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Cell free circulating cancer DNA

Ranjan Basak, Naveen Kumar Nair, Indraneel Mittra
There is extensive literature to show that nucleic acids can be taken up by cells under experimental conditions and that foetal DNA can be detected in maternal tissues. The uptaken DNA can integrate into host cell genomes and can be transcribed and translated into proteins. They can also cause chromosomal damage and karyotype alterations. Cell-free nucleic acids (cfNAs)-based non-invasive DNA diagnostic techniques are being extensively researched in the field of cancer with the potential to advance new prognostic parameters and direct treatment decisions...
October 12, 2016: Mutation Research
Changqing Yin, Changliang Luo, Wei Hu, Xu Ding, Chunhui Yuan, Fubing Wang
As part of "liquid biopsy," lots of literature indicated the potential diagnostic value of circulating cell-free DNA (cfDNA) in the management of prostate cancer (PCa). However, the literature on the accuracy of cfDNA detection in PCa has been inconsistent. Hence, we performed this meta-analysis to assess the diagnostic value of cfDNA in PCa. A total of 19 articles were included in this analysis according to the inclusion and exclusion criteria. We then investigated two main subgroups in this meta-analysis, including qualitative analysis of abnormal level of cfDNA and qualitative analysis of single-gene methylation alterations...
2016: Disease Markers
Sarah Hrebien, Ben O'Leary, Matthew Beaney, Gaia Schiavon, Charlotte Fribbens, Amarjit Bhambra, Richard Johnson, Isaac Garcia-Murillas, Nicholas Turner
Circulating tumor DNA (ctDNA) analysis has the potential to allow non-invasive analysis of tumor mutations in advanced cancer. In this study we assessed the reproducibility of digital PCR (dPCR) assays of circulating tumor DNA in a cohort of patients with advanced breast cancer and assessed delayed plasma processing using cell free DNA preservative tubes. We recruited a cohort of 96 paired samples from 71 women with advanced breast cancer who had paired blood samples processed either immediately or delayed in preservative tubes with processing 48-72 hours after collection...
2016: PloS One
Alexander Wolf, Katharina Beller, Sebastian Groemminger, Wera Hofmann, Matthias Sachse, Jana Fassunke
Increasing sample numbers for screening and diagnostics using circulating cell-free DNA (ccfDNA) as analyte demands an automated solution for ccfDNA extraction. The efficiency of a new, automated, large volume ccfDNA extraction method was evaluated against a manual reference method. The new kit for automated ccfDNA extraction on the QIAsymphony showed a comparable yield of total ccfDNA from healthy donors as well as a comparable recovery of circulating cancer and fetal DNA. In conclusion, a new kit for automated ccfDNA extraction was established successfully...
2016: Advances in Experimental Medicine and Biology
Jurgen Distler, Reimo Tetzner, Gunter Weiss, Thomas König, Anne Schlegel, Michal Bagrowski
For the subsequent analysis of the methylated mSEPT9 colorectal cancer screening marker in plasma, different blood collection tubes and blood storage conditions were investigated. The study demonstrated that methylated Septin 9 ((m)SEPT9) can be consistently detected in plasma samples derived from whole blood samples collected with S-Monovette® K3E and BD Vacutainer ® K2EDTA tubes stored at 2-8 °C for a maximum of 24 h and for samples collected in S-Monovette CPDA tubes stored at 18-25 °C for up to 48 h...
2016: Advances in Experimental Medicine and Biology
Vipulkumar Patel, Peter Celec, Magdalena Grunt, Heidi Schwarzenbach, Ingo Jenneckens, Timo Hillebrand
Circulating cell-free DNA (ccfDNA) is a promising diagnostic tool and its size fractionation is of interest. However, kits for isolation of ccfDNA available on the market are designed for small volumes hence processing large sample volumes is laborious. We have tested a new method that enables enrichment of ccfDNA from large volumes of plasma and subsequently allows size-fractionation of isolated ccfDNA into two fractions with individually established cut-off levels of ccfDNA length. This method allows isolation of low-abundant DNA as well as separation of long and short DNA molecules...
2016: Advances in Experimental Medicine and Biology
Jelena Belic, Marina Koch, Peter Ulz, Martina Auer, Teresa Gerhalter, Sumitra Mohan, Katja Fischereder, Edgar Petru, Thomas Bauernhofer, Jochen B Geigl, Michael R Speicher, Ellen Heitzer
Recent progress in the analysis of cell-free DNA fragments (cell-free circulating tumor DNA, ctDNA) now allows monitoring of tumor genomes by non-invasive means. However, previous studies with plasma DNA from patients with cancer demonstrated highly variable allele frequencies of ctDNA. Comprehensive genome-wide analysis of tumor genomes is greatly facilitated when plasma DNA has increased amounts of ctDNA. In order to develop a fast and cost-effective pre-screening method for the identification of plasma samples suitable for further extensive qualitative analysis, we adapted the recently described FAST-SeqS method...
2016: Advances in Experimental Medicine and Biology
Svetlana N Tamkovich, Oleg S Tutanov, Danil S Serdukov, Maxim S Belenikin, Anatoliy G Shlikht, Natalia A Kirushina, Vladimir E Voytsitskiy, Yuri P Tsentalovich, Vsevolod A Tkachuk, Pavel P Laktionov
In the current study we have investigated the protein content of blood plasma deoxyribonucleoprotein complexes. The complexes were isolated using affinity chromatography with immobilized polyclonal anti-histone antibodies. Proteins were separated by SDS PAAGE and identified by MALDI-TOF mass-spectrometry. 111 and 56 proteins (excluding histones), respectively, were identified with a good score in deoxyribonucleoprotein complexes of healthy females and breast cancer patients. However, only four of these proteins were found in 30 % of all samples...
2016: Advances in Experimental Medicine and Biology
Vasilina A Sergeeva, Svetlana V Kostyuk, Elizaveta S Ershova, Elena M Malinovskaya, Tatiana D Smirnova, Larisa V Kameneva, Natalia N Veiko
It has been established that cell-free DNA circulating in the bloodstream affects cells. The characteristics of cfDNA depend on the physiological state of the organism. As we showed previously, diseases can cause either GC-enrichment of the cell-free DNA pool or its oxidation. Thus, in cases of cerebral atherosclerosis, heart attack and rheumatic arthritis the cell-free DNA pool is GC-enriched and, in the case of cancer, both GC-enriched and oxidized. Herein we investigated the time-dependent effect of oxidized and GC-rich cell-free DNA on NF-kB and NRF2 signaling pathways in human mesenchymal stem cells and showed that they affect cells in different ways...
2016: Advances in Experimental Medicine and Biology
Svetlana N Tamkovich, Natalia A Kirushina, Vladimir E Voytsitskiy, Vsevolod A Tkachuk, Pavel P Laktionov
Size and termini of cell-free DNA molecules circulating in blood plasma and being bound with blood cell surface of healthy females and untreated breast cancer patients were investigated. The size and concentration of circulating blood DNA were analyzed by Agilent 2100 Bioanalyser (TM) and TaqMan PCR. The termini of circulating DNA were examined by ligation using biotinylated double-stranded oligonucleotide adapters with random 1-3 b overhangs of both chains and subsequent quantification by PCR. Short (180 bp) and longer (>8 kbp) DNA fragments were found in cell free DNA from both groups, but short were less represented in primary breast cancer patient plasma...
2016: Advances in Experimental Medicine and Biology
Elena Trujillo-Arribas, Hada C Macher, Pilar Jiménez-Arriscado, Fernando de la Portilla, Patrocinio Molinero, Juan M Guerrero, Amalia Rubio
Genomic characterization of cell-free circulating tumour DNA (ctDNA) may offer an opportunity to assess clonal dynamics throughout the course of a patient's illness. The existence of KRAS driver mutations in colon cancer patients is determinant to decide their treatment and to predict their outcome. DNA is extracted automatically from 400 μL of serum using the MagNa Pure Compact with the Nucleic Acid Isolation Kit I. DNA amplification, COLD-PCR and HRM were performed in the same run in the Light Cycler 480...
2016: Advances in Experimental Medicine and Biology
Erina Takai, Yasushi Totoki, Hiromi Nakamura, Mamoru Kato, Tatsuhiro Shibata, Shinichi Yachida
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies. The genomic landscape of the PDAC genome features four frequently mutated genes (KRAS, CDKN2A, TP53, and SMAD4) and dozens of candidate driver genes altered at low frequency, including potential clinical targets. Circulating cell-free DNA (cfDNA) is a promising resource to detect molecular characteristics of tumors, supporting the concept of "liquid biopsy".We determined the mutational status of KRAS in plasma cfDNA using multiplex droplet digital PCR in 259 patients with PDAC, retrospectively...
2016: Advances in Experimental Medicine and Biology
Inessa Skrypkina, Liudmyla Tsyba, Kateryna Onyshchenko, Dmytro Morderer, Olena Kashparova, Oleksii Nikolaienko, Grigory Panasenko, Sergii Vozianov, Alina Romanenko, Alla Rynditch
The critical point for successful treatment of cancer is diagnosis at early stages of tumor development. Cancer cell-specific methylated DNA has been found in the blood of cancer patients, indicating that cell-free DNA (cfDNA) circulating in the blood is a convenient tumor-associated DNA marker. Therefore methylated cfDNA can be used as a minimally invasive diagnostic marker. We analysed the concentration of plasma cfDNA and methylation of six tumor suppressor genes in samples of 27 patients with renal cancer and 15 healthy donors as controls...
2016: Disease Markers
Fumio Imamura, Junji Uchida, Yoji Kukita, Toru Kumagai, Kazumi Nishino, Takako Inoue, Madoka Kimura, Kikuya Kato
OBJECTIVES: Early evaluation of the effect of treatment is helpful in the management of cancer patients. Circulating biomarkers are an ideal tool for this if they are highly specific to tumors and respond rapidly to tumor volume changes. Circulating tumor DNA (ctDNA) is one such candidate. We conducted a prospective study to test the utility of EGFR ctDNA in early evaluation of EGFR-TKI effects. RESULTS: Twenty-one patients with EGFR-mutant lung cancer who were naïve to EGFR-TKI were enrolled...
September 30, 2016: Oncotarget
Florence Le Calvez-Kelm, Matthieu Foll, Magdalena B Wozniak, Tiffany M Delhomme, Geoffroy Durand, Priscilia Chopard, Maroulio Pertesi, Eleonora Fabianova, Zora Adamcakova, Ivana Holcatova, Lenka Foretova, Vladimir Janout, Maxime P Vallee, Sabina Rinaldi, Paul Brennan, James D McKay, Graham B Byrnes, Ghislaine Scelo
The utility of KRAS mutations in plasma circulating cell-free DNA (cfDNA) samples as non-invasive biomarkers for the detection of pancreatic cancer has never been evaluated in a large case-control series. We applied a KRAS amplicon-based deep sequencing strategy combined with analytical pipeline specifically designed for the detection of low-abundance mutations to screen plasma samples of 437 pancreatic cancer cases, 141 chronic pancreatitis subjects, and 394 healthy controls. We detected mutations in 21.1% (N=92) of cases, of whom 82 (89...
October 1, 2016: Oncotarget
Ao Huang, Xin Zhang, Shao-Lai Zhou, Ya Cao, Xiao-Wu Huang, Jia Fan, Xin-Rong Yang, Jian Zhou
PURPOSE: Circulating tumor DNA (ctDNA) is increasingly recognized as liquid biopsy to profile tumor genome. Droplet digital PCR (ddPCR) is a highly sensitive and easily operable platform for mutant detection. Here, we tried to detect ctDNA in hepatocellular carcinoma (HCC) patients using ddPCR. METHODS: Studies sequencing the genome of HCCs and COSMIC (Catalogue of Somatic Mutations in Cancer) database were reviewed to identify hotspot mutations. Circulating cell-free DNAs (cfDNAs) extracted from 1 ml preoperative plasma sample were analyzed to detect circulating mutants using ddPCR...
2016: Journal of Cancer
Ao Huang, Xin Zhang, Shao-Lai Zhou, Ya Cao, Xiao-Wu Huang, Jia Fan, Xin-Rong Yang, Jian Zhou
The clinical significance of circulating cell-free DNA (cfDNA) integrity as diagnostic and surveillance biomarker in hepatocellular carcinoma (HCC) was investigated and compared to that of alpha fetoprotein (AFP). Liver cancer patients had lower cfDNA integrity than those with benign diseases (P = 0.0167) and healthy individuals (P = 0.0025). Patients with HCC and non-HCC liver cancers (P = 0.7356), and patients with benign diseases and healthy individuals (P = 0.9138) had comparable cfDNA integrity respectively...
2016: Journal of Cancer
Fariz Nurwidya, Jamal Zaini, Andika Chandra Putra, Sita Andarini, Achmad Hudoyo, Elisna Syahruddin, Faisal Yunus
Circulating tumor cells (CTCs) are tumor cells that are separated from the primary site or metastatic lesion and disseminate in blood circulation. CTCs are considered to be part of the long process of cancer metastasis. As a 'liquid biopsy', CTC molecular examination and investigation of single cancer cells create an important opportunity for providing an understanding of cancer biology and the process of metastasis. In the last decade, we have seen dramatic development in defining the role of CTCs in lung cancer in terms of diagnosis, genomic alteration determination, treatment response and, finally, prognosis prediction...
September 2016: Chonnam Medical Journal
Jonathan Oh, Minal Barve, Carolyn M Matthews, E Colin Koon, Thomas P Heffernan, Bruce Fine, Elizabeth Grosen, Melanie K Bergman, Evelyn L Fleming, Leslie R DeMars, Loyd West, Daniel L Spitz, Howard Goodman, Kenneth C Hancock, Gladice Wallraven, Padmasini Kumar, Ernest Bognar, Luisa Manning, Beena O Pappen, Ned Adams, Neil Senzer, John Nemunaitis
OBJECTIVES: The majority of women with Stage III/IV ovarian cancer who achieve clinical complete response with frontline standard of care will relapse within 2years. Vigil immunotherapy, a GMCSF/bi-shRNA furin DNA engineered autologous tumor cell (EATC) product, demonstrated safety and induction of circulating activated T-cells against autologous tumor in Phase I trial Senzer et al. (2012, 2013) . Our objectives for this study include evaluation of safety, immune response and recurrence free survival (RFS)...
September 24, 2016: Gynecologic Oncology
T Rutkowski, A Mazurek, M Snietura, A Wygoda, U Bojko, P Widlak, K A Skladowski
No abstract text is available yet for this article.
October 1, 2016: International Journal of Radiation Oncology, Biology, Physics
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