Source Of cfDNA Research Articles

BIOM-16. LONGITUDINAL GLIOMA CEREBROSPINAL FLUID CELL-FREE DNA FOR MONITORING AND TREATMENT RESPONSE ASSESSMENT

Abstract Few methods exist via which to assess treatment response with high fidelity in gliomas. While CSF has previously been used as a source of cfDNA, it remains unknown how cfDNA abundance and sequencing changes throughout treatment and inevitable recurrence in gliomas. We utilized our biobank of longitudinal intracranial CSF specimens to determine the potential utility of CSF cfDNA as a monitoring tool for treatment response in patients with gliomas. Longitudinal CSF specimens were acquired via Ommaya reservoirs (NCT04692337) or ventriculoperitoneal shunts (NCT04692324) in patients with gliomas. cfDNA was extracted from 1-5 mL of CSF, and next-Generation sequencing or low-pass whole genome sequencing (LPWGS) was performed by Predicine, Inc. CSF acquired prior to versus after resection demonstrated an increase in quantified cfDNA (2.97x, range: 1.58-5.26x), consistent with the impact of increased parenchymal disruption and closer contact with CSF. Thereafter, CSF cfDNA continued to decrease throughout chemoradiation and adjuvant treatment and increased at recurrence, including in patients co-enrolled in immunotherapy trials for IL-7 agonists and pembrolizumab. Copy number burden (CNB) increased by the time of recurrence in three patients with known disease progression, and continued to decrease throughout immunotherapy treatment in one patient despite concerns of pseudoprogression. In one patient with a hypermutated glioblastoma, CSF cfDNA revealed over 59 genomic alterations, including MAP2K1, KIT, and PDGFRA, excluding even more variants of unknown significance, each of which had been detected in sequencing of the tissue acquired at resection and subsequently decreased with chemoradiation. In another patient with a known progressing EGFR-amplified GBM, over 200 new variants were identified by the patient’s final sample and EGFR copy number increased from 2 to over 30. In conclusion, cfDNA analysis over a patient’s disease course, including resection and treatment with standard-of-care and experimental therapies, may be of use for disease monitoring and treatment response.

Neutrophil extracellular traps-associated markers in malignant neoplasms of the female reproductive system after surgical treatment and adjuvant chemotherapy

Introduction. Studies evidence about a relation between increased circulating free DNA (cfDNA) concentrations and chemotherapy, the majority of which have been focused on considering a tumor as a source of cfDNA. It has been suggested that neutrophils also contribute to this process, as cancer-related cfDNA characteristics resemble those of neutrophil extracellular traps (NETs). Therefore, the elevated concentration of cfDNA observed in chemotherapy patients may be associated with NETosis.Aim: assessment of NETosis markers in surgical treatment and adjuvant chemotherapy of patients with malignant neoplasms of the female reproductive system.Materials and Methods. A prospective non-randomized interventional controlled study was carried out by enrolling 111 patients with malignant breast diseases and female genital organs of various localizations and stages hospitalized for elective surgical treatment or chemotherapy course. The control group included 33 healthy women. 69 patients underwent surgical treatment. Adjuvant chemotherapy with paclitaxel and carboplatin was performed in 25 patients with ovarian cancer and 17 patients with breast cancer. In cancer patients, citrullinated histone H3 (citH3) and myeloperoxidase (MPO) were chosen as NETosis biomarkers allowing to distinguish NETs from other tumor-derived cfDNA thereby improving quality of research study. The concentration of NETosis markers was assessed before surgery or onset of chemotherapy upon admission to hospital and 14 days after surgery or 14 days after the second course of chemotherapy.Results. In all patients, the concentrations of NETosis markers before the start of therapy were significantly increased compared to the control group as well as 14 days after surgical treatment and 14 days after the second course of chemotherapy. However, in surgical patients, no significantly increased concentration of NETosis markers postvs. pre-surgery magnitude was observed. Upon that, patients underwent 2 courses of chemotherapy vs. baseline level were found to have significantly elevated magnitude of NETosis markers.Conclusion. The study revealed the relationship between administration of paclitaxel-containing chemotherapy in patients with ovarian cancer and breast cancer and a rise in NETs level. Chemotherapy is an essential component for management of patients with malignant neoplasms of the female reproductive system, therefore, development of new strategies to lower a risk of thrombosis and resistance to it is of crucial importance.

#3486 CELL-FREE CIRCULATING DNA IN ANCA-ASSOCIATED VASCULITIS – A COMPARISON OF PATIENTS DURING ACTIVE DISEASE AND REMISSION

Abstract Background and Aims Patients with ANCA-associated vasculitis (AAV) undergo immunosuppressive treatment to thwart organ failure and avoid relapse. However, the treatment is associated with risk of infections and malignancy. There are currently no reliable biomarkers which can be used in the clinic to assess disease activity. Neutrophil extracellular traps containing nuclear (n) and/or mitochondrial (mt) DNA have been implied in the pathogenesis of AAV. The aim of this study was to explore whether there is a difference in levels of circulating cell-free DNA (cfDNA) amongst AAV patients during active disease and in remission. Method Paired samples from 7 male and 9 female patients with AAV, of which 10 were diagnosed with GPA, were obtained during both active disease and clinical remission as part of an ongoing observational prospective study. Participants’ ages ranged from 21.8 to 80.0 years (median = 64.9), and 11 participants had a history of kidney engagement. After DNA-extraction digital droplet PCR was performed to obtain levels of mtDNA and nDNA. Clinical diagnosis (GPA or MPA), ANCA-positivity, kidney involvement, and Birmingham vasculitis activity score (BVAS) were also assessed. Results There were no significant differences in levels of mtDNA or nDNA in patients with active disease compared to remission; mtDNA (median = 14 520 and 11 985 copies/µL respectively, p = .379) and nDNA (median = 4.45 and 4.70 copies/µL, p = .569). The ratio between mtDNA and nDNA did not differ either (median 2100 and 2400, p = .679). A strong correlation between mtDNA- and nDNA levels (r = .920, p < .001) was found, whereas no correlations were found between cfDNA and age, sex, clinical phenotype, ANCA positivity, kidney engagement or BVAS (Tables 1 and 2). Conclusion This study provides additional information regarding levels of mtDNA and nDNA comparing AAV patients during active disease and in clinical remission. The lack of association with disease activity and the correlation between nDNA and mtDNA may indicate cell damage as a source of cfDNA. To further delineate the contribution of NETs to the levels of cfDNA, and the mechanisms behind cellular injury and inflammation, studies with larger samples with longitudinal follow-up and healthy controls are needed.

Abstract 1967: Potential of aqueous humor as a liquid biopsy for uveal melanoma

Abstract Introduction: Uveal melanoma (UM) is the most common primary intraocular tumor in adults and arises from the uvea (iris, ciliary body and choroid). Although there are prognostic biomarkers available, identifying them requires intraocular tumor biopsy. Blood biopsy has emerged as a significantly less invasive alternative that also offers the ability to longitudinally track disease. However, blood biopsy has been unsuccessful for clinical use in identifying prognostic biomarkers in UM due to low detection rates. Thus, eye-specific aqueous humor (AH) biopsy may be a better alternative. Methods: This case series includes 20 primary UM patients with 13 (65%) choroid and 7 (35%) ciliary body (CB) tumors. AH samples were collected prior to brachytherapy plaque placement (n = 17), after brachytherapy (n = 19) and at enucleation (n = 1). A tumor wash sample (n = 1) was collected after routine fine needle aspiration biopsy. Nucleic acids ([NA], dsDNA, RNA, ssDNA and miRNA) were quantitated by Qubit Assay Kits. All AH samples and cells from tumor washing underwent DNA isolation and was followed by shallow whole-genome sequencing for copy-number profiling. Results: Comparison of pre- and post-radiation samples revealed significantly higher concentration of ssDNA (n = 10 pairs, P = 0.039) and miRNA (n = 10 pairs, P = 0.008) in choroid post- samples and significantly higher concentration of dsDNA (n = 7 pairs, P = 0.031) and miRNA (n = 7 pairs, P = 0.016) in CB post- samples. Between choroid (n = 12) and CB (n = 7) post- samples, there was a significantly higher concentration of dsDNA (P = 0.022) and RNA (P = 0.009) in post- CB samples, suggesting NA content is released from the disturbance of tumor cells by radiation and due to the proximity of the tumor to the AH in CB. Highly recurrent UM somatic copy number alterations (SCNAs) of monosomy 3, 6p gain, 6q loss and 8q gain were identified in post- AH samples. There was a significant difference between altered SCNA profiles in CB and choroid (P= 0.038). Altered SCNA profiles were found in 1/12 (8.3%) and 4/7 (57.1%) post-radiation AH samples of choroid and CB, respectively. No SCNAs were found in the same eyes’ pre-radiation sample. A high concordance of DNA profiles between a tumor wash and post- AH sample was identified (r = 0.978) and UM mutations GNAQ and BAP1 were detected in 3/6 (50%) post- AH with 2/5 (40%) matching tumor samples, demonstrating AH dsDNA’s tumor-origin. Conclusions: The AH is a source of cfDNA, with a higher yield of NAs after radiation in UM. Given the significant increase in NA concentration after radiation and in CB compared to choroid tumors, we hypothesize that all detected NAs post-radiation are tumor-derived due to apoptosis of tumor cells and subsequent release of cfDNA and due to the proximity of the CB tumor to AH. These results represent the first time that UM SCNAs and mutations were identified in cfDNA isolated from the AH, and this suggests that the AH can serve as a liquid biopsy for UM, especially in CB tumors. Citation Format: Deborah H. Im, Chen-Ching Peng, Liya Xu, Mary E. Kim, Dejerianne Ostrow, Venkata Yellapantula, Moiz Bootwalla, Jaclyn A. Biegel, Xiaowu Gai, Peter Kuhn, James Hicks, Jesse L. Berry. Potential of aqueous humor as a liquid biopsy for uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1967.

Influence of preanalytical variables on the quality of cell-free DNA. Biobanking of cell-free DNA material

The search for early disease markers and the development of diagnostic systems has recently been expanding within genomics. Genomic deoxyribonucleic acid (DNA), cell-free DNA (cfDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. It has been shown that cfDNA that enters the bloodstream, in particular, as a result of apoptosis, necrosis, active tumor secretion and metastasis, is of great importance for studying molecular mechanisms of the pathological process and application in clinical practice. Circulating nucleic acid analysis can be used to monitor response to treatment, assess drug resistance, and quantify minimal residual disease. The review article reflects the following information about the biomaterial: source of cfDNA, methods of cfDNA isolation, storage and use for the diagnosis of certain diseases. Cell-free DNA can be present in biological fluids such as blood, urine, saliva, synovial and cerebrospinal fluid. In most cases, cfDNA is isolated from blood derivatives (serum and plasma), while it is most correct to use blood plasma for cfDNA isolation. Optimal and economically justifiable is the use of ethylenediaminetetra-acetic acid tubes for taking blood and obtaining plasma with subsequent cfDNA isolation. There is evidence that the optimal shelf life in an ethylenediaminetetra-acetic acid tube from the moment of blood sampling to subsequent isolation is a 2-hour interval. After centrifugation, cfDNA in plasma (or serum) can be stored for a long time at a temperature of -80O C. Storage at -20O C is undesirable, since DNA fragmentation increases.

Abstract 10765: Plasma Cell-Free DNA Predicts Survival and Maps Tissue-Specific Sources of Injury in Pulmonary Arterial Hypertension

Background: Cell-free DNA (cfDNA) is a non-invasive marker of tissue injury. Although being incrementally used as a clinical biomarker, its significance in pulmonary arterial hypertension (PAH) is unknown. Methods: Plasma cfDNA was isolated in two independent PAH cohorts (A, n=48; B, n=161) and healthy controls (n=48). Clinical variables and survival status were collected for Registry to Evaluate Early And Long-term PAH Disease Management (REVEAL 2.0) scores and outcome determinations. Total cfDNA levels were compared amongst controls and PAH patients and also used to predict transplant-free survival. A subset of samples from cohort B (n=96) and controls (n=16) were subjected to bisulfite sequencing and methylation analysis to quantify tissue-specific sources of cfDNA. Results: Median (IQR) cfDNA concentrations were higher in cohort A PAH patients (exploratory cohort) compared to controls and increased according to REVEAL 2.0 risk group: controls 13.7 (10.8-18.8) vs low risk 14.4 (10.0-19.9) vs medium risk 14.6 (11.3-28.2) vs high risk 31.5 (17.2-45.6) ng/ml (P<0.01). cfDNA analysis in cohort B (validation cohort) demonstrated a similar cfDNA pattern: controls 13.7 (10.8-18.8) vs low risk 24.3 (16.0-57.9) vs medium risk 50.4 (29.4-70.9) vs high risk 51.5 (34.0-110.5) ng/ml (P<0.0001). cfDNA tertiles (Log-Rank; P=0.0001) and REVEAL 2.0 risk group (Log-Rank; P<0.0001) similarly predicted transplant-free survival, and the addition of cfDNA to REVEAL 2.0 improved model performance (AUC 0.64 to 0.70; P<0.05). Tissue-specific methylation analysis revealed increased cfDNA originating from vascular endothelium, cardiac myocytes, monocytes, erythrocyte progenitors, neutrophils, natural killer cells, and adipocytes (all P<0.005), but not colon, head/neck, liver, bladder, or kidney. With the exception of natural killer cells, cfDNA from enriched tissues also differentiated PAH patients of varying REVEAL 2.0 risk. Conclusions: cfDNA is elevated in PAH patients, correlates with disease severity and predicts worse survival. Methylation analysis of cfDNA in PAH patients is consistent with prevailing paradigms of disease pathogenesis. Thus, cfDNA may add prognostic power to PAH risk assessment and provide insight into disease progression.

Role of Cell-Free DNA and Deoxyribonucleases in Tumor Progression.

Many studies have reported an increase in the level of circulating cell-free DNA (cfDNA) in the blood of patients with cancer. cfDNA mainly comes from tumor cells and, therefore, carries features of its genomic profile. Moreover, tumor-derived cfDNA can act like oncoviruses, entering the cells of vulnerable organs, transforming them and forming metastatic nodes. Another source of cfDNA is immune cells, including neutrophils that generate neutrophil extracellular traps (NETs). Despite the potential eliminative effect of NETs on tumors, in some cases, their excessive generation provokes tumor growth as well as invasion. Considering both possible pathological contributions of cfDNA, as an agent of oncotransformation and the main component of NETs, the study of deoxyribonucleases (DNases) as anticancer and antimetastatic agents is important and promising. This review considers the pathological role of cfDNA in cancer development and the role of DNases as agents to prevent and/or prohibit tumor progression and the development of metastases.

Cell-Free DNA in Rheumatoid Arthritis.

Endogenous DNA derived from the nuclei or mitochondria is released into the bloodstream following cell damage or death. Extracellular DNA, called cell-free DNA (cfDNA), is associated with various pathological conditions. Recently, multiple aspects of cfDNA have been assessed, including cfDNA levels, integrity, methylation, and mutations. Rheumatoid arthritis (RA) is the most common form of autoimmune arthritis, and treatment of RA has highly varied outcomes. cfDNA in patients with RA is elevated in peripheral blood and synovial fluid and is associated with disease activity. Profiling of cfDNA in patients with RA may then be utilized in various aspects of clinical practice, such as the prediction of prognosis and treatment responses; monitoring disease state; and as a diagnostic marker. In this review, we discuss cfDNA in patients with RA, particularly the sources of cfDNA and the correlation of cfDNA with RA pathogenesis. We also highlight the potential of analyzing cfDNA profiles to guide individualized treatment approaches for RA.

Abstract 554: Aqueous humor as a liquid biopsy for uveal melanoma

Abstract Purpose: Metastatic Uveal Melanoma (UM) is usually fatal within one year of symptom onset. There are a variety of biomarkers that can stratify patients' metastatic risk, but identifying them requires intraocular tumor biopsy. Liquid biopsy offers a less invasive alterative without the risks of retinal detachment and intraocular hemorrhage. We investigated whether the aqueous humor (AH) has sufficient tumor-derived cell-free DNA (cfDNA) to function as a liquid biopsy for UM. Methods: This case series includes 12 AH samples from 7 eyes of 7 UM patients from whom AH was sampled during routine brachytherapy plaque placement and/or removal. Double stranded DNA (dsDNA), single stranded DNA (ssDNA), RNA, and microRNA (miRNA) were quantified with respective Qubit High Sensitivity Assay Kits (Thermo Fischer) for each sample. The lower limit of detection was 0.01 ng/µL for dsDNA, 0.05 ng/µL for ssDNA, 0.25 ng/µL for RNA, and 0.05 ng/µL for miRNA. CfDNA was then isolated and sequenced on an Illumina platform to assess genome-wide somatic copy number alterations (SCNAs). Results: Aqueous humor derived cfDNA was detected in all samples, ranging from 0.085-28.8 ng/µL (mean = 2.7 ng/µL). RNA was detected in 2 of 12 samples (mean = 1.6 ng/µL, range = 0.7-2.5 ng/µL), and miRNA was detected in 11 of 12 samples (mean = 1.7 ng/µL, range = 0.094-16.2 ng/µL). There was a significantly higher cfDNA concentration in post-radiation samples than pre-radiation samples, (median = 0.082 ng/µL in pre-radiation, 0.21 ng/µL in post-radiation, W = 1, z = -2.55, p < 0.05, Wilcoxon Signed-rank test). This finding was similar when comparing all nucleic acid concentrations (dsDNA, ssDNA, RNA, and miRNA) between pre- and post-radiation (median = 0.085 ng/µL in pre-radiation, 0.333 ng/µL in post-radiation, W = 1, z = -3.46, p = 0.00027). Confirmed UM genomic alterations of 6p gain, 6q loss, and 8q gain were identified in one post-radiation AH sample from an eye with an iridociliary body tumor. These SCNAs are characteristic of UM. No SCNAs were found in the AH from the pre-radiation sample in the same eye, or any of the other AH samples sequenced to date. Conclusions: The AH is a source of cfDNA in eyes with UM, with a higher yield of all nucleic acids detected after brachytherapy radiation treatment. UM associated SCNAs were identified in the AH of one eye with an iridociliary tumor after radiation only. We hypothesize this may be due to intratumoral necrosis from the radiation as well as the proximity of the primary tumor to the AH in the case where SCNAs were identified. These results represent the first time that UM SCNAs have been identified in cfDNA isolated from the AH, and this provides preliminary evidence that the AH can serve as a liquid biopsy for UM. Citation Format: Mary E. Kim, Liya Xu, Chen-Ching Peng, Peter Kuhn, James Hicks, Jesse L. Berry. Aqueous humor as a liquid biopsy for uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 554.

Abstract 2611: Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype

Abstract Our current understanding of solid tumors and their progression primarily relies on in vitro models, cell lines, patient-derived xenografts, and scarce data from invasive tissue biopsies from patients. The ability to monitor changes in chromatin structure and transcription factor binding in tumor cells using a minimally invasive approach in humans has the potential to revolutionize our understanding of disease progression and treatment resistance. In this study, we use the example of estrogen receptor (ER) positive breast cancer, the most common disease subtype, and define the ER axis from plasma cell-free DNA (cfDNA). While lymphoid/myeloid cell turnover represents the dominant source of cfDNA in the bloodstream, a detectable fraction of DNA from tumor tissue-of-origin can be found in patients with solid cancers. cfDNA is the product of the action of endogenous nucleases on chromatin; and retains the map of epigenomes from cells of origin. Our method therefore non-invasively captures TF-nucleosome dynamics in tumor tissue-of-origin using plasma cfDNA. First, we show that we can reliably identify the active binding of hematopoietic pioneer factor PU.1 and CTCF from cfDNA of healthy humans and cancer patients. Then to define cfDNA binding of disease specific TF ER, we used ER+ patient-derived xenograft (PDX) models allowing for a clear separation of tumor signal from hematopoietic background. This allowed us to establish the sensitivity and specificity of our approach. We also identified the subset of CUT&RUN-defined ER binding sites that feature the strongest binding in vivo from both lymphocyte background as well as cancer cells. Furthermore, we can define the active binding sites of pioneer factor FOXA1, which facilitates ER binding by opening the chromatin. Based on the TF protection levels from cfDNA we were able to define tumor as well as hematopoietic-specific TF binding sites that can serve as potential hotspots to monitor ER+ disease state at around 1% tumor fraction. These data demonstrate our ability to simultaneously monitor TF and nucleosome dynamics at disease sites just from plasma that can enable real-time monitoring of disease phenotype in a minimally invasive manner. Citation Format: Satyanarayan Rao, Amy Han, Alexis Zukowski, Etana Kopin, Peter Kabos, Srinivas Ramachandran. Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2611.

TP53 Targeted Deep Sequencing of Cell-Free DNA in Esophageal Squamous Cell Carcinoma Using Low-Quality Serum: Concordance with Tumor Mutation.

Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) and residents of the Asian cancer belt are examples of those malignancies and populations. Previous epidemiological studies using cfDNA have pointed to the need for high volumes of good quality plasma (i.e., >1 mL plasma with 0 or 1 cycles of freeze-thaw) rather than archival serum, which is often the main available source of cfDNA in retrospective studies. Here, we have investigated the concordance of TP53 mutations in tumor tissue and cfDNA extracted from archival serum left-over from 42 cases and 39 matched controls (age, gender, residence) in a high-risk area of Northern Iran (Golestan). Deep sequencing of TP53 coding regions was complemented with a specialized variant caller (Needlestack). Overall, 23% to 31% of mutations were concordantly detected in tumor and serum cfDNA (based on two false discovery rate thresholds). Concordance was positively correlated with high cfDNA concentration, smoking history (p-value = 0.02) and mutations with a high potential of neoantigen formation (OR; 95%CI = 1.9 (1.11–3.29)), suggesting that tumor DNA release in the bloodstream might reflect the effects of immune and inflammatory context on tumor cell turnover. We identified TP53 mutations in five controls, one of whom was subsequently diagnosed with ESCC. Overall, the results showed that cfDNA mutations can be reliably identified by deep sequencing of archival serum, with a rate of success comparable to plasma. Nonetheless, 70% non-identifiable mutations among cancer patients and 12% mutation detection in controls are the main challenges in applying cfDNA to detect tumor-related variants when blindly targeting whole coding regions of the TP53 gene in ESCC.

CfDNA in exhaled breath condensate (EBC) and contamination by ambient air: toward volatile biopsies

Exhaled breath is a source of volatile and nonvolatile biomarkers in the body that can be accessed non-invasively and used for monitoring. The collection of lung secretions by conventional methods such as bronchoalveolar lavage, induced sputum collection, and core biopsies is limited by the invasive nature of these methods. Non-invasive collection of exhaled breath condensate (EBC) provides fluid samples that are representative of airway lining fluids. Various volatile and nonvolatile biomarkers can be detected in volatile condensates, such as H2O2, nitric oxide, lipid mediators, cytokines, chemokines, DNA, and microRNAs. Studies have examined cell-free DNA (cfDNA) in plasma samples from non-small-cell lung cancer patients, offering to new insights and fostering development of the liquid biopsy. However, few studies have examined cfDNA in EBC samples. This study examined whether EBC is an appropriate source of cfDNA using housekeeping-gene-specific primer probes and quantitative real-time polymerase chain reaction in healthy subjects. Ambient (room) air is contaminated with DNA, so caution is needed. Preliminary studies indicated that volatile biopsies are becoming an important diagnostic tool in lung cancer.

Cell-free DNA: the role in pathophysiology and as a biomarker in kidney diseases.

Cell-free DNA (cfDNA) is present in various body fluids and originates mostly from blood cells. In specific conditions, circulating cfDNA might be derived from tumours, donor organs after transplantation or from the foetus during pregnancy. The analysis of cfDNA is mainly used for genetic analyses of the source tissue -tumour, foetus or for the early detection of graft rejection. It might serve also as a nonspecific biomarker of tissue damage in critical care medicine. In kidney diseases, cfDNA increases during haemodialysis and indicates cell damage. In patients with renal cell carcinoma, cfDNA in plasma and its integrity is studied for monitoring of tumour growth, the effects of chemotherapy and for prognosis. Urinary cfDNA is highly fragmented, but the technical hurdles can now be overcome and urinary cfDNA is being evaluated as a potential biomarker of renal injury and urinary tract tumours. Beyond its diagnostic application, cfDNA might also be involved in the pathogenesis of diseases affecting the kidneys as shown for systemic lupus, sepsis and some pregnancy-related pathologies. Recent data suggest that increased cfDNA is associated with acute kidney injury. In this review, we discuss the biological characteristics, sources of cfDNA, its potential use as a biomarker as well as its role in the pathogenesis of renal and urinary diseases.

Liquid biopsy in colon cancer: comparison of different circulating DNA extraction systems following absolute quantification of KRAS mutations using Intplex allele-specific PCR.

Non-invasive molecular analysis of circulating tumor DNA (ctDNA) is a promising application in personalized cancer management, although there is still much to learn about the biological characteristics of ctDNA. The present study compared absolute amounts of KRAS mutated ctDNA and total circulating cell-free DNA (cfDNA) in colorectal cancer (CRC) patients (n=50) from various stages and healthy controls (n=8) by Intplex allele-specific and digital droplet PCR. In addition, the impact of two prominent extraction techniques (silica-based membrane vs. magnetic beads) on cfDNA and ctDNA recovery was analyzed in 38 paired samples from CRC patients and specific spike-in DNA controls. CfDNA fragment size was assessed using the Agilent 2100 Bioanalyzer. Relative quantities of total cfDNA quantities were measured using the Qubit fluorometer. Statistical analysis on total cfDNA yield revealed a strong correlation (r=0.976) between Qubit and absolute Intplex allele-specific PCR measurements in cancer patients and healthy controls. Total cfDNA was significantly increased in cancer patients compared to healthy controls, with the highest yield in distant metastatic disease. In line, the highest amount of ctDNA (1.35 ng/μL) was found in patients with distant organ metastasis. Of great interest, the silica-based membrane method significantly promoted extraction of long cfDNA fragments. In contrast, the magnetic bead system more efficiently recovered short cfDNA fragments in serum of cancer patients. Further, a decreased KRAS allele frequency was observed in serum compared to plasma. This study suggests that the source of cfDNA and choice of pre-analytical extraction systems needs to be more carefully validated in routine clinical practice.

New evidence that a large proportion of human blood plasma cell-free DNA is localized in exosomes.

Cell-free DNA (cfDNA) in blood is used as a source of genetic material for noninvasive prenatal and cancer diagnostic assays in clinical practice. Recently we have started a project for new biomarker discovery with a view to developing new noninvasive diagnostic assays. While reviewing literature, it was found that exosomes may be a rich source of biomarkers, because exosomes play an important role in human health and disease. While characterizing exosomes found in human blood plasma, we observed the presence of cfDNA in plasma exosomes. Plasma was obtained from blood drawn into K3EDTA tubes. Exosomes were isolated from cell-free plasma using a commercially available kit. Sizing and enumeration of exosomes were done using electron microscopy and NanoSight particle counter. NanoSight and confocal microscopy was used to demonstrate the association between dsDNA and exosomes. DNA extracted from plasma and exosomes was measured by a fluorometric method and a droplet digital PCR (ddPCR) method. Size of extracellular vesicles isolated from plasma was heterogeneous and showed a mean value of 92.6 nm and a mode 39.7 nm. A large proportion of extracellular vesicles isolated from plasma were identified as exosomes using a fluorescence probe specific for exosomes and three protein markers, Hsp70, CD9 and CD63, that are commonly used to identify exosome fraction. Fluorescence dye that stain dsDNA showed the association between exosomes and dsDNA. Plasma cfDNA concentration analysis showed more than 93% of amplifiable cfDNA in plasma is located in plasma exosomes. Storage of a blood sample showed significant increases in exosome count and exosome DNA concentration. This study provide evidence that a large proportion of plasma cfDNA is localized in exosomes. Exosome release from cells is a metabolic energy dependent process, thus suggesting active release of cfDNA from cells as a source of cfDNA in plasma.

Abstract 5391: Low frequency variant detection and tissue-of-origin exploration using liquid biopsies

Abstract The promise of liquid biopsy assays lies in the non-invasive monitoring of diseases, such as cancer, through circulating, cell-free DNA (cfDNA) or circulating tumor cell DNA. This may assist in advancing early-stage diagnosis while simultaneously monitoring treatment response over time. Since these materials are often limited, most liquid biopsy assays incorporate targeted sequencing to enable cost-effective deep coverage of target loci for detection of low frequency pathogenic variants. Yet a critical aspect in attaining the necessary sensitivity is an assay that produces uniform, comprehensive coverage from low DNA input quantities. We have developed a liquid biopsy workflow to enable low frequency variant detection from a 10 mL blood draw using the Promega Maxwell RSC combined with Swift Biosciences Accel-NGS 2S® library preparation methodologies. In addition, we explore whether methylation patterns of the extracted cfDNA possess information of the tissue-of-origin. Whole blood samples were collected in Streck cell-free DNA BCT vials from patients with late stage cancer and cfDNA was extracted with the Promega Maxwell RSC. This instrument yielded DNA outputs ranging from 8-32 ng, with a size profile defined by a predominant peak of ~170bp and a mean Alu repeat qPCR integrity score of 0.22, characteristic of high quality cfDNA lacking cellular DNA content. A total of 20 ng cfDNA was used to make an Accel-NGS 2S Hyb library followed by hybridization capture using Agilent SureSelect Human All Exon probes. The Accel-NGS 2S Hyb Kit exhibits a 90% library conversion rate with cfDNA and provides high complexity libraries with uniform target coverage. In addition, molecular barcodes were incorporated to label each library molecule uniquely prior to PCR amplification. These molecular barcodes were utilized for accurate removal of PCR duplicates while simultaneously preserving naturally occurring fragmentation and strand duplicates to maximize data recovery. Secondly, these barcoded molecules were grouped to generate consensus sequences after removal of false positives originating from PCR and sequencing errors. Variant calling was performed using Vardict and Lofreq enabling highly sensitive and precise detection of variants down to a 0.5% allele frequency. In parallel, we have developed a workflow to determine if the epigenetic status of cfDNA can identify tissue-of-origin. This workflow utilizes the Accel-NGS Methyl-Seq DNA Library Kit to enable unbiased characterization from low (5 ng) cfDNA inputs. Through whole genome bisulfite sequencing, using a priori knowledge of differentially methylated regions characteristic of different human tissues, we can identify the predominant tissue source of cfDNA in blood. Citation Format: Justin S. Lenhart, Ashley Wood, Sukhinder Sandhu, Cassie Schumacher, Laurie Kurihara, Vladimir Makarov, Tim Harkins. Low frequency variant detection and tissue-of-origin exploration using liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5391. doi:10.1158/1538-7445.AM2017-5391

Abstract 421: Non reportable results - maternal neoplasm can alter results from non-invasive prenatal testing (NIPT)

Abstract Cell free DNA is a powerful new analyte for the detection of chromosomal abnormalities of fetuses from the plasma of pregnant women. In non-invasive prenatal testing (NIPT), cfDNA is contributed into the plasma by the placenta. In rare cases, these results are distorted by additional sources of cfDNA in the maternal bloodstream. For example, organ transplantation can severely affect the cfDNA levels and lead to uninterpretable results. Another source of cfDNA that can lead to similar difficulties and ultimately to a non-reportable NIPT results, can be a maternal neoplasm. In our clinical laboratory, we have processed samples from over 450,000 pregnant patients. In cases of uninterpretable findings due to aberrant genomic profiles, potential reasons for non-reportable results were discussed with the caregiving physician. When feedback about these cases was available, it was collected in a database. In summary, we observed non-reportable NIPT results with aberrant genomic profile for 55 cases. A set of 43 had sufficient information available to allow inclusion in this summary. In 40 cases, a maternal neoplasm was confirmed (18 malignant, 20 benign, and two with imaging but without pathological confirmation). These observational results support further investigation by prospective controlled trials. Citation Format: Daniel Grosu, Nilesh G. Dharajiya, Ron M. McCullough, Youting Sun, Juan-Sebastian Saldivar, Dirk van den Boom, Mathias Ehrich. Non reportable results - maternal neoplasm can alter results from non-invasive prenatal testing (NIPT). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 421.

Adjustments to the preanalytical phase of quantitative cell-free DNA analysis.

Evaluating the kinetics of cell-free DNA (cfDNA) in the blood of cancer patients could be a strong auxiliary component to the molecular characterization of cfDNA, but its potential clinical significance is obscured by the absence of an analytical consensus. To utilize quantitative cfDNA assessment with confidence, it is crucial that the preanalytical phase is standardized. In a previous publication, several preanalytical variables that may affect quantitative measurements of cfDNA were identified, and the most confounding variables were assessed further using the growth medium of cultured cancer cells as a source of cfDNA (“Cell-free DNA: Preanalytical variables” [1]). The data accompanying this report relates to these experiments, which includes numerous changes to the sample handling and isolation protocols, and can be used for the interpretation of these results and other similar experiments by different researchers.

Evaluation of Clinical Laboratory Methods for Plasma Cell-Free DNA Analysis in Suspected Septicaemia

Background: The amount and quality of plasma cell free DNA (cfDNA) changes in extreme physiological and pathological conditions. These changes could provide a basis for a novel prognostic biomarker in conditions as diverse as pregnancy, cancer, organ transplantation and septicaemia. Evaluation of current methods for cfDNA analysis is needed to identify the best practical approach to medical diagnostics. Methods: Initially, cf DNA was extracted from plasma of nine patients with febrile illness using both QIAamp Circulating Nucleic Acid and QI Aamp Mini Blood DNA kits. CfDNA concentration was determined by β-globin qPCR using PerfeCta and AmpliTaq mixes. Subsequently, Qubit fluorimetric and gel-on-a-chip assays were used to analyse plasma cfDNA from 64 additional patients with suspected septicaemia and positive blood cultures. Results: Determination of CfDNA concentration by β-globin gene qPCR using AmpliTaq mix was superior to the PerfeCta qPCR. Moreover, unlike PerfeCta AmpliTaq qPCR determined similar genome equivalent copy numbers in cfDNA isolated by either DNA extraction method. QIAamp Mini Blood kit and AmpliTaq qPCR were subsequently used in a larger prospective study for cfDNA isolation and quantification, respectively. However, qPCR was less suited for the detection of high plasma cfDNA levels when compared to direct DNA measurement by Qubit (mean 22.23 ng/ mL vs. 61.38 ng/mL, respectively) despite good correlation between the two methods. The DNA microfluidic chip method was then used to determine cfDNA fragments sizes and their relative concentrations revealing a presence of nucleosome-sized DNA fragments that were in strongly positive correlation with total cfDNA. Furthermore, apoptotic DNA was identified as a major DNA component in plasma with high cfDNA content. Conclusions: β-globin qPCR is more suited to detection of low plasma cfDNA concentrations, while the Qubit assay is a better choice for rapid identification of high plasma concentrations. Apoptosis is a major source of cfDNA in plasma with high cfDNA concentrations based on DNA chip analysis.

Superoxide Dismutase 2 (Sod2) is Overexpressed at an Early Stage During Colorectal Carcinogenesis: A Putative Target for Celecoxib Chemoprevention

Background: The occurence of circulating epithelial cells and cell-free tumor DNA (cfDNA) in peripheral blood of patients suffering from progressive forms of cancers has first been reported already in 1960s. With the great acceleration of genetic diagnostics by methods of polymerase chain reaction (PCR) the field of non-invasive examination of circulating molecular cancer biomarkers has recently been re-discovered. Aims: To investigate occurence of cfDNA as potential marker of regional and distant metastatic progression of colorectal cancer and to trace the source of cfDNA in patients undergoing surgery treatment at different levels of radicality. Methods: In a group of 165 patients in various stages of the disease tissue samples were initially acquired either as biopsies or resections. Samples were tested for a presence of the most frequent somatic colorectal cancer mutations within KRAS, APC, TP53, BRAF and PIK3CA genes. In addition, multiple plasma samples (n=789) were acquired over a time period covering (i) initial examination, (ii) immediately preceding a surgery (iv) postsurgery and (v) subsequent follow-up. Cell-free tumor DNA was traced in patient plasma by targeting mutations previously detected in tumor tissue. Results: Among patients who were positive for at least one of the detected somatic mutations in tumor tissue (102/165, 62%), cfDNA was present in 39 pre-surgery plasma samples. The frequency of cfDNA was correlated to the disease stage with 0% in Stages 0 and I, 9% in Stage II, 29% in Stage III and 94% in Stage IV. All cfDNA-positive patients (n=21) who underwent radical resection (R0) were free of cfDNA in subsequent testing of samples several days following surgery. All but 4 patients undergoing non-radical surgery, such as partial hepatic resections or paliative surgical treatment, remained cfDNA-positive also after the surgery. In some of the R0 patients, the cfDNA has re-appeared after a period of 18 22 months as a result of disease progression though local nodes or newly discovered metastases with continuous monitoring of the remainder of the group still in progress. Conclusion: Examination of a presence of cfDNA based on scanning plasma samples for presence of specific tumor mutations is a suitable tool for non-invasive monitoring of the disease progression as well as evaluation of surgery outcome. Supported by Czech Ministry of Health grant no. NS9809.