Your browser does not fully support modern features. Please upgrade for a smoother experience.
Submitted Successfully!
Thank you for your contribution! You can also upload a video entry or images related to this topic. For video creation, please contact our Academic Video Service.
Version Summary Created by Modification Content Size Created at Operation
1 Maria Panagopoulou + 4086 word(s) 4086 2021-03-11 03:54:14 |
2 format correction Peter Tang -1 word(s) 4085 2021-03-14 10:27:24 |

Video Upload Options

We provide professional Academic Video Service to translate complex research into visually appealing presentations. Would you like to try it?
Cite
If you have any further questions, please contact Encyclopedia Editorial Office.
Panagopoulou, M. Circulating Cell-Free DNA in BC. Encyclopedia. Available online: https://encyclopedia.pub/entry/7976 (accessed on 16 January 2026).
Panagopoulou M. Circulating Cell-Free DNA in BC. Encyclopedia. Available at: https://encyclopedia.pub/entry/7976. Accessed January 16, 2026.
Panagopoulou, Maria. "Circulating Cell-Free DNA in BC" Encyclopedia, https://encyclopedia.pub/entry/7976 (accessed January 16, 2026).
Panagopoulou, M. (2021, March 12). Circulating Cell-Free DNA in BC. In Encyclopedia. https://encyclopedia.pub/entry/7976
Panagopoulou, Maria. "Circulating Cell-Free DNA in BC." Encyclopedia. Web. 12 March, 2021.
Circulating Cell-Free DNA in BC
Edit

Breast cancer (BC) is the most common cancer among women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan.

breast cancer biomarker circulating cell-free DNA liquid biopsy prognosis monitoring

1. Introduction

Breast cancer (BC) remains in the very top of female oncology entities, with over 2 million new cases globally in 2018 [1]. BC is a heterogeneous disease of varying progression, while drug resistance and metastasis greatly reduce the survival rates. Current diagnostic/monitoring methods include mammography, ultrasound, tru-cut biopsy and ΜRI/CT scan. These techniques have several drawbacks (e.g., not suitable for all patients, low sensitivity and specificity, invasive and expensive).

Circulating biomarkers have been gaining ground as easy, minimally invasive choices for disease follow-up. The carcinogenic antigen CA 15-3 remains the “gold standard” for disease and therapy monitoring, although inadequate in sensitivity and specificity [2][3]. The FDA has recently approved the CellSearch system for measuring circulating cancer cells (CTCs), but only in metastatic disease [4][5]. Also, Oncotype DX, a 21-gene transcript-based assay, is currently used as a prognostic tool and for personalized treatment options in early stage ER + BC [6]. As an alternative, ccfDNA is currently the spearhead in biomedical research and provides the choice of non-invasive repetitive sampling for cancer monitoring. However, still limited clinical implementation [7], while a better understanding of its biology is expected to create an opportunity for its optimal exploitation in clinical routine. In the present review, we summarize the growing evidence that support this view, focusing in data specific for BC. Besides articles referring to ccfDNA, we also include findings from studies from other circulating complexes that contribute to the ‘pool’ of the ccfDNA, such as nucleosomes, vitrosomes and extracellular vesicles. Aberrant genetic alternations detected in ccfDNA are omitted, as thoroughly recently reviewed elsewhere [8][9].

2. Liquid Biopsy

During the life span of a tumor, cancer cells change constantly, acquiring genetic and epigenetic modifications and forming clones with different survival advantage resulting in the heterogeneity of cancer cell population [10][11]. The idea of discovering tools depicting these changes and monitoring them in «real time» is of obvious importance. Liquid biopsy is a minimally invasive approach in oncology, using peripheral blood as a source of biological material escaping the tumor and enriching circulation, such as ccfDNA, circulating tumor cells (CTCs) or extracellular vesicles (EVs) and platelets, assuming that they carry identical molecular characteristics of the parental tumor [12][13]. Liquid biopsies could reflect the heterogeneity of a primary tumor or the molecular evolution of a distant metastatic lesion, which is impossible using the conventional tissue biopsies. Another significant advantage is that upon sequential sampling due to its minimally invasive nature, it is possible to dynamically monitor disease and drug resistance acquisition. This approach could therefore offer a powerful tool in the field of clinical oncology of recognized value [14][15]. The initial steps on its actual implementation in clinical practice are taken and are expected to move forward longitudinally in the starting decade.

3. Circulating Cell-Free DNA

The first demonstration of circulating DNA in the bloodstream of healthy individuals was done by Mendel and Métais in 1948 [16]. Thirty years later, it was shown that the concentration of ccfDNA from cancer patients is greater than that from healthy individuals [17]. In 1989, Stroun et al. identified fragments of circulating DNA originating from cancer cells in the bloodstream, based on a technique that identified decreased strand stability [18]. These hallmarks brought circulating DNA in the center of the biomarker discovery field to aid precision medicine.

ccfDNA is DNA liberated from cells into biological fluids, e.g., blood, lymph, bile, milk, urine, saliva, mucous suspension, spinal fluid [19]. It is double or single stranded and can be either of nuclear or mitochondrial origin. In health, ccfDNA is mainly released from cells like hematopoietic, whereas in disease, it is enriched also from pathological tissues. Cancerous ccfDNA is called circulating tumor DNA (ctDNA) and represents only a fraction of the total ccfDNA in the blood [20]. ctDNA is liberated from tumor cells, metastatic sites and CTCs and it has been proved to reflect dynamically the genetic and epigenetic events in the tumor’s lifetime [21]. The detection of mutations, Loss of heterogeneity (LOH) and aberrant methylation is considered a mean of identification of the ctDNA fraction and could serve as diagnostic/prognostic/predictive indicators [14][22][23]. Minimally invasive consecutive sampling might therefore represent dynamically genetic and epigenetic characteristics of the tumor presenting a clear advantage over established biomarkers.

4. Methylation of ccfDNA

DNA methylation is defined as the covalent addition of a methyl group at the 5-carbon of the cytosine ring by DNA methyltransferases (DNMTs), mostly within CpG dinucleotides [24]. It is a well-defined epigenetic mechanism contributing to gene expression regulation [25]. DNA methylation is related to a variety of normal functions [24][26]. Also, promoter methylation of susceptible genes is associated with cancer [27][28][29] as well as hypomethylation [30] and their evaluation has been suggested as a potential clinical biomarker [31][32]. ccfDNA released from tumor cells has been shown to retain its epigenetic features [33][34]. Studies in multiple types of solid tumors have investigated the methylation profile of ccfDNA to evaluate its diagnostic, prognostic and predictive potential and add in their clinical management [14][22]. In breast cancer, the first documentation of aberrant methylation of ccfDNA was by Silva JM et al., in 1999, detecting the methylation of P16INK4A in plasma and in the corresponding tumor, indicating its cancer origin [35]. Since then, many studies reviewed below, have been performed to evaluate liquid methylation biomarkers in breast cancer associated with different clinical endpoints (Table 1). They differ significantly in the pre-analytical protocols for ccfDNA isolation as well as the methodology adopted for methylation detection assays and are often limited in a small cohort, still they accumulatively show that there is valuable information there awaiting further exploitation.

Table 1. Summary of studies evaluating ccfDNA methylation in BC diagnosis, prognosis and treatment response.

Table

Study Group

Clinical End-Point

Findings

References

Diagnostic Biomarkers

P16INK4A

- 35 BC patients

 

Tumor-related origin of ccfDNA

[35]

HIC-1, RARβ2, RASSF1A

-

20 BC women

-

15 women with fibroadenoma

-

10 healthy women

BC diagnosis

RARβ2 and RASSF1A methylation in combination with ccfDNA quantitative analysis could discriminate malignant from non-malignant disease.

[36]

gene panel

-

250 BC women

-

237 cancer-free women

-

59 women with benign breast disease

-

58 colon cancer women

BC diagnosis

ITIH5, DKK3, and RASSF1A methylation was correlated to early diagnosis

[37]

CST6

-

27 women with operable BC

-

46 women with MBC

-

37 healthy women

-

an independent cohort of 123 women with operable BC

clinicopathological parameters and outcome

CST6 is highly methylated in BC ccfDNA and could serve as biomarker

[38]

BRCA1, MGMT, GSTP1

-

100 BC women

-

30 healthy women

clinicopathological parameters and prognosis (DFS, OS)

Concordance between

tumor and ccfDNA methylation of BRCA1, MGMT, GSTP1, correlation between MGMT protein loss and promoter hypermethylation, prognostic value of BRCA1,GSTP1 methylation in ccfDNA

[39]

Gene panel

-

44 BC patients

-

39 healthy individuals

clinicopathological parameters and outcome(DFS, DSS), diagnosis

Diagnostic value of APC, FOXA1 and RASSF1A methylation of ccfDNA in BC (over 70% sensitivity, specificity)

[40]

Gene panel

-

108 BC women

-

72 CC women

-

73 LC women

Diagnosis of BC, CC and LC, correlation to clinical parametes

«PanCancer» panel (APC, FOXA1, RASSF1A) for detecting cancer (72% sensitivity and 74% specificity) and «CancerType» panel (SCGB3A1, SEPT9, SOX17) indicating cancer topography (over 80% specificity), RASSF1A and RARβ2 methylation correlated to clinical parameters in BC

[41]

Gene panel

-

86 BC patients

-

67 healthy women

BC diagnosis

EGFR, PPM1E and 8 gene-specific CpG sites were significantly hypermethylated in BC with sufficient performance for breast cancer detection (AUC 0.66 TO 0.75)

[42]

Methylation array

-

Public methylation data (32 normal people, 5 BC women and patients with other cancer types)

BC diagnosis

CancerLocator tool for determining presence and location of BC

[43]

9223 CpG sites

-

15 BC

-

22 NSCLC

-

12 Melanoma

-

29 CC patients

BC diagnosis, prognosis (OS), response to treatment (TTF)

Methylation scores could detect BC and classify the underlying cancer type with high accuracy (91.7% and 72.7% respectively), low methylation scores were associated with longer OS

[44]

Prognostic Biomarkers

Gene panel

- 101 BC women

Prognosis (OS, DFS), correlation to clinicopathological parameters

High methylation of seven genes was correlated to poor prognosis, Methylation of p16INK4A, BRCA1, GSTP1, PRB and RARβ2 were associated with unfavorable clinical parameters

[45]

ESR1

- 110 BC women

Correlation to clinicopathological parameters

High methylation of ESR1 was associated with ER negative receptor status and phenotypes with poor prognosis and could predict treatment response.

[46]

GSTP1, RASSF1A, RARβ2

- 336 ΒC women

Correlation to clinicopathological parameters, prognosis (OS, DFS)

Positive methylation of at least one of the three genes and high ccfDNA levels were associated with worse DFS and OS

[47]

GSTP1, RASSF1A, RARβ2

- 120 BC women

Correlation to clinicopathological parameters, prognosis (OS, DFS) and response to treatment

Positive methylation of at least one of the three genes and high ccfDNA levels were associated with worse DFS and OS and no response to treatment

[48]

Six BC specific DNAme patterns

-

460 women who developed BC within three years after serum donation

-

465 women who did not develop cancer the following five years

Prognosis (OS, DFS) and response to treatment

EFC#93 serum DNAme positivity was a poor prognostic factor and correlated to response to anti-hormonal treatment

[49]

Gene panel

-

200 BC women

-

35 healthy women

BC diagnosis, prognosis (OS, DFS) and treatment response

Methylation of SOX17, WNT5A, KLK10 was correlated to poor prognosis and two specific classifiers were constructed for prognosis of patients with metastatic BC (AUC 0.737). Another classifier could sufficiently discriminate BC disease (AUC 0.844). Positive methylation of at least 4 of any studied gene was correlated to the absence of chemotherapy response

[50]

Predictive Biomarkers

Gene panel

-

40 BC women (six sequential sera samples from each)

-

30 healthy women

Neoadjuvant treatment response, correlation to clinicopathological parameters

BRCA1 methylation status discriminate responders from non-responders

[51]

RASSF1A

-

148 BC patients (pretherapeutic and one-year-after surgery sampling)

Correlation to clinicopathological parameters, monitoring of adjuvant tamoxifen therapy response, prognosis (OS, DFS)

Methylation of RASSFIA was correlated to poor prognosis and resistance in tamoxifen treatment

[52]

ESR1, STRATIFIN

- 111 BC patients

Development of metastasis, response to treatment

Methylation of STRATIFIN could discriminate metastatic BC patients form those who were cancer free and was associated to treatment response (75% sensitivity and 66.7% specificity)

[53]

Gene panel

- 20 BC patients (sequential sampling)

Treatment monitoring

Methylation of PR, PROX, MDGI, PAX 5 and RARβ2 was diminished after surgery, especially in the combined treatment group (surgery and tamoxifen treatment). Surgery alone decreased methylation in PAX5 and RARβ2, while tamoxifen treatment changed ESR1 methylation

[54]

Gene panel (cMethDNA)

-

28 healthy, 24 BC women (training set)

-

27 healthy, 33 BC (Test set)

Treatment response

Cancer-specific methylated DNA was detected in recurrent stage ΙV BC patients (91% sensitivity and 96%specificity) and cMethDNA assay could reflect treatment response

[55]

Whole-genome bisulfite sequencing

-

80 BC patients

-

40 healthy individuals

Prediction of recurrence

Identification of 21 DNA hypermethylation hotspots associated with metastatic BC.

[56]

BC = Breast Cancer; CC = Colon Cancer; ccfDNA = circulating cell-free DNA; DFS = Disease Free Survival; DSS = Disease Specific Survival; LC = Lung Cancer; MBC = Metastatic Breast Cancer; NSCLC = Non-Small Cell Lung-Cancer; OS = Overall Survival; TTF = Time to Treatment Failure.

5. Hypomethylation in Breast Cancer

Breast cancer cells are highly hypomethylated [57][58][59] and global hypomethylation is correlated to clinicopathological characteristics of breast lesions [59]. A possible mechanism for DNA methylation loss in BC is through the formation of repressive chromatin at partially methylated domains (PMD) [60]. A recent study in BC reported that hypomethylation in PMD occurs in large fractions of the genome that display genetic and epigenetic alterations [61]. Only a few studies have investigated global hypomethylation of ccfDNA in BC. Genome-wide approaches have proved that ccfDNA is hypomethylated in metastatic breast cancer (MBC) [56][62]. Global hypomethylation was also detected in the plasma of BC patients by massively parallel bisulfite sequencing, which could be an attractive approach for diagnosis and disease monitoring [63].

6. Other Parameters of ccfDNA in Breast Cancer

The research on the development of ccfDNA-based biomarkers in cancer is not limited to the analysis of its sequence for identifying alterations (DNA methylation, mutations, LOH, etc.). Below, we present data from the study of other parameters such as quantity, protein content, integrity, release mechanism, etc. important features that could lead to the development of multi-parametric prognostic and predictive biomarkers in BC.

6.1. Quantity of ccfDNA

As aforementioned, small quantities of ccfDNA are detected in the plasma/serum of healthy individuals, but its concentration is notably increased in cancer or other pathological conditions [64][65]. The quantity of tumor-derived ccfDNA in the bloodstream differs and depends on tumor size and cancer type (blood-barrier in brain tumors). Also, it has been mentioned that DNAase activity often impaired in cancer patients is correlated to ccfDNA concentrations [66]. Clearance rates in liver, spleen, kidney and to a less extend degradation from blood nucleases are additional factors affecting quantity [67][68][69], while the half-life of ccfDNA could last from 15 min to a couple of hours [19].

Besides other characteristics, quantity of ccfDNA is by itself a parameter with potential value for diagnosis, classification and treatment monitoring. Several techniques have been proposed for total ccfDNA level measurements in blood, either direct in unpurified plasma [50][70][71] or after DNA isolation [72][73]. In our recent work in BC, we measured ccfDNA quantity directly, using a SYBR Green-based/Qubit assay; it is important to note that by this method, only free unbound ccfDNA is measured, as assay SYBR Green dye can only bind to free/naked DNA. In contrast, after isolation, all ccfDNA (naked, bound in nucleosomes, proteins or internalized in vesicles) is extracted and measured. The techniques mostly used so far for ccfDNA quantification is quantitative PCR (qPCR) in BC for the short and long sequences ALU115/247 [74][75] and LINE1 sequences [76] or using the reference gene GAPDH [77][78]. Both methods have repetitively confirmed higher ccfDNA levels in BC in relation to healthy individuals [73][75][76][78][79][80][81][82][83][84][85][86][87]. Increased levels of ccfDNA in BC have also been correlated to metastasis [50][75][80], tumor size [73][76][77][78], other histopathological parameters [73][83] and BC outcome [50][84]. In our recent study, elevated levels of ccfDNA were correlated to the incidence of death, shorter PFS and non-response to pharmacotherapy in metastatic patients [50]. Most interestingly from a clinical aspect is the construction of a single-parametric linear model using ccfDNA plasma concentration values with great discriminating power to predict response to chemotherapy [50]. However, in our patient group we did not detect correlations of quantity to clinicopathological parameters, possibly due to the different quantification methods and patient classification criteria, in concordance with some researchers [80][82]. Other studies have assessed the ccfDNA quantity in relation to diagnosis. In a study, researchers developed a qPCR assay using telomere, centromere and LINE primers and showed that the shortening of telomeric ccfDNA in plasma was correlated to BC [88]. The circulating levels of the longer fragment of ALU247 have also been shown to hold a diagnostic potential, shown to discriminate the cancer from non-cancer subjects [81]. Also, it has been shown that ccfDNA was superior to other circulating biomarkers in detecting BC. it has been found that ccfDNA as measured by qPCR for the GAPDH gene, was superior to serum vascular endothelial growth factor measured by ELISA in discriminating healthy from BC women [89]. A study in MBC showed that ccfDNA was superior to CTCs or CA 15-3 for disease monitoring, as levels showed greater correlation with changes in tumor burden and detected earlier than CA 15-3 or CTCs treatment response [90], proving its superiority over other innovative or established circulating biomarkers. This was further confirmed by studies using ALU and LINE1 levels to quantify ccfDNA [91][92]. It was earlier proposed that cancerous ccfDNA fragment measurements could serve as a reliable tool to monitor tumor dynamics in the course of disease and therapy [15] and indeed a recent meta-analysis of 13 studies concluded that the concentration of ccfDNA had great sensitivity and specificity [87% (95% CI, 73–94%) and 87% (95% CI, 79–93%), respectively] for BC diagnosis [93]. Furthermore, Catarino et al. using a real-time PCR probe assay for the hTERT gene, quantified ccfDNA of BC patients before and after surgery. They showed that ccfDNA levels were significantly decreased after surgery, successfully reflecting the tumor removal [79]. In accordance to that, Agassi et al. used a SYBR Gold-based fluorescence assay for ccfDNA quantification and confirmed that ccfDNA quantity was diminished after tumor resection [94]. Recently, researchers using the same quantification technique found that the reduction of ccfDNA levels were correlated to surgical removal or tumor reduction by chemotherapy, confirming once again previous studies. However, in the same study ccfDNA levels could not discriminate between patients with BC and healthy individuals for diagnostic purposes [95]. Maybe this discrepancy could be attributed to the use of the SYBR Gold-technique for ccfDNA quantification which can be quite sensitive, but lacks in specificity due to RNA interference. Very recently, Moss et al. compared genome wide methylation data of different tissues and cell types and found a breast-unique methylation pattern of three genes (znf296, krt19, lmx1b) which was used to quantify breast derived-ccfDNA in plasma using massive parallel sequencing. This approach could sufficiently discriminate between healthy individuals and cancer patients (AUC: 90.44% (95% CI: 78.51%–100%)), while no breast molecules were identified in healthy individuals. Also, breast derived-cfDNA levels were associated with tumor aggressiveness and a decrease was noticed during neo-adjuvant treatment. Notably, the persistent presence of breast derived-ccfDΝA after treatment indicated the existence of minimal residual disease [96]. This is an excellent proof showing that the tissue specificity of methylation could precisely reflect and monitor tumor burden. A more sophisticated approach for optimal feature selection such as automated machine learning would be a more appropriate methodological choice to deliver tissue specific signatures.

Obviously, high levels of ccfDNA in the bloodstream could be due to the presence of a solid tumor but could also be related to other pathologies such as autoimmune disorders, inflammation and others. Hence, ccfDNA concentration can be proposed to serve diagnostic proposes in BC or reflecting removal of a primary breast tumor only adjunct to other tissue of origin or cancer related markers and clinical manifestations. On the other hand, due to its high sensitivity in MBC and in predicting treatment response [50][90], it could be envisaged to offer a reliable and simple solution for treatment monitoring. Validation in a clinical setting is highly anticipated to speed up application.

6.2. Integrity of ccfDNA

In 1989, Stroun et al. showed that ccfDNA of cancer patients is shorter than the ccfDNA of healthy individuals [18] implying that the study of ccfDNA integrity could aid the discrimination of cancerous ccfDNA from total ccfDNA but also biomarker discovery. Many studies have been conducted analyzing ccfDNA Integrity (cfDI) as the ratio between longer and shorter DNA fragments, with controversial findings so far. The most widely used method for cfDI assessment is the measurement of non-coding DNA integrity, such as repetitive elements ALU and LINE. In a 2006 study, researchers using the ALU247/ALU115 ratio found that patients having breast cancer of stage I, II and III showed greater integrity of ccfDNA as compared to healthy individuals [83]. Similarly, Iqbal et al. showed that ALU247/ALU115 was higher in stage IV breast cancer than in earlier stages and declined after surgery, suggesting it as a clinically relevant prognostic biomarker [84]. Kamel et al. found that cfDI was significantly higher in breast cancer than in benign breast patients and healthy individuals, using different amplicons of β-actin and was correlated to TNM stage [97]. Similar studies have been conducted in breast cancer and other cancer types confirming the finding that cfDI is greater in cancer [83][87][98][99].

These results however were not confirmed by several other studies, showing in contrast that healthy individuals showed greater cfDI than BC patients. Madhavan et al. suggested that it is the reduced cfDI that can serve as diagnostic marker for primary and metastatic breast cancer [100]. In a later study, researchers using the long and short fragment of HER2, MYC, BCAS1 and PI3KCA genes showed that BC patients had lower integrity than healthy individuals [85]. Cheng et al. using the ALU/LINE1 method proved that in BC the cfDI was significantly lower in recurrent patients, discriminating them from the non-recurrent patients [101]. Also, the same researchers reported that MBC patients showed increased cfDI after the first cycle of therapy and that it can be an independent prognostic marker [91] in contrast to earlier findings showing that the distribution of the cfDI in BC patients did not change after adjuvant chemotherapy [102]. Both Cheng’s and Madhavan’s studies used greater BC cohorts [100][101] than previous studies [83], adding to the power of their findings, however this controversial matter needs further elucidation.

Massive parallel sequencing added considerable to the deeper understanding of ccfDNA integrity. Jiang et al. proved that fragments originating from cancer cells were smaller than the fragments from healthy cells in patients with hepatocellular carcinoma. In the same study, patients having greater quantity of cancerous ccfDNA had a more fragmented DNA profile [103], in concordance with two previous studies in metastatic colorectal cancer [104] and pancreatic cancer [105]. In our BC study, we showed via capillary electrophoresis that patients at advanced stage that started neo-adjuvant or first line therapy had fragments sized from 22 to 160 bp, whereas this pattern was not observed in healthy individuals. We also showed that patients with higher total levels of ccfDNA had a greater number of short fragments (<160 bp). Finally, tumor size and the incidence of death were correlated with greater DNA fragmentation [50]. We assume that the pattern of fragments (22 to 160 bp) that we found in advanced BC is the result of degradation after ccfDNA liberation during cell death or active release. Most recently, researchers used a genome-wide approach for analyzing the fragmentation patterns of ccfDNA for early detection of BC and six different cancer types (DELFI study). They found that healthy individual ccfDNA patterns were correlated to nucleosomal DNA fragments originating from lymphocytes, while cancer patient fragmentation patterns were more variable, with shorter median overall length, in concordance with our findings. Most interestingly, using the DELFI approach they could recognize with high sensitivity a specific cancer type among others [106].

cFDI assessment could have a clinical application, although there is still discrepancy between researchers, some claiming that longer fragments represent the tumorous DNA while others the opposite. We assume that the main reason for these controversial findings is the selection of different methods for measuring cfDI (ALU247/ALU115 vs. others), as different fragments are quantified. Other reasons possibly depend on the differences in studied patient groups, with varying disease stage representation. Tumor growth kinetics may cause significant differences in the cellular release of ccfDNA and degradation. The pre-analytical process chosen in each study might as well represent a source of discrepancy, as shown in a study comparing different extraction methods of ccfDNA from plasma (phenol-chloroform isoamyl vs. QIAamp DNA Blood Mini Kit) that found different fragment lengths in the elutant of each method [71]. Despite the fact that ccfDNA is systematically investigated, until now different groups have not agreed to a standard operational pre-analytical procedure (e.g., sample collection, DNA extraction method), leading to variations and often in opposite findings between studies. In conclusion, for valid conclusions drawn from ccfDNA integrity studies, but also in general, it is important for the different methods to be compared in the same cohort of samples, as well as the establishment of a widely-accepted pre-analytical procedure.

6.3. ccfDNA Releasing Mechanism

Both apoptosis [107] and necrosis [65] have been suggested as mechanisms of cellular release of ccfDNA, whereas active release from viable cells [108] has also been described. Different ways of cell death are also sources of ccfDNA. For example, macrophages which engulf and degradate necrotic and apoptotic cells liberate degraded DNA [109]. An ischemic cell death (oncosis) has also been described in cancer [110] and could alternatively release DNA fragments. ccfDNA of 166 bp or multiples (single, di-, tri- and polynucleosomes) is possibly released through apoptosis and is the result of the action of a caspase-dependent endonuclease that cleaves DNA between nucleosomes. It is more or less accepted that the larger fraction of ccfDNA in human plasma is produced via apoptosis [ 109], fragments sized 10,000 or bigger derive from necrosis, while active release delivers a fragments of 2000 bp [111][112], although it is clear that the exact pathways of ccfDNA production in each case still needs to be clarified. Our study evaluated fragment size distribution by capillary electrophoresis and showed all above types of fragments (160 bp, 2000 bp and 10,000 bp) present in the plasma of BC patients, indicating all three releasing mechanisms (apoptosis, active release and necrosis) responsible for the liberation of ccfDNA [50]. This was further confirmed by our in vitro studies using the human breast cancer cell line MCF-7, where fragment—size profiling was indicative of active release, whereas exposure to the demethylating agent 5—AZA—CR induced the release of additional shorter fragments, indicative of apoptosis (see below) [34].

References

  1. Bray, F.; Ferlay, J.; Soerjomataram, I.; Siegel, R.L.; Torre, L.A.; Jemal, A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA A Cancer J. Clin. 2018, 68, 394–424.
  2. Pedersen, A.C.; Sorensen, P.D.; Jacobsen, E.H.; Madsen, J.S.; Brandslund, I. Sensitivity of CA 15-3, CEA and serum HER2 in the early detection of recurrence of breast cancer. Clin. Chem. Lab. Med. 2013, 51, 1511–1519.
  3. Duffy, M.J.; Evoy, D.; McDermott, E.W. CA 15-3: Uses and limitation as a biomarker for breast cancer. Clin. Chim. Acta Int. J. Clin. Chem. 2010, 411, 1869–1874.
  4. Cristofanilli, M. Circulating tumor cells, disease progression, and survival in metastatic breast cancer. Semin. Oncol. 2006, 33, S9–S14.
  5. Bidard, F.C.; Peeters, D.J.; Fehm, T.; Nolé, F.; Gisbert-Criado, R.; Mavroudis, D.; Grisanti, S.; Generali, D.; Garcia-Saenz, J.A.; Stebbing, J.; et al. Clinical validity of circulating tumour cells in patients with metastatic breast cancer: A pooled analysis of individual patient data. Lancet Oncol. 2014, 15, 406–414.
  6. Chen, C.; Dhanda, R.; Tseng, W.Y.; Forsyth, M.; Patt, D.A. Evaluating use characteristics for the oncotype dx 21-gene recurrence score and concordance with chemotherapy use in early-stage breast cancer. J. Oncol. Pract. 2013, 9, 182–187.
  7. Lamb, Y.N.; Dhillon, S. Epi proColon(®) 2.0 CE: A Blood-Based Screening Test for Colorectal Cancer. Mol. Diagn. Ther. 2017, 21, 225–232.
  8. Jansen, M.P.; Martens, J.W.; Helmijr, J.C.; Beaufort, C.M.; van Marion, R.; Krol, N.M.; Monkhorst, K.; Trapman-Jansen, A.M.; Meijer-van Gelder, M.E.; Weerts, M.J.; et al. Cell-free DNA mutations as biomarkers in breast cancer patients receiving tamoxifen. Oncotarget 2016, 7, 43412–43418.
  9. Takeshita, T.; Yamamoto, Y.; Yamamoto-Ibusuki, M.; Tomiguchi, M.; Sueta, A.; Murakami, K.; Iwase, H. Clinical significance of plasma cell-free DNA mutations in PIK3CA, AKT1, and ESR1 gene according to treatment lines in ER-positive breast cancer. Mol. Cancer 2018, 17, 67.
  10. Gupta, G.P.; Massagué, J. Cancer metastasis: Building a framework. Cell 2006, 127, 679–695.
  11. Chaffer, C.L.; Weinberg, R.A. A perspective on cancer cell metastasis. Science 2011, 331, 1559–1564.
  12. Mader, S.; Pantel, K. Liquid Biopsy: Current Status and Future Perspectives. Oncol. Res. Treat. 2017, 40, 404–408.
  13. Speicher, M.R.; Pantel, K. Tumor signatures in the blood. Nat. Biotechnol. 2014, 32, 441–443.
  14. Balgkouranidou, I.; Chimonidou, M.; Milaki, G.; Tsaroucha, E.; Kakolyris, S.; Georgoulias, V.; Lianidou, E. SOX17 promoter methylation in plasma circulating tumor DNA of patients with non-small cell lung cancer. Clin. Chem. Lab. Med. 2016, 54, 1385–1393.
  15. Diehl, F.; Schmidt, K.; Choti, M.A.; Romans, K.; Goodman, S.; Li, M.; Thornton, K.; Agrawal, N.; Sokoll, L.; Szabo, S.A.; et al. Circulating mutant DNA to assess tumor dynamics. Nat. Med. 2008, 14, 985–990.
  16. Mandel, P.; Metais, P. Nuclear Acids in Human Blood Plasma. Comptes Rendus Seances Soc. Biol. Fil. 1948, 142, 241–243.
  17. Leon, S.A.; Shapiro, B.; Sklaroff, D.M.; Yaros, M.J. Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res. 1977, 37, 646–650.
  18. Stroun, M.; Anker, P.; Maurice, P.; Lyautey, J.; Lederrey, C.; Beljanski, M. Neoplastic characteristics of the DNA found in the plasma of cancer patients. Oncology 1989, 46, 318–322.
  19. Fleischhacker, M.; Schmidt, B. Circulating nucleic acids (CNAs) and cancer—A survey. Biochim. Biophys. Acta 2007, 1775, 181–232.
  20. Kidess, E.; Jeffrey, S.S. Circulating tumor cells versus tumor-derived cell-free DNA: Rivals or partners in cancer care in the era of single-cell analysis? Genome Med. 2013, 5, 70.
  21. Lu, J.L.; Liang, Z.Y. Circulating free DNA in the era of precision oncology: Pre- and post-analytical concerns. Chronic Dis. Transl. Med. 2016, 2, 223–230.
  22. Matthaios, D.; Balgkouranidou, I.; Karayiannakis, A.; Bolanaki, H.; Xenidis, N.; Amarantidis, K.; Chelis, L.; Romanidis, K.; Chatzaki, A.; Lianidou, E.; et al. Methylation status of the APC and RASSF1A promoter in cell-free circulating DNA and its prognostic role in patients with colorectal cancer. Oncol. Lett. 2016, 12, 748–756.
  23. Anker, P.; Lefort, F.; Vasioukhin, V.; Lyautey, J.; Lederrey, C.; Chen, X.Q.; Stroun, M.; Mulcahy, H.E.; Farthing, M.J. K-ras mutations are found in DNA extracted from the plasma of patients with colorectal cancer. Gastroenterology 1997, 112, 1114–1120.
  24. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002, 16, 6–21.
  25. Herceg, Z.; Hainaut, P. Genetic and epigenetic alterations as biomarkers for cancer detection, diagnosis and prognosis. Mol. Oncol. 2007, 1, 26–41.
  26. Slotkin, R.K.; Martienssen, R. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 2007, 8, 272–285.
  27. Kulis, M.; Esteller, M. DNA methylation and cancer. Adv. Genet. 2010, 70, 27–56.
  28. Klutstein, M.; Nejman, D.; Greenfield, R.; Cedar, H. DNA Methylation in Cancer and Aging. Cancer Res. 2016, 76, 3446–3450.
  29. Baylin, S.B.; Jones, P.A. Epigenetic Determinants of Cancer. Cold Spring Harb. Perspect. Biol. 2016, 8.
  30. Ehrlich, M. DNA methylation in cancer: Too much, but also too little. Oncogene 2002, 21, 5400–5413.
  31. Panagopoulou, M.; Lambropoulou, M.; Balgkouranidou, I.; Nena, E.; Karaglani, M.; Nicolaidou, C.; Asimaki, A.; Konstantinidis, T.; Constantinidis, T.C.; Kolios, G.; et al. Gene promoter methylation and protein expression of BRMS1 in uterine cervix in relation to high-risk human papilloma virus infection and cancer. Tumour Biol. 2017, 39, 1010428317697557.
  32. Kioulafa, M.; Balkouranidou, I.; Sotiropoulou, G.; Kaklamanis, L.; Mavroudis, D.; Georgoulias, V.; Lianidou, E.S. Methylation of cystatin M promoter is associated with unfavorable prognosis in operable breast cancer. Int. J. Cancer 2009, 125, 2887–2892.
  33. Fece de la Cruz, F.; Corcoran, R.B. Methylation in cell-free DNA for early cancer detection. Ann. Oncol. 2018, 29, 1351–1353.
  34. Panagopoulou, M.; Karaglani, M.; Balgkouranidou, I.; Pantazi, C.; Kolios, G.; Kakolyris, S.; Chatzaki, E. Circulating cell-free DNA release in vitro: Kinetics, size profiling, and cancer-related gene methylation. Cell. Physiol. 2019, 234, 14079–14089.
  35. Silva, J.M.; Dominguez, G.; Villanueva, M.J.; Gonzalez, R.; Garcia, J.M.; Corbacho, C.; Provencio, M.; España, P.; Bonilla, F. Aberrant DNA methylation of the p16INK4a gene in plasma DNA of breast cancer patients. Br. J. Cancer 1999, 80, 1262–1264.
  36. Skvortsova, T.E.; Rykova, E.Y.; Tamkovich, S.N.; Bryzgunova, O.E.; Starikov, A.V.; Kuznetsova, N.P.; Vlassov, V.V.; Laktionov, P.P. Cell-free and cell-bound circulating DNA in breast tumours: DNA quantification and analysis of tumour-related gene methylation. Br. J. Cancer 2006, 94, 1492–1495.
  37. Kloten, V.; Becker, B.; Winner, K.; Schrauder, M.G.; Fasching, P.A.; Anzeneder, T.; Veeck, J.; Hartmann, A.; Knüchel, R.; Dahl, E. Promoter hypermethylation of the tumor-suppressor genes ITIH5, DKK3, and RASSF1A as novel biomarkers for blood-based breast cancer screening. Breast Cancer Res. 2013, 15, R4.
  38. Chimonidou, M.; Tzitzira, A.; Strati, A.; Sotiropoulou, G.; Sfikas, C.; Malamos, N.; Georgoulias, V.; Lianidou, E. CST6 promoter methylation in circulating cell-free DNA of breast cancer patients. Clin. Biochem. 2013, 46, 235–240.
  39. Sharma, G.; Mirza, S.; Parshad, R.; Srivastava, A.; Gupta, S.D.; Pandya, P.; Ralhan, R. Clinical significance of promoter hypermethylation of DNA repair genes in tumor and serum DNA in invasive ductal breast carcinoma patients. Life Sci. 2010, 87, 83–91.
  40. Salta, S.; Nunes, S.P.; Fontes-Sousa, M.; Lopes, P.; Freitas, M.; Caldas, M.; Antunes, L.; Castro, F.; Antunes, P.; Palma de Sousa, S.; et al. A DNA Methylation-Based Test for Breast Cancer Detection in Circulating Cell-Free DNA. J. Clin. Med. 2018, 7, 420.
  41. Nunes, S.P.; Moreira-Barbosa, C.; Salta, S.; Palma de Sousa, S.; Pousa, I.; Oliveira, J.; Soares, M.; Rego, L.; Dias, T.; Rodrigues, J.; et al. Cell-Free DNA Methylation of Selected Genes Allows for Early Detection of the Major Cancers in Women. Cancers 2018, 10, 357.
  42. Li, Z.; Guo, X.; Tang, L.; Peng, L.; Chen, M.; Luo, X.; Wang, S.; Xiao, Z.; Deng, Z.; Dai, L.; et al. Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing. Tumour Biol. 2016, 37, 13111–13119.
  43. Kang, S.; Li, Q.; Chen, Q.; Zhou, Y.; Park, S.; Lee, G.; Grimes, B.; Krysan, K.; Yu, M.; Wang, W.; et al. CancerLocator: Non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA. Genome Biol. 2017, 18, 53.
  44. Liu, L.; Toung, J.M.; Jassowicz, A.F.; Vijayaraghavan, R.; Kang, H.; Zhang, R.; Kruglyak, K.M.; Huang, H.J.; Hinoue, T.; Shen, H.; et al. Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification. Ann. Oncol. 2018, 29, 1445–1453.
  45. Sharma, G.; Mirza, S.; Yang, Y.-H.; Parshad, R.; Hazrah, P.; Datta Gupta, S.; Ralhan, R. Prognostic relevance of promoter hypermethylation of multiple genes in breast cancer patients. Cell. Oncol. 2009, 31, 487–500.
  46. Martínez-Galán, J.; Torres-Torres, B.; Núñez, M.I.; López-Peñalver, J.; Del Moral, R.; Ruiz De Almodóvar, J.M.; Menjón, S.; Concha, A.; Chamorro, C.; Ríos, S.; et al. ESR1 gene promoter region methylation in free circulating DNA and its correlation with estrogen receptor protein expression in tumor tissue in breast cancer patients. BMC Cancer 2014, 14, 59.
  47. Fujita, N.; Nakayama, T.; Yamamoto, N.; Kim, S.J.; Shimazu, K.; Shimomura, A.; Maruyama, N.; Morimoto, K.; Tamaki, Y.; Noguchi, S. Methylated DNA and total DNA in serum detected by one-step methylation-specific PCR is predictive of poor prognosis for breast cancer patients. Oncology 2012, 83, 273–282.
  48. Fujita, N.; Kagara, N.; Yamamoto, N.; Shimazu, K.; Shimomura, A.; Shimoda, M.; Maruyama, N.; Naoi, Y.; Morimoto, K.; Oda, N.; et al. Methylated DNA and high total DNA levels in the serum of patients with breast cancer following neoadjuvant chemotherapy are predictive of a poor prognosis. Oncol. Lett. 2014, 8, 397–403.
  49. Widschwendter, M.; Evans, I.; Jones, A.; Ghazali, S.; Reisel, D.; Ryan, A.; Gentry-Maharaj, A.; Zikan, M.; Cibula, D.; Eichner, J.; et al. Methylation patterns in serum DNA for early identification of disseminated breast cancer. Genome Med. 2017, 9, 115.
  50. Panagopoulou, M.; Karaglani, M.; Balgkouranidou, I.; Biziota, E.; Koukaki, T.; Karamitrousis, E.; Nena, E.; Tsamardinos, I.; Kolios, G.; Lianidou, E.; et al. Circulating cell-free DNA in breast cancer: Size profiling, levels, and methylation patterns lead to prognostic and predictive classifiers. Oncogene 2019, 38, 3387–3401.
  51. Sharma, G.; Mirza, S.; Parshad, R.; Gupta, S.D.; Ralhan, R. DNA methylation of circulating DNA: A marker for monitoring efficacy of neoadjuvant chemotherapy in breast cancer patients. Tumour Biol. 2012, 33, 1837–1843.
  52. Fiegl, H.; Millinger, S.; Mueller-Holzner, E.; Marth, C.; Ensinger, C.; Berger, A.; Klocker, H.; Goebel, G.; Widschwendter, M. Circulating tumor-specific DNA: A marker for monitoring efficacy of adjuvant therapy in cancer patients. Cancer Res. 2005, 65, 1141–1145.
  53. Zurita, M.; Lara, P.C.; del Moral, R.; Torres, B.; Linares-Fernández, J.L.; Arrabal, S.R.; Martínez-Galán, J.; Oliver, F.J.; Ruiz de Almodóvar, J.M. Hypermethylated 14-3-3-sigma and ESR1 gene promoters in serum as candidate biomarkers for the diagnosis and treatment efficacy of breast cancer metastasis. BMC Cancer 2010, 10, 217.
  54. Liggett, T.E.; Melnikov, A.A.; Marks, J.R.; Levenson, V.V. Methylation patterns in cell-free plasma DNA reflect removal of the primary tumor and drug treatment of breast cancer patients. Int. J. Cancer 2011, 128, 492–499.
  55. Fackler, M.J.; Lopez Bujanda, Z.; Umbricht, C.; Teo, W.W.; Cho, S.; Zhang, Z.; Visvanathan, K.; Jeter, S.; Argani, P.; Wang, C.; et al. Novel methylated biomarkers and a robust assay to detect circulating tumor DNA in metastatic breast cancer. Cancer Res. 2014, 74, 2160–2170.
  56. Legendre, C.; Gooden, G.C.; Johnson, K.; Martinez, R.A.; Liang, W.S.; Salhia, B. Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer. Clin. Epigenetics 2015, 7, 100.
  57. Bernardino, J.; Roux, C.; Almeida, A.; Vogt, N.; Gibaud, A.; Gerbault-Seureau, M.; Magdelenat, H.; Bourgeois, C.A.; Malfoy, B.; Dutrillaux, B. DNA hypomethylation in breast cancer: An independent parameter of tumor progression? Cancer Genet. Cytogenet. 1997, 97, 83–89.
  58. Jackson, K.; Yu, M.C.; Arakawa, K.; Fiala, E.; Youn, B.; Fiegl, H.; Müller-Holzner, E.; Widschwendter, M.; Ehrlich, M. DNA hypomethylation is prevalent even in low-grade breast cancers. Cancer Biol. Ther. 2004, 3, 1225–1231.
  59. Soares, J.; Pinto, A.E.; Cunha, C.V.; André, S.; Barão, I.; Sousa, J.M.; Cravo, M. Global DNA hypomethylation in breast carcinoma: Correlation with prognostic factors and tumor progression. Cancer 1999, 85, 112–118.
  60. Hon, G.C.; Hawkins, R.D.; Caballero, O.L.; Lo, C.; Lister, R.; Pelizzola, M.; Valsesia, A.; Ye, Z.; Kuan, S.; Edsall, L.E.; et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012, 22, 246–258.
  61. Brinkman, A.B.; Nik-Zainal, S.; Simmer, F.; Rodríguez-González, F.G.; Smid, M.; Alexandrov, L.B.; Butler, A.; Martin, S.; Davies, H.; Glodzik, D.; et al. Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation. Nat. Commun. 2019, 10, 1749.
  62. Tang, Q.; Cheng, J.; Cao, X.; Surowy, H.; Burwinkel, B. Blood-based DNA methylation as biomarker for breast cancer: A systematic review. Clin. Epigenetics 2016, 8, 115.
  63. Chan, K.C.; Jiang, P.; Chan, C.W.; Sun, K.; Wong, J.; Hui, E.P.; Chan, S.L.; Chan, W.C.; Hui, D.S.; Ng, S.S.; et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc. Natl. Acad. Sci. USA 2013, 110, 18761–18768.
  64. Bartoloni, E.; Ludovini, V.; Alunno, A.; Pistola, L.; Bistoni, O.; Crinò, L.; Gerli, R. Increased levels of circulating DNA in patients with systemic autoimmune diseases: A possible marker of disease activity in Sjögren’s syndrome. Lupus 2011, 20, 928–935.
  65. Schwarzenbach, H.; Hoon, D.S.; Pantel, K. Cell-free nucleic acids as biomarkers in cancer patients. Nat. Rev. Cancer 2011, 11, 426–437.
  66. Cherepanova, A.V.; Tamkovich, S.N.; Bryzgunova, O.E.; Vlassov, V.V.; Laktionov, P.P. Deoxyribonuclease activity and circulating DNA concentration in blood plasma of patients with prostate tumors. Ann. N. Y. Acad. Sci. 2008, 1137, 218–221.
  67. Tamkovich, S.N.; Cherepanova, A.V.; Kolesnikova, E.V.; Rykova, E.Y.; Pyshnyi, D.V.; Vlassov, V.V.; Laktionov, P.P. Circulating DNA and DNase activity in human blood. Ann. N. Y. Acad. Sci. 2006, 1075, 191–196.
  68. Minchin, R.F.; Carpenter, D.; Orr, R.J. Polyinosinic acid and polycationic liposomes attenuate the hepatic clearance of circulating plasmid DNA. J. Pharmacol. Exp. Ther. 2001, 296, 1006–1012.
  69. Lo, Y.M.; Zhang, J.; Leung, T.N.; Lau, T.K.; Chang, A.M.; Hjelm, N.M. Rapid clearance of fetal DNA from maternal plasma. Am. J. Hum. Genet. 1999, 64, 218–224.
  70. Szpechcinski, A.; Struniawska, R.; Zaleska, J.; Chabowski, M.; Orlowski, T.; Roszkowski, K.; Chorostowska-Wynimko, J. Evaluation of fluorescence-based methods for total vs. amplifiable DNA quantification in plasma of lung cancer patients. J. Physiol. Pharmacol. 2008, 59 Suppl 6, 675–681.
  71. Breitbach, S.; Tug, S.; Helmig, S.; Zahn, D.; Kubiak, T.; Michal, M.; Gori, T.; Ehlert, T.; Beiter, T.; Simon, P. Direct quantification of cell-free, circulating DNA from unpurified plasma. PLoS ONE 2014, 9, e87838.
  72. Zanetti-Dällenbach, R.A.; Schmid, S.; Wight, E.; Holzgreve, W.; Ladewing, A.; Hahn, S.; Zhong, X.Y. Levels of circulating cell-free serum DNA in benign and malignant breast lesions. Int. J. Biol. Markers 2007, 22, 95–99.
  73. Hashad, D.; Sorour, A.; Ghazal, A.; Talaat, I. Free circulating tumor DNA as a diagnostic marker for breast cancer. J. Clin. Lab. Anal. 2012, 26, 467–472.
  74. Umetani, N.; Kim, J.; Hiramatsu, S.; Reber, H.A.; Hines, O.J.; Bilchik, A.J.; Hoon, D.S. Increased integrity of free circulating DNA in sera of patients with colorectal or periampullary cancer: Direct quantitative PCR for ALU repeats. Clin. Chem. 2006, 52, 1062–1069.
  75. Tang, Z.; Li, L.; Shen, L.; Shen, X.; Ju, S.; Cong, H. Diagnostic Value of Serum Concentration and Integrity of Circulating Cell-Free DNA in Breast Cancer: A Comparative Study with CEA and CA15-3. Lab. Med. 2018, 49, 323–328.
  76. Sunami, E.; Vu, A.T.; Nguyen, S.L.; Giuliano, A.E.; Hoon, D.S. Quantification of LINE1 in circulating DNA as a molecular biomarker of breast cancer. Ann. N. Y. Acad. Sci. 2008, 1137, 171–174.
  77. Gong, B.; Xue, J.; Yu, J.; Li, H.; Hu, H.; Yen, H.; Hu, J.; Dong, Q.; Chen, F. Cell-free DNA in blood is a potential diagnostic biomarker of breast cancer. Oncol. Lett. 2012, 3, 897–900.
  78. Kohler, C.; Radpour, R.; Barekati, Z.; Asadollahi, R.; Bitzer, J.; Wight, E.; Bürki, N.; Diesch, C.; Holzgreve, W.; Zhong, X.Y. Levels of plasma circulating cell free nuclear and mitochondrial DNA as potential biomarkers for breast tumors. Mol. Cancer 2009, 8, 105.
  79. Catarino, R.; Ferreira, M.M.; Rodrigues, H.; Coelho, A.; Nogal, A.; Sousa, A.; Medeiros, R. Quantification of free circulating tumor DNA as a diagnostic marker for breast cancer. DNA Cell Biol. 2008, 27, 415–421.
  80. Nicolini, C.; Ens, C.; Cerutti, T.; Roehe, A.V.; Agnes, G.; Damin, A.P.; Alexandre, C.O. Elevated level of cell-free plasma DNA is associated with advanced-stage breast cancer and metastasis. Clin. Chem. Lab. Med. 2013, 51, e277–e278.
  81. Agostini, M.; Enzo, M.V.; Bedin, C.; Belardinelli, V.; Goldin, E.; Del Bianco, P.; Maschietto, E.; D’Angelo, E.; Izzi, L.; Saccani, A.; et al. Circulating cell-free DNA: A promising marker of regional lymphonode metastasis in breast cancer patients. Cancer Biomark. 2012, 11, 89–98.
  82. Huang, Z.H.; Li, L.H.; Hua, D. Quantitative analysis of plasma circulating DNA at diagnosis and during follow-up of breast cancer patients. Cancer Lett. 2006, 243, 64–70.
  83. Umetani, N.; Giuliano, A.E.; Hiramatsu, S.H.; Amersi, F.; Nakagawa, T.; Martino, S.; Hoon, D.S. Prediction of breast tumor progression by integrity of free circulating DNA in serum. J. Clin. Oncol. 2006, 24, 4270–4276.
  84. Iqbal, S.; Vishnubhatla, S.; Raina, V.; Sharma, S.; Gogia, A.; Deo, S.S.; Mathur, S.; Shukla, N.K. Circulating cell-free DNA and its integrity as a prognostic marker for breast cancer. SpringerPlus 2015, 4, 265.
  85. Maltoni, R.; Casadio, V.; Ravaioli, S.; Foca, F.; Tumedei, M.M.; Salvi, S.; Martignano, F.; Calistri, D.; Rocca, A.; Schirone, A.; et al. Cell-free DNA detected by "liquid biopsy" as a potential prognostic biomarker in early breast cancer. Oncotarget 2017, 8, 16642–16649.
  86. Arko-Boham, B.; Aryee, N.A.; Blay, R.M.; Owusu, E.D.A.; Tagoe, E.A.; Doris Shackie, E.S.; Debrah, A.B.; Adu-Aryee, N.A. Circulating cell-free DNA integrity as a diagnostic and prognostic marker for breast and prostate cancers. Cancer Genet. 2019, 235–236, 65–71.
  87. Stötzer, O.J.; Lehner, J.; Fersching-Gierlich, D.; Nagel, D.; Holdenrieder, S. Diagnostic relevance of plasma DNA and DNA integrity for breast cancer. Tumour Biol. 2014, 35, 1183–1191.
  88. Wu, X.; Tanaka, H. Aberrant reduction of telomere repetitive sequences in plasma cell-free DNA for early breast cancer detection. Oncotarget 2015, 6, 29795–29807.
  89. El Tarhouny, S.; Seefeld, M.; Fan, A.X.; Hahn, S.; Holzgreve, W.; Zhong, X.Y. Comparison of serum VEGF and its soluble receptor sVEGFR1 with serum cell-free DNA in patients with breast tumor. Cytokine 2008, 44, 65–69.
  90. Dawson, S.J.; Tsui, D.W.; Murtaza, M.; Biggs, H.; Rueda, O.M.; Chin, S.F.; Dunning, M.J.; Gale, D.; Forshew, T.; Mahler-Araujo, B.; et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N. Engl. J. Med. 2013, 368, 1199–1209.
  91. Cheng, J.; Holland-Letz, T.; Wallwiener, M.; Surowy, H.; Cuk, K.; Schott, S.; Trumpp, A.; Pantel, K.; Sohn, C.; Schneeweiss, A.; et al. Circulating free DNA integrity and concentration as independent prognostic markers in metastatic breast cancer. Breast Cancer Res. Treat. 2018, 169, 69–82.
  92. Lehner, J.; Stötzer, O.J.; Fersching, D.; Nagel, D.; Holdenrieder, S. Circulating plasma DNA and DNA integrity in breast cancer patients undergoing neoadjuvant chemotherapy. Clin. Chim. Acta 2013, 425, 206–211.
  93. Yu, D.; Tong, Y.; Guo, X.; Feng, L.; Jiang, Z.; Ying, S.; Jia, J.; Fang, Y.; Yu, M.; Xia, H.; et al. Diagnostic Value of Concentration of Circulating Cell-Free DNA in Breast Cancer: A Meta-Analysis. Front. Oncol. 2019, 9, 95.
  94. Agassi, R.; Czeiger, D.; Shaked, G.; Avriel, A.; Sheynin, J.; Lavrenkov, K.; Ariad, S.; Douvdevani, A. Measurement of circulating cell-free DNA levels by a simple fluorescent test in patients with breast cancer. Am. J. Clin. Pathol. 2015, 143, 18–24.
  95. Peled, M.; Agassi, R.; Czeiger, D.; Ariad, S.; Riff, R.; Rosenthal, M.; Lazarev, I.; Novack, V.; Yarza, S.; Mizrakli, Y.; et al. Cell-free DNA concentration in patients with clinical or mammographic suspicion of breast cancer. Sci. Rep. 2020, 10, 14601.
  96. Moss, J.; Zick, A.; Grinshpun, A.; Carmon, E.; Maoz, M.; Ochana, B.L.; Abraham, O.; Arieli, O.; Germansky, L.; Meir, K.; et al. Circulating breast-derived DNA allows universal detection and monitoring of localized breast cancer. Ann. Oncol. 2020, 31, 395–403.
  97. Kamel, A.M.; Teama, S.; Fawzy, A.; El Deftar, M. Plasma DNA integrity index as a potential molecular diagnostic marker for breast cancer. Tumour Biol. 2016, 37, 7565–7572.
  98. Chan, K.C.; Leung, S.F.; Yeung, S.W.; Chan, A.T.; Lo, Y.M. Persistent aberrations in circulating DNA integrity after radiotherapy are associated with poor prognosis in nasopharyngeal carcinoma patients. Clin. Cancer Res. 2008, 14, 4141–4145.
  99. Ellinger, J.; Wittkamp, V.; Albers, P.; Perabo, F.G.; Mueller, S.C.; von Ruecker, A.; Bastian, P.J. Cell-free circulating DNA: Diagnostic value in patients with testicular germ cell cancer. J. Urol. 2009, 181, 363–371.
  100. Madhavan, D.; Wallwiener, M.; Bents, K.; Zucknick, M.; Nees, J.; Schott, S.; Cuk, K.; Riethdorf, S.; Trumpp, A.; Pantel, K.; et al. Plasma DNA integrity as a biomarker for primary and metastatic breast cancer and potential marker for early diagnosis. Breast Cancer Res. Treat. 2014, 146, 163–174.
  101. Cheng, J.; Cuk, K.; Heil, J.; Golatta, M.; Schott, S.; Sohn, C.; Schneeweiss, A.; Burwinkel, B.; Surowy, H. Cell-free circulating DNA integrity is an independent predictor of impending breast cancer recurrence. Oncotarget 2017, 8, 54537–54547.
  102. Deligezer, U.; Eralp, Y.; Akisik, E.Z.; Akisik, E.E.; Saip, P.; Topuz, E.; Dalay, N. Effect of adjuvant chemotherapy on integrity of free serum DNA in patients with breast cancer. Ann. N. Y. Acad. Sci. 2008, 1137, 175–179.
  103. Jiang, P.; Chan, C.W.; Chan, K.C.; Cheng, S.H.; Wong, J.; Wong, V.W.; Wong, G.L.; Chan, S.L.; Mok, T.S.; Chan, H.L.; et al. Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients. Proc. Natl. Acad. Sci. USA 2015, 112, E1317–E1325.
  104. Mouliere, F.; Robert, B.; Arnau Peyrotte, E.; Del Rio, M.; Ychou, M.; Molina, F.; Gongora, C.; Thierry, A.R. High fragmentation characterizes tumour-derived circulating DNA. PLoS ONE 2011, 6, e23418.
  105. Lapin, M.; Oltedal, S.; Tjensvoll, K.; Buhl, T.; Smaaland, R.; Garresori, H.; Javle, M.; Glenjen, N.I.; Abelseth, B.K.; Gilje, B.; et al. Fragment size and level of cell-free DNA provide prognostic information in patients with advanced pancreatic cancer. J. Transl. Med. 2018, 16, 300.
  106. Cristiano, S.; Leal, A.; Phallen, J.; Fiksel, J.; Adleff, V.; Bruhm, D.C.; Jensen, S.O.; Medina, J.E.; Hruban, C.; White, J.R.; et al. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature 2019, 570, 385–389.
  107. Stroun, M.; Lyautey, J.; Lederrey, C.; Olson-Sand, A.; Anker, P. About the possible origin and mechanism of circulating DNA apoptosis and active DNA release. Clin. Chim. Acta 2001, 313, 139–142.
  108. Anker, P.; Stroun, M.; Maurice, P.A. Spontaneous release of DNA by human blood lymphocytes as shown in an in vitro system. Cancer Res. 1975, 35, 2375–2382.
  109. Choi, J.J.; Reich, C.F., 3rd; Pisetsky, D.S. The role of macrophages in the in vitro generation of extracellular DNA from apoptotic and necrotic cells. Immunology 2005, 115, 55–62.
  110. Hernandez, A.M.; Rodriguez, N.; Gonzalez, J.E.; Reyes, E.; Rondon, T.; Grinan, T.; Macias, A.; Alfonso, S.; Vazquez, A.M.; Perez, R. Anti-NeuGcGM3 antibodies, actively elicited by idiotypic vaccination in nonsmall cell lung cancer patients, induce tumor cell death by an oncosis-like mechanism. J. Immunol. 2011, 186, 3735–3744.
  111. Jahr, S.; Hentze, H.; Englisch, S.; Hardt, D.; Fackelmayer, F.O.; Hesch, R.D.; Knippers, R. DNA fragments in the blood plasma of cancer patients: Quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res. 2001, 61, 1659–1665.
  112. Wu, T.L.; Zhang, D.; Chia, J.H.; Tsao, K.; Sun, C.F.; Wu, J.T. Cell-free DNA: Measurement in various carcinomas and establishment of normal reference range. Clin. Chim. Acta 2002, 321, 77–87.
More
Upload a video for this entry
Information
Subjects: Oncology
Contributor MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register : Maria Panagopoulou
View Times: 693
Revisions: 2 times (View History)
Update Date: 15 Mar 2021
Notice
You are not a member of the advisory board for this topic. If you want to update advisory board member profile, please contact office@encyclopedia.pub.
OK
Confirm
Only members of the Encyclopedia advisory board for this topic are allowed to note entries. Would you like to become an advisory board member of the Encyclopedia?
Yes
No
${ textCharacter }/${ maxCharacter }
Submit
Cancel
There is no comment~
${ textCharacter }/${ maxCharacter }
Submit
Cancel
${ selectedItem.replyTextCharacter }/${ selectedItem.replyMaxCharacter }
Submit
Cancel
Confirm
Are you sure to Delete?
Yes No
Academic Video Service