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Pallares RM, Kong SL, Hui Ru T, Thanh NTK, Lu Y, Su X. A plasmonic nanosensor with inverse sensitivity for circulating cell-free DNA quantification. Chem Commun (Camb) 2015; 51:14524-7. [DOI: 10.1039/c5cc05331e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A plasmonic nanosensor (using gold nanorods) with inverse sensitivity is presented for circulating cell-free DNA quantification.
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Affiliation(s)
- Roger M. Pallares
- Department of Chemistry
- University College London
- London
- UK
- Institute of Materials Research and Engineering
| | - Say Li Kong
- Genome Institute of Singapore
- A*STAR
- Singapore, 138672
| | - Tan Hui Ru
- Institute of Materials Research and Engineering
- A*STAR (Agency for Science, Technology and Research)
- 3 Research Link
- Singapore, 117602
| | - Nguyên T. K. Thanh
- Biophysics Group
- Department of Physics and Astronomy
- University College London
- London
- UK
| | - Yi Lu
- Department of Chemistry
- University of Illinois at Urbana-Champaign
- Illinois
- USA
| | - Xiaodi Su
- Institute of Materials Research and Engineering
- A*STAR (Agency for Science, Technology and Research)
- 3 Research Link
- Singapore, 117602
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Bryzgunova OE, Laktionov PP. Generation of blood circulating DNAs: Sources, features of struction and circulation. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2014. [DOI: 10.1134/s1990750814030020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Kapitskaya KY, Azhikina TL, Ponomaryova AA, Cherdyntseva NV, Vlasov VV, Laktionov PP, Rykova EY. MIRA analysis of RARβ2 gene methylation in DNA circulating in the blood in lung cancer. Bull Exp Biol Med 2014; 157:516-9. [PMID: 25110096 DOI: 10.1007/s10517-014-2604-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 11/25/2022]
Abstract
Analysis of DNA epigenetic mutations in the blood circulating DNA is a prospective trend for creation of noninvasive methods for the diagnosis and treatment efficiency monitoring in cancer. The methylation status of target genes in circulating DNA was evaluated by methods based on preliminary bisulfite conversion of DNA. We used a different approach based on selection of hypermethylated sequences of circulating DNA by means of DNA-methyl-binding protein (methylated CpG island recovery assay, MIRA). Methylation was evaluated for RARβ2 tumor suppression gene in circulating DNA in lung cancer and a trend was detected to higher methylation of this gene in the patients in comparison with healthy donors.
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Affiliation(s)
- K Yu Kapitskaya
- Institute of Organic Biochemistry, the Russian Academy of Sciences, Moscow, Russia
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Ralla B, Stephan C, Meller S, Dietrich D, Kristiansen G, Jung K. Nucleic acid-based biomarkers in body fluids of patients with urologic malignancies. Crit Rev Clin Lab Sci 2014; 51:200-31. [PMID: 24878357 DOI: 10.3109/10408363.2014.914888] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review focuses on the promising potential of nucleic acids in body fluids such as blood and urine as diagnostic, prognostic, predictive and monitoring biomarkers in urologic malignancies. The tremendous progress in the basic knowledge of molecular processes in cancer, as shown in the companion review on nucleic acid-based biomarkers in tissue of urologic tumors, provides a strong rationale for using these molecular changes as non-invasive markers in body fluids. The changes observed in body fluids are an integrative result, reflecting both tissue changes and processes occurring in the body fluids. The availability of sensitive methods has only recently made possible detailed studies of DNA- and RNA-based markers in body fluids. In addition to these biological aspects, methodological aspects of the determination of nucleic acids in body fluids, i.e. pre-analytical, analytical and post-analytical issues, are particularly emphasized. The characteristic changes of RNA (differential mRNA and miRNA expression) and DNA (concentrations, integrity index, mutations, microsatellite and methylation alterations) in serum/plasma and urine samples of patients suffering from the essential urologic cancers of the prostate, bladder, kidney and testis are summarized and critically discussed below. To translate the promising results into clinical practice, laboratory scientists and clinicians have to collaborate to resolve the challenges of harmonized and feasible pre-analytical and analytical conditions for the selected markers and to validate these markers in well-designed and sufficiently powered multi-center studies.
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Affiliation(s)
- Bernhard Ralla
- Department of Urology, Charité - Universitätsmedizin Berlin , Berlin , Germany
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Information handling by the brain: proposal of a new "paradigm" involving the roamer type of volume transmission and the tunneling nanotube type of wiring transmission. J Neural Transm (Vienna) 2014; 121:1431-49. [PMID: 24866694 DOI: 10.1007/s00702-014-1240-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/06/2014] [Indexed: 12/13/2022]
Abstract
The current view on the organization of the central nervous system (CNS) is basically anchored to the paradigm describing the brain as formed by networks of neurons interconnected by synapses. Synaptic contacts are a fundamental characteristic for describing CNS operations, but increasing evidence accumulated in the last 30 years pointed to a refinement of this view. A possible overcoming of the classical "neuroscience paradigm" will be here outlined, based on the following hypotheses: (1) the basic morpho-functional unit in the brain is a compartment of tissue (functional module) where different resident cells (not only neurons) work as an integrated unit; (2) in these complex networks, a spectrum of intercellular communication processes is exploited, that can be classified according to a dichotomous criterion: wiring transmission (occurring through physically delimited channels) and volume transmission (exploiting diffusion in the extracellular space); (3) the connections between cells can themselves be described as a network, leading to an information processing occurring at different levels from cell network down to molecular level; (4) recent evidence of the existence of specialized structures (microvesicles and tunneling nanotubes) for intercellular exchange of materials, could allow a further type of polymorphism of the CNS networks based on at least transient changes in cell phenotype. When compared to the classical paradigm, the proposed scheme of cellular organization could allow a strong increase of the degrees of freedom available to the whole system and then of its plasticity. Furthermore, long range coordination and correlation can be more easily accommodated within this framework.
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Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery. PLoS One 2014; 9:e86993. [PMID: 24489824 PMCID: PMC3906086 DOI: 10.1371/journal.pone.0086993] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/16/2013] [Indexed: 12/11/2022] Open
Abstract
Pregnant women carry a mixture of cell-free DNA fragments from self and fetus (non-self) in their circulation. In recent years multiple independent studies have demonstrated the ability to detect fetal trisomies such as trisomy 21, the cause of Down syndrome, by Next-Generation Sequencing of maternal plasma. The current clinical tests based on this approach show very high sensitivity and specificity, although as yet they have not become the standard diagnostic test. Here we describe improvements to the analysis of the sequencing data by reducing GC bias and better handling of the genomic repeats. We show substantial improvements in the sensitivity of the standard trisomy 21 statistical tests, which we measure by artificially reducing read coverage. We also explore the bias stemming from the natural cleavage of plasma DNA by examining DNA motifs and position specific base distributions. We propose a model to correct this fragmentation bias and observe that incorporating this bias does not lead to any further improvements in the detection of fetal trisomy. The improved bias corrections that we demonstrate in this work can be readily adopted into existing fetal trisomy detection protocols and should also lead to improvements in sub-chromosomal copy number variation detection.
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57
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The concentration of cell-free DNA in focal epilepsy. Epilepsy Res 2013; 105:292-8. [DOI: 10.1016/j.eplepsyres.2013.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/21/2013] [Accepted: 03/17/2013] [Indexed: 12/21/2022]
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Smythies J, Edelstein L. Interactions between the spike code and the epigenetic code during information processing in the brain. Front Mol Neurosci 2013; 6:17. [PMID: 23847467 PMCID: PMC3703540 DOI: 10.3389/fnmol.2013.00017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 06/18/2013] [Indexed: 12/03/2022] Open
Affiliation(s)
- John Smythies
- Department of Psychology, Center for Brain and Cognition, University of California San Diego La Jolla, CA, USA
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Arnalich F, Maldifassi MC, Ciria E, Codoceo R, Renart J, Fernández-Capitán C, Herruzo R, Garcia-Rio F, López-Collazo E, Montiel C. Plasma levels of mitochondrial and nuclear DNA in patients with massive pulmonary embolism in the emergency department: a prospective cohort study. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2013; 17:R90. [PMID: 23705965 PMCID: PMC3707013 DOI: 10.1186/cc12735] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/24/2013] [Indexed: 01/17/2023]
Abstract
Introduction Cell-free plasma mitochondrial DNA (mt-DNA) and nuclear DNA (n-DNA) are biomarkers with prognostic utility in conditions associated with a high rate of cell death. This exploratory study aimed to determine the plasma levels of both nucleic acids in patients with massive and submassive pulmonary embolism (PE) and to compare them with other biomarkers, such as heart-type fatty acid-binding protein (H-FABP) and troponin I (Tn-I) Methods This was a prospective observational study of 37 consecutive patients with massive PE, 37 patients with submassive PE, and 37 healthy subjects. Quantifications of plasma mt-DNA and n-DNA with real-time quantitative polymerase chain reaction (PCR), and plasma H-FABP and Tn-I by commercial assays, were done on blood samples drawn within 4 hours after presentation at the emergency department. Results Plasma mt-DNA and n-DNA concentrations were much higher in patients with massive PE (median, 2,970 GE/ml; interquartile range (IQR), 1,050 to 5,485; and 3,325 GE/ml, IQR: 1,080 to 5,790, respectively) than in patients with submassive PE (870 GE/ml and 1,245 GE/ml, respectively; P < 0.01) or controls (185 GE/ml and 520 GE/ml, respectively). Eighteen patients with massive PE died of a PE-related cause by day 15 of observation. Plasma mt-DNA and n-DNA values were 2.3-fold and 1.9-fold higher in the subgroup of nonsurviving patients than in survivors. H-FABP and Tn-I values were also higher in patients with massive PE who died (7.3 ng/ml and 0.023 ng/ml, respectively) than in those who survived (6.4 ng/ml, and 0.016 ng/ml, respectively). By receiver operating curve (ROC) analysis, the best cutoff values for predicting 15-day mortality were 3,380 GE/ml for mt-DNA, 6.8 ng/ml for H-FABP, 3,625 GE/ml for n-DNA, and 0.020 ng/ml for Tn-I, based on the calculated areas under the curve (AUCs) of 0.89 (95% confidence interval (CI), 0.78 to 0.99), 0.76 (95% CI, 0.69 to 093), 0.73 (95% CI, 0.58 to 0.91), and 0.59 (95% CI, 0.41 to 0.79), respectively. By stepwise logistic regression, a plasma mt-DNA concentration greater than 3,380 GE/ml (adjusted odds ratio (OR), 8.22; 95% CI, 1.72 to 39.18; P < 0.001) and a plasma value of H-FBAP >6.8 ng/ml (OR, 5.36; 95% CI, 1.06 to 27.08; P < 0.01) were the only independent predictors of mortality. Conclusions mt-DNA and H-FBAP might be promising markers for predicting 15-day mortality in massive PE, with mt-DNA having better prognostic accuracy.
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Eph receptors and their ligands: promising molecular biomarkers and therapeutic targets in prostate cancer. Biochim Biophys Acta Rev Cancer 2013; 1835:243-57. [PMID: 23396052 DOI: 10.1016/j.bbcan.2013.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/21/2013] [Accepted: 01/25/2013] [Indexed: 01/01/2023]
Abstract
Although at present, there is a high incidence of prostate cancer, particularly in the Western world, mortality from this disease is declining and occurs primarily only from clinically significant late stage tumors with a poor prognosis. A major current focus of this field is the identification of new biomarkers which can detect earlier, and more effectively, clinically significant tumors from those deemed "low risk", as well as predict the prognostic course of a particular cancer. This strategy can in turn offer novel avenues for targeted therapies. The large family of Receptor Tyrosine Kinases, the Ephs, and their binding partners, the ephrins, has been implicated in many cancers of epithelial origin through stimulation of oncogenic transformation, tumor angiogenesis, and promotion of increased cell survival, invasion and migration. They also show promise as both biomarkers of diagnostic and prognostic value and as targeted therapies in cancer. This review will briefly discuss the complex roles and biological mechanisms of action of these receptors and ligands and, with regard to prostate cancer, highlight their potential as biomarkers for both diagnosis and prognosis, their application as imaging agents, and current approaches to assessing them as therapeutic targets. This review demonstrates the need for future studies into those particular family members that will prove helpful in understanding the biology and potential as targets for treatment of prostate cancer.
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Dvořáková M, Karafiát V, Pajer P, Kluzáková E, Jarkovská K, Peková S, Krutílková L, Dvořák M. DNA released by leukemic cells contributes to the disruption of the bone marrow microenvironment. Oncogene 2012; 32:5201-9. [PMID: 23222712 DOI: 10.1038/onc.2012.553] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 12/22/2022]
Abstract
Reciprocal interactions between a tumor and its microenvironment control expansion of tumor cells. Here we show a specific type of interaction in which blasts of experimental leukemia destroy the bone marrow (BM) structures and kill stromal cells. The in vitro experiments showed that the cytotoxic agent released by leukemic cells is the fragmented DNA derived from their genome and occurring in nucleosome-like complexes. This DNA entered nuclei of BM or other cells and induced H2A.X phosphorylation at serine 139, similar to double-strand break-inducing agents. There was a correlation between large amounts of acquired DNA and death of recipient cells. Moreover, the DNA integrated into chromosomal DNA of recipient cells. Primary human acute myeloid leukemia cells also released fragmented DNA that penetrated the nuclei of other cells both in vitro and in vivo. We suggest that DNA fragments released from leukemic and also perhaps other types of tumor cells can activate DNA repair mechanisms or death in recipient cells of a tumor microenvironment, depending on the amount of the acquired DNA. This can impair DNA stability and viability of tumor stromal cells, undermine homeostatic capacity of tumor microenvironment and facilitate tumor progression.
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Affiliation(s)
- M Dvořáková
- Institute of Molecular Genetics, AS CR, Prague, Czech Republic
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Abstract
It has been estimated that 10(11) -10(12) cells, primarily of haematogenous origin, die in the adult human body daily, and a similar number is regenerated to maintain homeostasis. Despite the presence of an efficient scavenging system for dead cells, considerable amounts of fragmented genetic material enter the circulation in healthy individuals. Elevated blood levels of extracellular nucleic acids have been reported in various disease conditions; such as ageing and age-related degenerative disorders, cancer; acute and chronic inflammatory conditions, severe trauma and autoimmune disorders. In addition to genomic DNA and nucleosomes, mitochondrial DNA is also found in circulation, as are RNA and microRNA. There is extensive literature that suggests that extraneously added nucleic acids have biological actions. They can enter into cells in vitro and in vivo and induce genetic transformation and cellular and chromosomal damage; and experimentally added nucleic acids are capable of activating both innate and adaptive immune systems and inducing a sterile inflammatory response. The possibility as to whether circulating nucleic acids may, likewise, have biological activities has not been explored. In this review we raise the question as to whether circulating nucleic acids may have damaging effects on the host and be implicated in ageing and diverse acute and chronic human pathologies.
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Ronquist GK, Larsson A, Stavreus-Evers A, Ronquist G. Prostasomes are heterogeneous regarding size and appearance but affiliated to one DNA-containing exosome family. Prostate 2012; 72:1736-45. [PMID: 22539202 DOI: 10.1002/pros.22526] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/13/2012] [Indexed: 12/23/2022]
Abstract
BACKGROUND Prostate acinar epithelial cells release microvesicles (prostasomes) that possess pleiotropic biological effects relevant for successful fertilization. Prostasomes are formed in a similar way as exosomes but are heterogeneous as regards size and appearance. Like exosomes they are thought to be mediators of intercellular communication. METHODS We prepared seminal prostasomes in accordance with the prevailing protocol for exosome preparation including passage through a 0.2 µm filter and centrifugation in a sucrose gradient. RESULTS We compared the "filterable prostasomes" with those trapped on the filter ("nonfilterable prostasomes") and, qualitatively, no conspicuous differences were apparent regarding ultrastructure and SDS-PAGE banding pattern. Moreover, both types of prostasomes contained DNA fragments and Western blot revealed presence of prostate specific membrane antigen (PSMA), CD38, and annexin A1. CONCLUSIONS Reasonably, prostasomes could be included in the exosome family and be regarded as one entity containing chromosomal DNA.
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Affiliation(s)
- Göran K Ronquist
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden.
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Kostjuk S, Loseva P, Chvartatskaya O, Ershova E, Smirnova T, Malinovskaya E, Roginko O, Kuzmin V, Izhevskaia V, Baranova A, Ginter E, Veiko N. Extracellular GC-rich DNA activates TLR9- and NF-kB-dependent signaling pathways in human adipose-derived mesenchymal stem cells (haMSCs). Expert Opin Biol Ther 2012; 12 Suppl 1:S99-111. [PMID: 22594608 DOI: 10.1517/14712598.2012.690028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION The content of GC-rich ribosomal repeats (rDNA) in cell-free DNA (cfDNA) of patients with various diseases is several times higher as compared with genomic DNA (gDNA) and cfDNA of healthy donors. rDNA may act as Toll-like receptor 9 (TLR9) ligands and affect human adipose-derived mesenchymal stem cells (haMSCs). Here we explore effects of human cfDNAs and model rDNA fragments on cultured haMSCs. AREAS COVERED Both cfDNAs and cloned rDNA stimulate expression of TLR9 (qRT-PCR). Treatment with cloned rDNA leads to an increase in the number of TLR9(+) cells (FACS), expression levels for both TLR9 and Myd88, the translocation of nuclear factor-kappa B to the nuclei and up-regulation of TNFα and IL-10 cytokines (ELISA). As shown by an analysis of γH2AX-foci and MTT test, the preconditioning of haMSCs with cloned rDNA fragment increases the resistance of these cells to irradiation at 2Gy, while the treatments with control gDNA did not stimulate either TLR9- or NF-kB-dependent signaling pathways. EXPERT OPINION GC-rich sequences present in cfDNA stimulate endogenous stems cells when body is exposed to adverse conditions. GC-rich fragments of human DNA may be used for preconditioning of therapeutic MSCs aiming at an increase in their survival in the ailing body.
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Affiliation(s)
- Svetlana Kostjuk
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
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Peters DL, Pretorius PJ. Continuous adaptation through genetic communication – a putative role for cell-free DNA. Expert Opin Biol Ther 2012; 12 Suppl 1:S127-32. [DOI: 10.1517/14712598.2012.668518] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Rykova EY, Morozkin ES, Ponomaryova AA, Loseva EM, Zaporozhchenko IA, Cherdyntseva NV, Vlassov VV, Laktionov PP. Cell-free and cell-bound circulating nucleic acid complexes: mechanisms of generation, concentration and content. Expert Opin Biol Ther 2012; 12 Suppl 1:S141-53. [PMID: 22500614 DOI: 10.1517/14712598.2012.673577] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Extracellular nucleic acids are found in human blood and cell culture medium as cell-free or being adsorbed at cell surface. In the last years, the circulating extracellular nucleic acids in blood were shown to be associated with certain diseases. Attempts are made to develop non-invasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA. AREAS COVERED This article reviews accumulating data regarding cell-free and cell-surface-bound extracellular nucleic acid nature and generation mechanisms. Their existence as a constituent of the naturally occurring complexes with proteins or membrane-bearing particles is discussed with regard to their homeostatic concentration and distribution in healthy donor blood which are significantly altered in cancer patients. Gene-target and whole-genome studies reveal significant differences in gene representation between extracellular DNA and genome DNA. Overrepresentation of regions with high transcription activity has led to proposal that extracellular DNA generation is strongly dependent on the parent genome functionality, which is associated with chromosome packaging and DNA methylation levels. EXPERT OPINION Recent studies provide evidence of the circulating nucleome organization complexity indicating that discovery of extracellular DNA generation and circulation patterns in healthy condition and cancer is essential to enable the development of proper approaches for the selection of valid diagnostic markers.
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Affiliation(s)
- Elena Y Rykova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Acad. Lavrentyev Prosp., Novosibirsk, Russia.
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Jylhävä J, Lyytikäinen LP, Kähönen M, Hutri-Kähönen N, Kettunen J, Viikari J, Raitakari OT, Lehtimäki T, Hurme M. A genome-wide association study identifies UGT1A1 as a regulator of serum cell-free DNA in young adults: The Cardiovascular Risk in Young Finns Study. PLoS One 2012; 7:e35426. [PMID: 22511988 PMCID: PMC3325226 DOI: 10.1371/journal.pone.0035426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 03/16/2012] [Indexed: 01/13/2023] Open
Abstract
Introduction Circulating cell-free DNA (cf-DNA) is a useful indicator of cell death, and it can also be used to predict outcomes in various clinical disorders. Several innate immune mechanisms are known to be involved in eliminating DNA and chromatin-related material as part of the inhibition of potentially harmful autoimmune responses. However, the exact molecular mechanism underlying the clearance of circulating cf-DNA is currently unclear. Methods To examine the mechanisms controlling serum levels of cf-DNA, we carried out a genome-wide association analysis (GWA) in a cohort of young adults (aged 24–39 years; n = 1841; 1018 women and 823 men) participating in the Cardiovascular Risk in Young Finns Study. Genotyping was performed with a custom-built Illumina Human 670 k BeadChip. The Quant-iTTM high sensitivity DNA assay was used to measure cf-DNA directly from serum. Results The results revealed that 110 single nucleotide polymorphisms (SNPs) were associated with serum cf-DNA with genome-wide significance (p<5×10−8). All of these significant SNPs were localised to chromosome 2q37, near the UDP-glucuronosyltransferase 1 (UGT1) family locus, and the most significant SNPs localised within the UGT1 polypeptide A1 (UGT1A1) gene region. Conclusion The UGT1A1 enzyme catalyses the detoxification of several drugs and the turnover of many xenobiotic and endogenous compounds by glucuronidating its substrates. These data indicate that UGT1A1-associated processes are also involved in the regulation of serum cf-DNA concentrations.
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Affiliation(s)
- Juulia Jylhävä
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.
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