cfDNA subsets is expected to drive further innovation in liquid biopsy and its integration into routine clinical practice.

Increased amounts of cell-free DNA released from a culture with a high content of cancer stem cells

Background

The study and characterization of cell-free DNA (cfDNA) has gained significant importance due to its clinical applications as a diagnostic and prognostic marker. However, it remains unclear whether all cell populations within a tumor or culture contribute equally to its release. This pioneering research analyzes the contribution of cancer stem cells (CSCs) in colon cancer cell lines to the amount of cfDNA released and its role in cellular transformation.

Methods

The CSC population derived from the SW480 colon cancer cell line was enriched using a non-adhesive culture system to assess the quantity and electrophoretic profile of the released cfDNA. Subsequently, in vitro transformation assays were conducted to compare the transforming capacity of the cfDNA obtained from enriched cultures with that from non-enriched cultures. Group differences were analyzed using analysis of variance (ANOVA), followed by post hoc interpretation with Tukey's test.

Results

Our study revealed that cultures with CSCs released greater amounts of cfDNA, displaying a distinct fragment profile. Additionally, cfDNA from different cellular origins influenced the transformation characteristics of NIH3T3 cells. This is the first demonstration of a link between CSC proportions and cfDNA release, suggesting that CSCs and microenvironmental conditions can affect cfDNA quantity and its potential to induce transformation.

Conclusion

These findings highlight the importance of cfDNA in carcinogenesis and its potential as a biomarker and therapeutic target, especially given the role of CSCs in drug resistance and tumor aggressiveness.

An appropriate DNA input for bisulfite conversion reveals LINE-1 and Alu hypermethylation in tissues and circulating cell-free DNA from cancers

The autonomous and active Long-Interspersed Element-1 (LINE-1, L1) and the non-autonomous Alu retrotransposon elements, contributing to 30% of the human genome, are the most abundant repeated sequences. With more than 90% of their sequences being methylated in normal cells, these elements undeniably contribute to the global DNA methylation level and constitute a major part of circulating-cell-free DNA (cfDNA). So far, the hypomethylation status of LINE-1 and Alu in cellular and extracellular DNA has long been considered a prevailing hallmark of ageing-related diseases and cancer. This study demonstrated that errors in LINE-1 and Alu methylation level measurements were caused by an excessive input quantity of genomic DNA used for bisulfite conversion. Using the minuscule DNA amount of 0.5 ng, much less than what has been used and recommended so far (500 ng-2 μg) or 1 μL of cfDNA extracted from 1 mL of blood, we revealed hypermethylation of LINE-1 and Alu in 407 tumour samples of primary breast, colon and lung cancers when compared with the corresponding pair-matched adjacent normal tissue samples (P < 0.05-0.001), and in cfDNA from 296 samples of lung cancers as compared with 477 samples from healthy controls (P < 0.0001). More importantly, LINE-1 hypermethylation in cfDNA is associated with healthy ageing. Our results have not only contributed to the standardized bisulfite-based protocols for DNA methylation assays, particularly in applications on repeated sequences but also provided another perspective for other repetitive sequences whose epigenetic properties may have crucial impacts on genome architecture and human health.

Genome-wide repeat landscapes in cancer and cell-free DNA

Genetic changes in repetitive sequences are a hallmark of cancer and other diseases, but characterizing these has been challenging using standard sequencing approaches. We developed a de novo kmer finding approach, called ARTEMIS (Analysis of RepeaT EleMents in dISease), to identify repeat elements from whole-genome sequencing. Using this method, we analyzed 1.2 billion kmers in 2837 tissue and plasma samples from 1975 patients, including those with lung, breast, colorectal, ovarian, liver, gastric, head and neck, bladder, cervical, thyroid, or prostate cancer. We identified tumor-specific changes in these patients in 1280 repeat element types from the LINE, SINE, LTR, transposable element, and human satellite families. These included changes to known repeats and 820 elements that were not previously known to be altered in human cancer. Repeat elements were enriched in regions of driver genes, and their representation was altered by structural changes and epigenetic states. Machine learning analyses of genome-wide repeat landscapes and fragmentation profiles in cfDNA detected patients with early-stage lung or liver cancer in cross-validated and externally validated cohorts. In addition, these repeat landscapes could be used to noninvasively identify the tissue of origin of tumors. These analyses reveal widespread changes in repeat landscapes of human cancers and provide an approach for their detection and characterization that could benefit early detection and disease monitoring of patients with cancer.

Targeted Sequencing of Human Satellite 2 Repeat Sequences in Plasma cfDNA Reveals Potential Breast Cancer Biomarkers

Liquid biopsies are revolutionizing the detection and management of malignant diseases. While repetitive DNA sequences, such as LINE-1 and ALU are established in cell-free DNA (cfDNA) research, their clinical applications remain limited. In this study, we explore human satellite 2 (HSATII), a prevalent repeat DNA sequence in plasma that exhibits increased levels in cancer patients, thereby positioning it as a potential pan-cancer biomarker. We employed targeted sequencing and copy number variation (CNV) analysis using two primer pairs to assess the differential abundance of HSATII sequences in the plasma of breast cancer patients compared to healthy individuals. PCR amplicons of HSATII from 10 patients and 10 control subjects were sequenced, generating 151 bp paired-end reads. By constructing a pooled reference dataset, HSATII copy ratios were estimated in the patients. Our analysis revealed several significant CNVs in HSATII, with certain sequences displaying notable gains and losses across all breast cancer patients, suggesting their potential as biomarkers. However, we observed pronounced fragmentation of cfDNA in cancer, leading to the loss of longer PCR amplicons (>180 bp). While not all observed losses can be attributed to fragmentation artifacts, this phenomenon does introduce complexity in interpreting CNV data. Notably, this research marks the first instance of targeted HSATII sequencing in a liquid biopsy context. Our findings lay the groundwork for developing sequencing-based assays to detect differentially represented HSATII sequences, potentially advancing the field of minimally-invasive cancer screening.

Biochemical profiling of the follicular environment to predict oocyte competence in cattle

To identify markers of oocyte competence, we compared the biochemical characteristics of fluid and cells from follicles containing oocytes with different capacities to form an embryo. Follicles (5-6 mm) were dissected, and follicular fluid (FF), granulosa cells (GC), cumulus cells (CC) from immature and mature cumulus-oocyte-complexes (COC) were individually collected. The oocytes were matured, fertilized, and cultured individually until day 8 (D8) of development. On D8, the samples were grouped according to embryo production into those that gave rise to blastocysts (EMB) and those that did not reach the blastocyst stage (NEMB). In CCs from immature and mature COCs and GCs, expression of CASP3, SERPINE2, VCAN, LUM, FSHR, EGFR, PGR, and GHR genes was quantified. Cell-free DNA (cfDNA), progesterone, and estradiol concentrations in the FF were determined. Data were analyzed by Mann-Whitney U test (GraphPad Prism 9). GHR was highly expressed in immature CCs from the EMB group, whereas CASP3 was highly expressed in mature CCs from the NEMB group (P<0.05). During maturation, the expression of CASP3 and GHR genes increased only in the NEMB group. ART2 cfDNA was highly detected in FF of the NEMB compared to the EMB group. Progesterone concentration was similar between the groups, whereas estradiol concentration was higher (P<0.05) in the EMB than in the NEMB group. It was concluded that a higher level of GHR transcripts in immature CCs, lower CASP3 expression in CCs from matured COCs, lower levels of ART2, and higher estradiol concentrations in FF may indicate oocytes with greater potential for development.

Kan Plazmasında Satellit-2 Tekrar Elementi DNA Dizilerinin Karakterizasyonu

Amaç: Son yıllarda tıp biliminin farklı disiplinlerinde sıkça karşılaşılan kavramlardan biri olan “sıvı biyopsi”, hastaların tanı, prognoz analizi ve tedaviye cevabını değerlendirme gibi konularda girişimsel doku biyopsisi yerine, kan ve çeşitli vücut sıvılarındaki moleküler ve epigenetik biyobelirteçlerin kullanılmasını içerir. Dolaşımda serbest halde dolaşan DNA’da (‘cell-free DNA’, cfDNA) kanser hücrelerine özgü gen mutasyonlarının saptanması, kanser hücrelerinin içeriğinin vücut sıvılarına geçtiğinin kesin kanıtı olarak kabul edilmektedir. cfDNA’nın bileşiminin belirlenmesine yönelik dizileme çalışmaları, perisentrik satellit DNA dizilerinin, cfDNA’da genom oranlarına kıyasla daha fazla oranda temsil edildiğini bildirmiştir. Bu çalışmada, kanser açısından spesifik dizilerin saptanması amacıyla, Sat-2 dizilerinin polimeraz zincir reaksiyonunda (PCR) çoğaltılmaları sonrasında daha detaylı karakterizasyonu amaçlanmıştır.Yöntem: Çalışmada, sağlıklı ve metastatik meme kanserli hastaların plazmalarından 1. ve 10. kromozoma spesifik Sat-2 dizileri PCR ile çoğaltıldıktan sonra, otomatik elektroforez sisteminde ayrıştırıldılar.Bulgular: Yapılan büyüklük analizinde, iki bölgeden çok sayıda amplikon oluştuğu, bunların yaklaşık %50’ni sırasıyla 143 ve 115 bç uzunluğunda ürünlerin oluşturduğu belirlenmiştir. Bu iki PCR amplikonunun miktarı meme kanserli hastalarda daha yüksek olarak hesaplandı. Onuncu kromozoma özgü 115 bç’lik fargman dışındaki Sat-2 dizileri açısından kontroller ile hastalar arasında önemli farklar olduğu belirlenmiştir.Sonuç: Çalışma kapsamında elde edilen bulgular, Sat-2 tekrar elementine ait DNA dizilerinin sekanslanması sonrası kansere spesifik hedef bölgelerin saptanabileceğini ortaya koymaktadır. 

Uterosomes: The lost ring of telegony?

Telegony refers to the appearance of some characteristics of the female's previously mated male in her subsequent offspring by another male. According to evidence, telegony may occur either through the infiltration of sperm into the somatic tissues of the female genital tract or the presence of fetal genes in the mother's blood. It is highlighted that sperm penetrates into the mucosa of the uterine and possibly alters the genetic structure, affecting the embryo and enduring from one pregnancy to the next, which may be one of the potential mechanisms of telegony. Uterine fluid, uterine gland-derived histotroph, supplies key nutrients for successful embryo implantation and it is important during the first trimester, especially, because of its susceptibility to maternal states. The presence of EVs in uterine fluid (uterosomes) was reported in mice, sheep, and humans, including a wide range of biomolecules, such as proteins, and non-coding RNAs. In this review article, we presented a new idea to explain telegony. Based on our idea, after the previous male sperm entry into the female reproductive system, those sperm which do not participate in fertilization penetrate into the somatic cells of the uterus and store their genetic/epigenetic information there. The sperm of the next partner reaches a location in the female reproductive canal where it exchanges information with the uterosomes and obtains the proteins and non-coding RNAs required for fertilization, development, and implantation.

New Perspectives on the Importance of Cell-Free DNA Biology

Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.

The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies

Liquid biopsy is a broad term that refers to the testing of body fluids for biomarkers that correlate with a pathological condition. While a variety of body-fluid components (e.g., circulating tumor cells, extracellular vesicles, RNA, proteins, and metabolites) are studied as potential liquid biopsy biomarkers, cell-free DNA (cfDNA) has attracted the most attention in recent years. The total cfDNA population in a typical biospecimen represents an immensely rich source of biological and pathological information and has demonstrated significant potential as a versatile biomarker in oncology, non-invasive prenatal testing, and transplant monitoring. As a significant portion of cfDNA is composed of repeat DNA sequences and some families (e.g., pericentric satellites) were recently shown to be overrepresented in cfDNA populations vs their genomic abundance, it holds great potential for developing liquid biopsy-based biomarkers for the early detection and management of patients with cancer. By outlining research that employed cell-free repeat DNA sequences, in particular the ALU and LINE-1 elements, we highlight the clinical potential of the repeat-element content of cfDNA as an underappreciated marker in the cancer liquid biopsy repertoire.

In Vitro Analysis of Biological Activity of Circulating Cell-Free DNA Isolated from Blood Plasma of Schizophrenic Patients and Healthy Controls

Schizophrenia is associated with low-grade systemic inflammation. Circulating cell-free DNA (c-cfDNA) belongs to the DAMP class. The major research question was: can the c-cfDNA of schizophrenic patients (sz-cfDNA) stimulate the DNA sensor genes, which control the innate immunity? We investigated the in vitro response of ten human skin fibroblast (HSF) lines to five DNA probes containing different amounts of a GC-rich marker (the ribosomal repeat) and a DNA oxidation marker (8-oxodG) including sz-cfDNA and healthy control c-cfDNA (hc-cfDNA) probes. After 1 h, 3 h, and 24 h of incubation, the expression of 6 protein genes responsible for cfDNA transport into the cell (EEA1 and HMGB1) and the recognition of cytosolic DNA (TLR9, AIM2, STING and RIG-I) was analyzed at the transcriptional (RT-qPCR) and protein level (flow cytometry and fluorescence microscopy). Additionally, we analyzed changes in the RNA amount of 32 genes (RT-qPCR), which had been previously associated with different cellular responses to cell-free DNA with different characteristics. Adding sz-cfDNA and hc-cfDNA to the HSF medium in equal amounts (50 ng/mL) blocked endocytosis and stimulated TLR9 and STING gene expression while blocking RIG-I and AIM2 expression. Sz-cfDNA and hc-cfDNA, compared to gDNA, demonstrated much stronger stimulated transcription of genes that control cell proliferation, cytokine synthesis, apoptosis, autophagy, and mitochondrial biogenesis. No significant difference was observed in the response of the cells to sz-cfDNA and hc-cfDNA. Sz-cfDNA and hc-cfDNA showed similarly high biological activity towards HSFs, stimulating the gene activity of TLR9 and STING DNA sensor proteins and blocking the activity of the AIM2 protein gene. Since the sz-cfDNA content in the patients’ blood is several times higher than the hc-cfDNA content, sz-cfDNA may upregulate pro-inflammatory cytokines in schizophrenia.

Standardization of DNA amount for bisulfite conversion for analyzing the methylation status of LINE-1 in lung cancer

Highly methylated Long Interspersed Nucleotide Elements 1 (LINE-1) constitute approximately 20% of the human genome, thus serving as a surrogate marker of global genomic DNA methylation. To date, there is still lacking a consensus about the precise location in LINE-1 promoter and its methylation threshold value, making challenging the use of LINE-1 methylation as a diagnostic, prognostic markers in cancer. This study reports on a technical standardization of bisulfite-based DNA methylation analysis, which ensures the complete bisulfite conversion of repeated LINE-1 sequences, thus allowing accurate LINE-1 methylation value. In addition, the study also indicated the precise location in LINE-1 promoter of which significant variance in methylation level makes LINE-1 methylation as a potential diagnostic biomarker for lung cancer. A serial concentration of 5-50-500 ng of DNA from 275 formalin-fixed paraffin-embedded lung tissues were converted by bisulfite; methylation level of two local regions (at nucleotide position 300–368 as LINE-1.1 and 368–460 as LINE-1.2) in LINE-1 promoter was measured by real time PCR. The use of 5 ng of genomic DNA but no more allowed to detect LINE-1 hypomethylation in lung cancer tissue (14.34% versus 16.69% in non-cancerous lung diseases for LINE-1.1, p < 0.0001, and 30.28% versus 32.35% for LINE-1.2, p < 0.05). Our study thus highlighted the optimal and primordial concentration less than 5 ng of genomic DNA guarantees the complete LINE-1 bisulfite conversion, and significant variance in methylation level of the LINE-1 sequence position from 300 to 368 allowed to discriminate lung cancer from non-cancer samples.

Epididymosomes: the black box of Darwin’s pangenesis?

Darwin, in the pangenesis theory, imagined particles, named as ‘gemmules’, which are released from all (‘pan’) cells of the body. By cell–cell communication and also circulation through the body, they finally reach the germ cells to participate in the generation (‘genesis’) of the new individual. It has been shown that circulatory exosomes are affected by environmental stressors and they can reach the parental germ cells. Therefore, in the mirror of his theory, circulatory exosomes could interact with epididymosomes: epididymis-derived exosomes which have a wide spectrum of variation in content and size, are very sensitive to environmental stressors, and may be involved in translating external information to the germ cells. The protein and RNA cargo would be transferred by epididymosomes to sperm during sperm maturation, which would be then delivered to the embryo at fertilization and inherited by offspring. Therefore, in this study, we will briefly discuss Darwin’s pangenesis theory and its possible relation with epididymosomes. We believed that epididymosomes could be considered as an attractive candidate for the storage of RNA contents, changing the epigenome of the next generations, and allowing the reappearance acquired characteristics of ancestors. Therefore, epididymosomes, as a black box of Darwin’s pangenesis, may unravel parental life history and also disclose the historical events that affect the life of offspring.

Aging-associated distinctive DNA methylation changes of LINE-1 retrotransposons in pure cell-free DNA from human blood

LINE-1 hypomethylation of cell-free DNA has been described as an epigenetic biomarker of human aging. However, in the past, insufficient differentiation between cellular and cell-free DNA may have confounded analyses of genome-wide methylation levels in aging cells. Here we present a new methodological strategy to properly and unambiguously extract DNA methylation patterns of repetitive, as well as single genetic loci from pure cell-free DNA from peripheral blood. Since this nucleic acid fraction originates mainly in apoptotic, senescent and cancerous cells, this approach allows efficient analysis of aged and cancerous cell-specific DNA methylation patterns for diagnostic and prognostic purposes. Using this methodology, we observe a significant age-associated erosion of LINE-1 methylation in cfDNA suggesting that the threshold of hypomethylation sufficient for relevant LINE-1 activation and consequential harmful retrotransposition might be reached at higher age. We speculate that this process might contribute to making aging the main risk factor for many cancers.

Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms

Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.