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Tutanov O, Shefer A, Shefer E, Ruzankin P, Tsentalovich Y, Tamkovich S. DNA-Binding Proteins and Passenger Proteins in Plasma DNA-Protein Complexes: Imprint of Parental Cells or Key Mediators of Carcinogenesis Processes? Int J Mol Sci 2024; 25:5165. [PMID: 38791202 PMCID: PMC11121045 DOI: 10.3390/ijms25105165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Knowledge of the composition of proteins that interact with plasma DNA will provide a better understanding of the homeostasis of circulating nucleic acids and the various modes of interaction with target cells, which may be useful in the development of gene targeted therapy approaches. The goal of the present study is to shed light on the composition and architecture of histone-containing nucleoprotein complexes (NPCs) from the blood plasma of healthy females (HFs) and breast cancer patients (BCPs) and to explore the relationship of proteins with crucial steps of tumor progression: epithelial-mesenchymal transition (EMT), cell proliferation, invasion, cell migration, stimulation of angiogenesis, and immune response. MALDI-TOF mass spectrometric analysis of NPCs isolated from blood samples using affine chromatography was performed. Bioinformatics analysis showed that the shares of DNA-binding proteins in the compositions of NPCs in normal and cancer patients are comparable and amount to 40% and 33%, respectively; in total, we identified 38 types of DNA-binding motifs. Functional enrichment analysis using FunRich 3.13 showed that, in BCP blood, the share of DNA-binding proteins involved in nucleic acid metabolism increased, while the proportion of proteins involved in intercellular communication and signal transduction decreased. The representation of NPC passenger proteins in breast cancer also changes: the proportion of proteins involved in transport increases and the share of proteins involved in energy biological pathways decreases. Moreover, in the HF blood, proteins involved in the processes of apoptosis were more represented in the composition of NPCs and in the BCP blood-in the processes of active secretion. For the first time, bioinformatics approaches were used to visualize the architecture of circulating NPCs in the blood and to show that breast cancer has an increased representation of passenger proteins involved in EMT, cell proliferation, invasion, cell migration, and immune response. Using breast cancer protein data from the Human Protein Atlas (HPA) and DEPC, we found that 86% of NPC proteins in the blood of BCPs were not previously annotated in these databases. The obtained data may indirectly indicate directed protein sorting in NPCs, which, along with extracellular vesicles, can not only be diagnostically significant molecules for liquid biopsy, but can also carry out the directed transfer of genetic material from donor cells to recipient cells.
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Affiliation(s)
- Oleg Tutanov
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA;
| | - Aleksei Shefer
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Evgenii Shefer
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Laboratory of Applied Inverse Problems, Sobolev Institute of Mathematics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Ruzankin
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Laboratory of Applied Inverse Problems, Sobolev Institute of Mathematics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Yuri Tsentalovich
- Laboratory of Proteomics and Metabolomics, International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Svetlana Tamkovich
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Novosibirsk State University, 630090 Novosibirsk, Russia
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2
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Smalheiser NR. Mobile circular DNAs regulating memory and communication in CNS neurons. Front Mol Neurosci 2023; 16:1304667. [PMID: 38125007 PMCID: PMC10730651 DOI: 10.3389/fnmol.2023.1304667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Stimuli that stimulate neurons elicit transcription of immediate-early genes, a process which requires local sites of chromosomal DNA to form double-strand breaks (DSBs) generated by topoisomerase IIb within a few minutes, followed by repair within a few hours. Wakefulness, exploring a novel environment, and contextual fear conditioning also elicit turn-on of synaptic genes requiring DSBs and repair. It has been reported (in non-neuronal cells) that extrachromosomal circular DNA can form at DSBs as the sites are repaired. I propose that activated neurons may generate extrachromosomal circular DNAs during repair at DSB sites, thus creating long-lasting "markers" of that activity pattern which contain sequences from their sites of origin and which regulate long-term gene expression. Although the population of extrachromosomal DNAs is diverse and overall associated with pathology, a subclass of small circular DNAs ("microDNAs," ∼100-400 bases long), largely derives from unique genomic sequences and has attractive features to act as stable, mobile circular DNAs to regulate gene expression in a sequence-specific manner. Circular DNAs can be templates for the transcription of RNAs, particularly small inhibitory siRNAs, circular RNAs and other non-coding RNAs that interact with microRNAs. These may regulate translation and transcription of other genes involved in synaptic plasticity, learning and memory. Another possible fate for mobile DNAs is to be inserted stably into chromosomes after new DSB sites are generated in response to subsequent activation events. Thus, the insertions of mobile DNAs into activity-induced genes may tend to inactivate them and aid in homeostatic regulation to avoid over-excitation, as well as providing a "counter" for a neuron's activation history. Moreover, activated neurons release secretory exosomes that can be transferred to recipient cells to regulate their gene expression. Mobile DNAs may be packaged into exosomes, released in an activity-dependent manner, and transferred to recipient cells, where they may be templates for regulatory RNAs and possibly incorporated into chromosomes. Finally, aging and neurodegenerative diseases (including Alzheimer's disease) are also associated with an increase in DSBs in neurons. It will become important in the future to assess how pathology-associated DSBs may relate to activity-induced mobile DNAs, and whether the latter may potentially contribute to pathogenesis.
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Affiliation(s)
- Neil R. Smalheiser
- Department of Psychiatry, University of Illinois College of Medicine, Chicago, IL, United States
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3
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Chauhan US, Kohale MG, Jaiswal N, Wankhade R. Emerging Applications of Liquid Biopsies in Ovarian Cancer. Cureus 2023; 15:e49880. [PMID: 38174205 PMCID: PMC10762500 DOI: 10.7759/cureus.49880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Liquid biopsy is a new diagnostic tool in precision oncology that can be used as a complementary or alternative method to surgical biopsies. It is a cutting-edge sampling technique that examines distinct cancer components, such as exosomes and circulating tumor cells discharged into the peripheral circulation, to identify tumor biomarkers through various methods, including polymerase chain reaction (PCR). Liquid biopsy has several benefits, including its non-invasiveness and practicality, which permit serial sampling and long-term monitoring of dynamic tumor changes. Ovarian cancer (OC), the most lethal gynecologic malignancy in the world, is typically diagnosed at stages II and III, which makes recovery and treatment extremely difficult. Relapsed OC and chemotherapy resistance of ovarian tumor cells are other clinical challenges. Although liquid biopsy is not a routinely used diagnostic test, it should be utilized in the diagnosis and prognosis of OC for early detection and treatment. It is less intrusive than conventional tissue biopsies, allowing for the continuous collection of serial blood samples to track cancer development in real time. Before therapeutic application, more investigation is required to pinpoint the particular release processes, the source tissue, and the biological significance of the bulk of liquid biopsy contents.
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Affiliation(s)
- Urvi S Chauhan
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Mangesh G Kohale
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Neha Jaiswal
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Rashmi Wankhade
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
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4
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Tutanov O, Shefer A, Tsentalovich Y, Tamkovich S. Comparative Analysis of Molecular Functions and Biological Role of Proteins from Cell-Free DNA-Protein Complexes Circulating in Plasma of Healthy Females and Breast Cancer Patients. Int J Mol Sci 2023; 24:ijms24087279. [PMID: 37108441 PMCID: PMC10138639 DOI: 10.3390/ijms24087279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Cell-free DNA (cfDNA) circulates in the bloodstream packed in membrane-coated structures (such as apoptotic bodies) or bound to proteins. To identify proteins involved in the formation of deoxyribonucleoprotein complexes circulating in the blood, native complexes were isolated using affinity chromatography with immobilized polyclonal anti-histone antibodies from plasma of healthy females (HFs) and breast cancer patients (BCPs). It was found that the nucleoprotein complexes (NPCs) from HF plasma samples contained shorter DNA fragments (~180 bp) than BCP NPCs. However, the share of DNA in the NPCs from cfDNA in blood plasma in HFs and BCPs did not differ significantly, as well as the share of NPC protein from blood plasma total protein. Proteins were separated by SDS-PAGE and identified by MALDI-TOF mass spectrometry. Bioinformatic analysis showed that in the presence of a malignant tumor, the proportion of proteins involved in ion channels, protein binding, transport, and signal transduction increased in the composition of blood-circulating NPCs. Moreover, 58 (35%) proteins are differentially expressed in a number of malignant neoplasms in the NPCs of BCPs. Identified NPC proteins from BCP blood can be recommended for further testing as breast cancer diagnostic/prognostic biomarkers or as being useful in developing gene-targeted therapy approaches.
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Affiliation(s)
- Oleg Tutanov
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksei Shefer
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Yuri Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
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5
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The Prognostic Value of a Single, Randomly Timed Circulating Tumor DNA Measurement in Patients with Metastatic Melanoma. Cancers (Basel) 2022; 14:cancers14174158. [PMID: 36077695 PMCID: PMC9455041 DOI: 10.3390/cancers14174158] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary In this study, we investigated the associations of circulating tumor DNA (ctDNA), measured at a random time point during the patient’s treatment, with tumor progression and routine blood markers (protein S100, lactate dehydrogenase (LDH), and C-reactive protein (CRP)) in a cohort of patients with metastatic melanoma. Detectable ctDNA was associated with the presence of extracerebral disease, tumor progression, and poorer overall survival (OS). Elevated S100 and CRP was correlated with detectable ctDNA, whereas LDH was not. Our results further support the use of ctDNA in the clinical management of patients with metastatic melanoma. Abstract Melanoma currently lacks validated blood-based biomarkers for monitoring and predicting treatment efficacy. Circulating tumor DNA (ctDNA), originating from tumor cells and detectable in plasma, has emerged as a possible biomarker in patients with metastatic melanoma. In this retrospective, single-center study, we collected 129 plasma samples from 79 patients with stage IIIB–IV melanoma as determined by the American Joint Committee on Cancer (AJCC, 8th edition). For the determination of ctDNA levels, we used eight different assays of droplet digital polymerase chain reaction (ddPCR) to detect the most common hotspot mutations in the BRAF and NRAS genes. The aim of the study was to investigate the association of the detectability of ctDNA at a non-prespecified time point in a patient’s treatment with tumor progression, and to correlate ctDNA with commonly used biomarkers (protein S100, LDH, and CRP). Patients with detectable ctDNA progressed more frequently in PET-CT within 12 months than those without detectable ctDNA. Detectability of ctDNA was associated with shorter OS in univariate and multivariate analyses. ctDNA was detectable in a statistically significantly larger proportion of patients with distant metastases (79%) than in patients with no distant metastases or only intracranial metastases (32%). Elevated protein S100 and CRP correlated better with detectable ctDNA than LDH. This study supports the potential of ctDNA as a prognostic biomarker in patients with metastatic melanoma. However, additional prospective longitudinal studies with quantitative assessments of ctDNA are necessary to investigate the limitations and strengths of ctDNA as a biomarker.
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6
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Mishra S, Dubey DB, Agarwal K, Dubey DB, Verma S, Shabbir N, Kushwaha R, Reddy DH, Singh US, Ali W. Circulating Cell-Free DNA Level in Prediction of COVID-19 Severity and Mortality: Correlation of with Haematology and Serum Biochemical Parameters. Indian J Clin Biochem 2022; 38:172-181. [PMID: 36032561 PMCID: PMC9392861 DOI: 10.1007/s12291-022-01082-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/22/2022] [Indexed: 01/08/2023]
Abstract
Lymphocyte dysregulation in coronavirus disease-19 (COVID-19) is a major contributing factor linked to disease severity and mortality. Apoptosis results in the accumulation of cell-free DNA (cfDNA) in circulation. COVID-19 has a heterogeneous clinical course. The role of cfDNA levels was studied to assess the severity and outcome of COVID-19 patients and correlated with other laboratory parameters. The current case series included 100 patients with mild COVID-19 (MCOV-19) and 106 patients with severe COVID-19 (SCOV-19). Plasma cfDNA levels were quantified using SYBR green quantitative real-time PCR through amplification of the β-actin gene. CfDNA level was significantly higher in SCOV-19 at 706.7 ng/ml (522.6–1258) as compared to MCOV-19 at 219.8 ng/ml (167.7–299.6). The cfDNA levels were significantly higher in non-survivor than in survivors (p = 0.0001). CfDNA showed a significant correlation with NLR, ferritin, LDH, procalcitonin, and IL-6. The diagnostic sensitivity and specificity of cfDNA in the discrimination of SCOV-19 from MCOV-19 were 90.57% & 80%, respectively. CfDNA showed a sensitivity of 94.74% in the differentiation of non-survivors from survivors. CfDNA levels showed a significant positive correlation with other laboratory and inflammatory markers of COVID-19. CfDNA levels, NLR, and other parameters may be used to stratify and monitor COVID-19 patients and predict mortality. CfDNA may be used to predict COVID-19 severity with higher diagnostic sensitivity.
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Affiliation(s)
- Sridhar Mishra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Gomti Nagar, Lucknow, Uttar Pradesh 22610 India
| | - Devanshi B. Dubey
- Department of Pathology, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
| | - Krachi Agarwal
- Department of Pathology, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
| | - Deval B. Dubey
- Department of Pathology, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
| | - Shweta Verma
- Department of Pathology, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
| | - Nida Shabbir
- Department of Pathology, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
| | - Rashmi Kushwaha
- Department of Pathology, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
| | - D Himanshu Reddy
- Department of Internal Medicine, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
| | - Uma Shankar Singh
- Department of Pathology, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
| | - Wahid Ali
- Department of Pathology, King George Medical University, Lucknow, Chowk, Uttar Pradesh 226003 India
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7
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Zhu JW, Charkhchi P, Akbari MR. Potential clinical utility of liquid biopsies in ovarian cancer. Mol Cancer 2022; 21:114. [PMID: 35545786 PMCID: PMC9092780 DOI: 10.1186/s12943-022-01588-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. One of the main challenges in the management of OC is the late clinical presentation of disease that results in poor survival. Conventional tissue biopsy methods and serological biomarkers such as CA-125 have limited clinical applications. Liquid biopsy is a novel sampling method that analyzes distinctive tumour components released into the peripheral circulation, including circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free RNA (cfRNA), tumour-educated platelets (TEPs) and exosomes. Increasing evidence suggests that liquid biopsy could enhance the clinical management of OC by improving early diagnosis, predicting prognosis, detecting recurrence, and monitoring response to treatment. Capturing the unique tumour genetic landscape can also guide treatment decisions and the selection of appropriate targeted therapies. Key advantages of liquid biopsy include its non-invasive nature and feasibility, which allow for serial sampling and longitudinal monitoring of dynamic tumour changes over time. In this review, we outline the evidence for the clinical utility of each liquid biopsy component and review the advantages and current limitations of applying liquid biopsy in managing ovarian cancer. We also highlight future directions considering the current challenges and explore areas where more studies are warranted to elucidate its emerging clinical potential.
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Affiliation(s)
- Jie Wei Zhu
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada.,Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Parsa Charkhchi
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada. .,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada. .,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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8
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Chen Y, Zhao Y, Yin Y, Jia X, Mao L. Mechanism of cargo sorting into small extracellular vesicles. Bioengineered 2021; 12:8186-8201. [PMID: 34661500 PMCID: PMC8806638 DOI: 10.1080/21655979.2021.1977767] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are special membranous structures released by almost every cell type that carry and protect some biomolecules from being degraded. They transport important signaling molecules involved in cell communication, migration, and numerous physiological processes. EVs can be categorized into two main types according to their size: i) small extracellular vesicles (sEVs), such as exosomes (30-150 nm), released from the fusion of multivesicular bodies (MVBs) with the plasma membrane, and ii) large EVs, such as microvesicles (100-1000 nm). These are no longer considered a waste product of cells, but regulators of intercellular communication, as they can transport specific repertoires of cargos, such as proteins, lipids, and nucleic acids to receptor cells to achieve cell-to-cell communication. This indicates the existence of different mechanisms, which controls the cargos sorting into EVs. This review mainly gives a description about the biological roles of the cargo and the sorting mechanisms of sEVs, especially exosomes.
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Affiliation(s)
- Yiwen Chen
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yuxue Zhao
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yiqian Yin
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaonan Jia
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Lingxiang Mao
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
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9
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Bellassai N, D’Agata R, Marti A, Rozzi A, Volpi S, Allegretti M, Corradini R, Giacomini P, Huskens J, Spoto G. Detection of Tumor DNA in Human Plasma with a Functional PLL-Based Surface Layer and Plasmonic Biosensing. ACS Sens 2021; 6:2307-2319. [PMID: 34032412 PMCID: PMC8294610 DOI: 10.1021/acssensors.1c00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022]
Abstract
Standard protocols for the analysis of circulating tumor DNA (ctDNA) include the isolation of DNA from the patient's plasma and its amplification and analysis in buffered solutions. The application of such protocols is hampered by several factors, including the complexity and time-constrained preanalytical procedures, risks for sample contamination, extended analysis time, and assay costs. A recently introduced nanoparticle-enhanced surface plasmon resonance imaging-based assay has been shown to simplify procedures for the direct detection of tumor DNA in the patient's plasma, greatly simplifying the cumbersome preanalytical phase. To further simplify the protocol, a new dual-functional low-fouling poly-l-lysine (PLL)-based surface layer has been introduced that is described herein. The new PLL-based layer includes a densely immobilized CEEEEE oligopeptide to create a charge-balanced system preventing the nonspecific adsorption of plasma components on the sensor surface. The layer also comprises sparsely attached peptide nucleic acid probes complementary to the sequence of circulating DNA, e.g., the analyte that has to be captured in the plasma from cancer patients. We thoroughly investigated the contribution of each component of the dual-functional polymer to the antifouling properties of the surface layer. The low-fouling property of the new surface layer allowed us to detect wild-type and KRAS p.G12D-mutated DNA in human plasma at the attomolar level (∼2.5 aM) and KRAS p.G13D-mutated tumor DNA in liquid biopsy from a cancer patient with almost no preanalytical treatment of the patient's plasma, no need to isolate DNA from plasma, and without PCR amplification of the target sequence.
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Affiliation(s)
- Noemi Bellassai
- Department
of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95122 Catania, Italy
| | - Roberta D’Agata
- Department
of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95122 Catania, Italy
- INBB,
Istituto Nazionale di Biostrutture e Biosistemi, Viale delle Medaglie d’Oro, 305, 00136 Roma, Italy
| | - Almudena Marti
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science & Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Andrea Rozzi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 17/A, 43124 Parma, Italy
| | - Stefano Volpi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 17/A, 43124 Parma, Italy
| | - Matteo Allegretti
- Oncogenomics
and Epigenetics, IRCCS Regina Elena National
Cancer Institute, Via
Elio Chianesi, 53, 00144 Rome, Italy
| | - Roberto Corradini
- INBB,
Istituto Nazionale di Biostrutture e Biosistemi, Viale delle Medaglie d’Oro, 305, 00136 Roma, Italy
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 17/A, 43124 Parma, Italy
| | - Patrizio Giacomini
- Oncogenomics
and Epigenetics, IRCCS Regina Elena National
Cancer Institute, Via
Elio Chianesi, 53, 00144 Rome, Italy
| | - Jurriaan Huskens
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science & Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Giuseppe Spoto
- Department
of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95122 Catania, Italy
- INBB,
Istituto Nazionale di Biostrutture e Biosistemi, Viale delle Medaglie d’Oro, 305, 00136 Roma, Italy
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10
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Moradi-Marjaneh R, Asgharzadeh F, Khordad E, Marjaneh MM. The Clinical Impact of Quantitative Cell-free DNA, KRAS, and BRAF Mutations on Response to Anti-EGFR Treatment in Patients with Metastatic Colorectal Cancer. Curr Pharm Des 2021; 27:942-952. [PMID: 33030125 DOI: 10.2174/1381612826666201007163116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
Colorectal cancer (CRC) is one of the most common leading causes of cancer death in the world. Although EGFR inhibitors have established efficacy in metastatic colorectal cancer (mCRC), some patients do not respond to this treatment. The EGFR inhibitors' failure and acquired resistance are partly due to KRAS and BRAF mutations. Thus, prognostic biomarkers that help to select eligible patients are highly in demand. To improve patient selection, assessment of mutational status in circulating cell free DNA (cfDNA), which possibly represents the dynamicity of tumor genetic status better than tumor tissue, could be advantageous. This review summarizes the current knowledge of the prognostic value of cfDNA in patients with mCRC treated with EGFR inhibitors with emphasis on the clinical importance of identification of KRAS and BRAF mutations.
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Affiliation(s)
- Reyhaneh Moradi-Marjaneh
- Department of Basic Sciences, Faculty of Medicine, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Fereshteh Asgharzadeh
- Department of Physiology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Khordad
- Department of Physiology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
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11
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Hammad R, Eldosoky MAER, Fouad SH, Elgendy A, Tawfeik AM, Alboraie M, Abdelmaksoud MF. Circulating cell-free DNA, peripheral lymphocyte subsets alterations and neutrophil lymphocyte ratio in assessment of COVID-19 severity. Innate Immun 2021; 27:240-250. [PMID: 33646058 PMCID: PMC8054149 DOI: 10.1177/1753425921995577] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cell destruction results in plasma accumulation of cell-free DNA (cfDNA). Dynamic changes in circulating lymphocytes are features of COVID-19. We aimed to investigate if cfDNA level can serve in stratification of COVID-19 patients, and if cfDNA level is associated with alterations in lymphocyte subsets and neutrophil-to-lymphocyte ratio (NLR). This cross-sectional comparative study enrolled 64 SARS-CoV-2-positive patients. Patients were subdivided to severe and non-severe groups. Plasma cfDNA concentration was determined by real-time quantitative PCR. Lymphocyte subsets were assessed by flow cytometry. There was significant increase in cfDNA among severe cases when compared with non-severe cases. cfDNA showed positive correlation with NLR and inverse correlation with T cell percentage. cfDNA positively correlated with ferritin and C-reactive protein. The output data of performed ROC curves to differentiate severe from non-severe cases revealed that cfDNA at cut-off ≥17.31 ng/µl and AUC of 0.96 yielded (93%) sensitivity and (73%) specificity. In summary, excessive release of cfDNA can serve as sensitive COVID-19 severity predictor. There is an association between cfDNA up-regulation and NLR up-regulation and T cell percentage down-regulation. cfDNA level can be used in stratification and personalized monitoring strategies in COVID-19 patients.
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Affiliation(s)
- Reham Hammad
- Clinical Pathology Department, Faculty of Medicine (for Girls), Al-Azhar University, Egypt
| | | | - Shaimaa Hani Fouad
- Internal Medicine Allergy and Clinical Immunology, Ain-Shams University, Egypt
| | - Abdelaleem Elgendy
- Clinical Pathology Department, Faculty of Medicine (for Boys), Al-Azhar University, Egypt
| | - Amany M Tawfeik
- Microbiology and Immunology Department, Faculty of Medicine (for Girls), Al-Azhar University, Egypt
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12
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Vasilyeva I, Bespalov V, Baranova A, Voznyuk I, Baranenko D. Differential Dynamics of the Levels of Low Molecular Weight DNA Fragments in the Plasma of Patients With Ischemic and Hemorrhagic Strokes. Basic Clin Neurosci 2020; 11:805-810. [PMID: 33850617 PMCID: PMC8019841 DOI: 10.32598/bcn.11.6.1639.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/10/2019] [Accepted: 02/16/2019] [Indexed: 11/23/2022] Open
Abstract
Introduction: To evaluate Low-Molecular-weight (LMW) DNA as a possible prognostic biomarker in acute ischemic and hemorrhagic stroke. Methods: LMW DNA samples were isolated from plasma and cerebrospinal fluid by phenol deproteinization, analyzed by gradient polyacrylamide electrophoresis and quantified by spectrophotometry. Results: Two common types of stroke, i.e. ischemic and hemorrhagic, differ by the temporal dynamics of cell-free DNA (cfDNA) accumulation. In hemorrhagic stroke, an initial increase in LMW DNA levels, most likely reflects an extent of the tissue damage, while in ischemic patients, the LMW DNA levels increase in parallel with the damage caused by hypoxia and subsequent compensatory reperfusion. Conclusion: These time-course data specify optimal assessment windows with maximum differentiating power for stroke outcomes: 24–48 hours post-event for ischemic stroke, and as close as possible to the moment of hospital admission for hemorrhagic stroke. These data also indicate the role of apoptosis in the formation of ischemic focus.
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Affiliation(s)
- Irina Vasilyeva
- Laboratory of Cancer Chemoprevention and Oncopharmacology, N.N.Petrov National Medical Research Center of Oncology, St.-Petersburg, Russia.,International Research Center 'Biotechnologies of the Third Millennium' ITMO University, St.-Petersburg, Russia
| | - Vladimir Bespalov
- Laboratory of Cancer Chemoprevention and Oncopharmacology, N.N.Petrov National Medical Research Center of Oncology, St.-Petersburg, Russia.,International Research Center 'Biotechnologies of the Third Millennium' ITMO University, St.-Petersburg, Russia
| | - Ancha Baranova
- Department of George, School of Systemic Biology, George Mason University, Fairfax, VA, USA.,Laboratory of Functional Genomics, Research Center for Medical Genetics, Moscow, Russia.,Scientific Council, Atlas Biomed Group, Moscow, Russia
| | - Igor Voznyuk
- Department of Acute Cerebrovascular Pathology and Emergency Neurology, Saint-Petersburg I.I. Dzhanelidze Research Institute for Emergency Medicine, St.-Petersburg, Russia
| | - Denis Baranenko
- Department of Acute Cerebrovascular Pathology and Emergency Neurology, Saint-Petersburg I.I. Dzhanelidze Research Institute for Emergency Medicine, St.-Petersburg, Russia
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13
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Direct plasmonic detection of circulating RAS mutated DNA in colorectal cancer patients. Biosens Bioelectron 2020; 170:112648. [PMID: 33010708 DOI: 10.1016/j.bios.2020.112648] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/01/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022]
Abstract
RAS mutations in the blood of colorectal cancer (CRC) patients are emerging as biomarkers of acquired resistance to Epidermal Growth Factor Receptor therapy. Unfortunately, reliable assays granting fast, real-time monitoring of treatment response, capable of refining retrospective, tissue-based analysis, are still needed. Recently, several methods for detecting blood RAS mutations have been proposed, generally relying on multi-step and PCR-based, time-consuming and cost-ineffective procedures. By exploiting a liquid biopsy approach, we developed an ultrasensitive nanoparticle-enhanced plasmonic method for detecting ~1 aM RAS single nucleotide variants (SNVs) in the plasma of CRC patients. The assay does not require the extraction of tumor DNA from plasma and detects it in volumes as low as 40 μL of plasma, which is at least an order of magnitude smaller than that required by state of the art liquid biopsy technologies. The most prevalent RAS mutations are detected in DNA from tumor tissue with 100% sensitivity and 83.33% specificity. Spike-in experiments in human plasma further encouraged assay application on clinical specimens. The assay was proven in plasma from CRC patients and healthy donors, and full discrimination between mutated DNA from patients over wild-type DNA from healthy volunteers was obtained thus demonstrating its promising avenue for cancer monitoring based on liquid biopsy.
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14
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Truszewska A, Wirkowska A, Gala K, Truszewski P, Krzemień-Ojak Ł, Perkowska-Ptasińska A, Mucha K, Pączek L, Foroncewicz B. Cell-free DNA profiling in patients with lupus nephritis. Lupus 2020; 29:1759-1772. [DOI: 10.1177/0961203320957717] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Increased level of cell-free DNA (cf-DNA) is associated with systemic lupus erythematosus (SLE) and might be related to disease activity. The aim of this study was to evaluate whether cfDNA integrity, size distribution and concentration of different cfDNA fractions is associated with lupus activity and kidney involvement. Methods Blood samples were collected from 43 SLE patients and 50 healthy controls. Nuclear and mitochondrial fractions of cfDNA and intracellular DNA were quantified by real-time qPCR. Sizing and quantification of total cfDNA level was performed on Bioanalyzer. Results We determined four parameters that characterized cfDNA profile: fragmentation index, ratio of intra- to extracellular mtDNA copy number, cfDNA concentration, and presence of 54–149 bp and 209–297 bp fragments. Patients with healthy-like cfDNA profile had higher eGFR ( P = 0.009) and more often no indications for kidney biopsy or less advanced lupus nephritis (LN) ( P = 0.037). In contrary, SLE patients with distinct cfDNA profile (characterized by increased cfDNA concentration and fragmentation, higher discrepancy between intra- to extracellular mtDNA copy number, and the presence of 54–149 bp and 209–297 bp fragments) had lower eGFR ( P = 0.005) and more often advanced LN or history of renal transplantation ( P = 0.001). Conclusions We showed that cfDNA profiling may help to distinguish SLE patients with renal involvement and severe disease course from patients with more favorable outcomes. We suggest cfDNA profile a promising SLE biomarker.
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Affiliation(s)
- Anna Truszewska
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Wirkowska
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Gala
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Truszewski
- Department of Orthopedics and Traumatology of Musculoskeletal System, Baby Jesus Clinical Hospital, Warsaw, Poland
| | - Łucja Krzemień-Ojak
- Laboratory of the Molecular Biology of Cancer, Centre of New Technologies, Warsaw, Poland
| | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Foroncewicz
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
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15
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Shmarina GV, Ershova ES, Simashkova NV, Nikitina SG, Chudakova JM, Veiko NN, Porokhovnik LN, Basova AY, Shaposhnikova AF, Pukhalskaya DA, Pisarev VM, Korovina NJ, Gorbachevskaya NL, Dolgikh OA, Bogush M, Kutsev SI, Kostyuk SV. Oxidized cell-free DNA as a stress-signaling factor activating the chronic inflammatory process in patients with autism spectrum disorders. J Neuroinflammation 2020; 17:212. [PMID: 32677958 PMCID: PMC7364812 DOI: 10.1186/s12974-020-01881-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/25/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Autism spectrum disorders (ASD) are known to be associated with an inflammatory process related to immune system dysfunction. This study's aim was to investigate the role of cell-free DNA in chronic inflammatory process in ASD patients. METHODS The study included 133 ASD patients and 27 healthy controls. Sixty-two ASD patients were demonstrated to have mild-to-moderate disease severity (group I) and 71 individuals to have severe ASD (group II). Plasma cell-free (cf) DNA characteristics, plasma cytokine concentrations, expression of the genes for NFкB1 transcription factor and pro-inflammatory cytokines TNFα, IL-1β and IL-8 in peripheral blood lymphocytes (PBL) of ASD patients, and unaffected controls were investigated. Additionally, in vitro experiments with oxidized DNA supplementation to PBL cultures derived from ASD patients and healthy controls were performed. RESULTS The data indicates that ASD patients have demonstrated increased cfDNA concentration in their circulation. cfDNA of patients with severe ASD has been characterized by a high abundance of oxidative modification. Furthermore, ASD patients of both groups have shown elevated plasma cytokine (IL-1β, IL-8, IL-17A) levels and heightened expression of genes for NFкB1 nuclear factor and pro-inflammatory cytokines TNFα, IL-1β, and IL-8 in PBL. In vitro experiments have shown that NF-κB/cytokine mRNA expression profiles of ASD patient PBL treated with oxidized DNA fragments were significantly different from those of healthy controls. CONCLUSIONS It may be proposed that oxidized cfDNA plays a role of stress-signaling factor activating the chronic inflammatory process in patients with ASD.
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Affiliation(s)
- Galina V Shmarina
- Research Centre for Medical Genetics, Moscow, Russia.
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.
- G.N. Gabrichevsky Institute of Epidemiology and Microbiology, Moscow, Russia.
| | - Elizaveta S Ershova
- Research Centre for Medical Genetics, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | | | | | | | | | - Anna Y Basova
- G.E. Sukhareva Scientific-Practical Centre for Mental Health of Children and Adolescents, Moscow, Russia
| | - Antonina F Shaposhnikova
- G.E. Sukhareva Scientific-Practical Centre for Mental Health of Children and Adolescents, Moscow, Russia
| | | | - Vladimir M Pisarev
- V. A. Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Natalia J Korovina
- G.E. Sukhareva Scientific-Practical Centre for Mental Health of Children and Adolescents, Moscow, Russia
| | - Natalia L Gorbachevskaya
- G.E. Sukhareva Scientific-Practical Centre for Mental Health of Children and Adolescents, Moscow, Russia
| | | | - Marina Bogush
- Rowan University Biological Sciences Department, Science Hall, Glassboro, NJ, USA
| | | | - Svetlana V Kostyuk
- Research Centre for Medical Genetics, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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16
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Delmonico L, Alves G, Bines J. Cell free DNA biology and its involvement in breast carcinogenesis. Adv Clin Chem 2020; 97:171-223. [PMID: 32448434 DOI: 10.1016/bs.acc.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid biopsy represents a procedure for minimally invasive analysis of non-solid tissue, blood and other body fluids. It comprises a set of analytes that includes circulating tumor cells (CTCs) and circulating free DNA (cfDNA), RNA, long noncoding RNA (lncRNA) and micro RNA (miRNA), as well as extracellular vesicles. These novel analytes represent an alternative tool to complement diagnosis and monitor and predict response to treatment of the tumoral process and may be used for other disease processes such viral and parasitic infection. This review focuses on the biologic and molecular characteristics of cfDNA in general and the molecular changes (mutational and epigenetic) proven useful in oncologic practice for diagnosis, monitoring and treatment of breast cancer specifically.
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Affiliation(s)
- Lucas Delmonico
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Gilda Alves
- Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - José Bines
- Instituto Nacional de Câncer (INCA-HCIII), Rio de Janeiro, Brazil
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17
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Bingham N, Spencer A. The role of cell free DNA and liquid biopsies in haematological conditions. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:521-531. [PMID: 35582436 PMCID: PMC8992501 DOI: 10.20517/cdr.2019.93] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cell free nucleic acids (CFNAs) are nucleic acids released from cells that circulate within bodily fluids. Recent advances in molecular techniques have led the ability to interrogate CFNAs in a clinically meaningful way, for example the identification and assessment of foetal CFNAs in maternal blood, allowing minimally invasive testing for foetal genetic abnormalities. The majority of CFNAs arise from haemopoietic cells, making it a particularly rich source of genetic information in haematological conditions. Furthermore, the innate genetic heterogeneity of haematological malignancies, as epitomised by multiple myeloma, lend itself well to “liquid biopsies”. This approach promises to provide a more wholistic assessment of whole disease genetics, especially when contrasted against the current gold-standard of single site tissue biopsies. This review briefly summarises the definitions and physiology of CFNAs, both cell free DNA (cfDNA) and extracellular RNA (exRNA), before exploring the literature surrounding the current and future roles of cfDNA in the haematological malignancies and patient care.
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Affiliation(s)
- Nicholas Bingham
- Australian Centre for Blood Diseases, Monash University, Victoria 3181, Australia
| | - Andrew Spencer
- Australian Centre for Blood Diseases, Monash University, Victoria 3181, Australia
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18
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Sierra J, Marrugo-Ramírez J, Rodriguez-Trujillo R, Mir M, Samitier J. Sensor-Integrated Microfluidic Approaches for Liquid Biopsies Applications in Early Detection of Cancer. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1317. [PMID: 32121271 PMCID: PMC7085501 DOI: 10.3390/s20051317] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/13/2022]
Abstract
Cancer represents one of the conditions with the most causes of death worldwide. Common methods for its diagnosis are based on tissue biopsies-the extraction of tissue from the primary tumor, which is used for its histological analysis. However, this technique represents a risk for the patient, along with being expensive and time-consuming and so it cannot be frequently used to follow the progress of the disease. Liquid biopsy is a new cancer diagnostic alternative, which allows the analysis of the molecular information of the solid tumors via a body fluid draw. This fluid-based diagnostic method displays relevant advantages, including its minimal invasiveness, lower risk, use as often as required, it can be analyzed with the use of microfluidic-based platforms with low consumption of reagent, and it does not require specialized personnel and expensive equipment for the diagnosis. In recent years, the integration of sensors in microfluidics lab-on-a-chip devices was performed for liquid biopsies applications, granting significant advantages in the separation and detection of circulating tumor nucleic acids (ctNAs), circulating tumor cells (CTCs) and exosomes. The improvements in isolation and detection technologies offer increasingly sensitive and selective equipment's, and the integration in microfluidic devices provides a better characterization and analysis of these biomarkers. These fully integrated systems will facilitate the generation of fully automatized platforms at low-cost for compact cancer diagnosis systems at an early stage and for the prediction and prognosis of cancer treatment through the biomarkers for personalized tumor analysis.
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Affiliation(s)
- Jessica Sierra
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC) Barcelona Institute of Science and Technology (BIST), 12 Baldiri Reixac 15-21, 08028 Barcelona, Spain; (J.S.); (R.R.-T.); (J.S.)
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
| | - José Marrugo-Ramírez
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
| | - Romen Rodriguez-Trujillo
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC) Barcelona Institute of Science and Technology (BIST), 12 Baldiri Reixac 15-21, 08028 Barcelona, Spain; (J.S.); (R.R.-T.); (J.S.)
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
| | - Mònica Mir
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC) Barcelona Institute of Science and Technology (BIST), 12 Baldiri Reixac 15-21, 08028 Barcelona, Spain; (J.S.); (R.R.-T.); (J.S.)
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain
| | - Josep Samitier
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC) Barcelona Institute of Science and Technology (BIST), 12 Baldiri Reixac 15-21, 08028 Barcelona, Spain; (J.S.); (R.R.-T.); (J.S.)
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain
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19
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Shmarina GV, Orlova MD, Ershova ES, Jestkova EM, Martynov AV, Veiko NN, Konkova MS, Dolgikh OA, Filev AD, Kostyuk SV. NRF2 and HMOX1 Gene Expression against the Background of Systemic Oxidative Stress in Patients with Acute Psychosis. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542001010x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Pallares RM, Thanh NTK, Su X. Sensing of circulating cancer biomarkers with metal nanoparticles. NANOSCALE 2019; 11:22152-22171. [PMID: 31555790 DOI: 10.1039/c9nr03040a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The analysis of circulating cancer biomarkers, including cell-free and circulating tumor DNA, circulating tumor cells, microRNA and exosomes, holds promise in revolutionizing cancer diagnosis and prognosis using body fluid analysis, also known as liquid biopsy. To enable clinical application of these biomarkers, new analytical tools capable of detecting them in very low concentrations in complex sample matrixes are needed. Metal nanoparticles have emerged as extraordinary analytical scaffolds because of their unique optoelectronic properties and ease of functionalization. Hence, multiple analytical techniques have been developed based on these nanoparticles and their plasmonic properties. The aim of this review is to summarize and discuss the present development on the use of metal nanoparticles for the analysis of circulating cancer biomarkers. We examine how metal nanoparticles can be used as (1) analytical transducers in various sensing principles, such as aggregation induced colorimetric assays, plasmon resonance energy transfer, surface enhanced Raman spectroscopy, and refractive index sensing, and (2) signal amplification elements in surface plasmon resonance spectroscopy and electrochemical detection. We critically discuss the clinical relevance of each category of circulating biomarkers, followed by a thorough analysis of how these nanoparticle-based designs have overcome some of the main challenges that gold standard analytical techniques currently face, and what new directions the field may take in the future.
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Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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21
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Rice A, Del Rio Hernandez A. The Mutational Landscape of Pancreatic and Liver Cancers, as Represented by Circulating Tumor DNA. Front Oncol 2019; 9:952. [PMID: 31608239 PMCID: PMC6769086 DOI: 10.3389/fonc.2019.00952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
The mutational landscapes of pancreatic and liver cancers share many common genetic alterations which drive cancer progression. However, these mutations do not occur in all cases of these diseases, and this tumoral heterogeneity impedes diagnosis, prognosis, and therapeutic development. One minimally invasive method for the evaluation of tumor mutations is the analysis of circulating tumor DNA (ctDNA), released through apoptosis, necrosis, and active secretion by tumor cells into various body fluids. By observing mutations in those genes which promote transformation by controlling the cell cycle and oncogenic signaling pathways, a representation of the mutational profile of the tumor is revealed. The analysis of ctDNA is a promising technique for investigating these two gastrointestinal cancers, as many studies have reported on the accuracy of ctDNA assessment for diagnosis and prognosis using a variety of techniques.
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Affiliation(s)
- Alistair Rice
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Armando Del Rio Hernandez
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
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22
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Lázaro-Ibáñez E, Lässer C, Shelke GV, Crescitelli R, Jang SC, Cvjetkovic A, García-Rodríguez A, Lötvall J. DNA analysis of low- and high-density fractions defines heterogeneous subpopulations of small extracellular vesicles based on their DNA cargo and topology. J Extracell Vesicles 2019; 8:1656993. [PMID: 31497265 PMCID: PMC6719264 DOI: 10.1080/20013078.2019.1656993] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cells, thereby influencing the recipient cell's phenotype. While the role of RNAs in EVs has been extensively studied, the function of DNA remains elusive. Here, we distinguished novel heterogeneous subpopulations of small extracellular vesicles (sEVs) based on their DNA content and topology. Low- and high-density sEV subsets from a human mast cell line (HMC-1) and an erythroleukemic cell line (TF-1) were separated using high-resolution iodixanol density gradients to discriminate the nature of the DNA cargo of the sEVs. Paired comparisons of the sEV-associated DNA and RNA molecules showed that RNA was more abundant than DNA and that most of the DNA was present in the high-density fractions, demonstrating that sEV subpopulations have different DNA content. DNA was predominately localised on the outside or surface of sEVs, with only a small portion being protected from enzymatic degradation. Whole-genome sequencing identified DNA fragments spanning all chromosomes and mitochondrial DNA when sEVs were analysed in bulk. Our work contributes to the understanding of how DNA is associated with sEVs and thus provides direction for distinguishing subtypes of EVs based on their DNA cargo and topology.
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Affiliation(s)
- Elisa Lázaro-Ibáñez
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Cecilia Lässer
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Ganesh Vilas Shelke
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Rossella Crescitelli
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Su Chul Jang
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Aleksander Cvjetkovic
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Anaís García-Rodríguez
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
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23
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Tamkovich S, Laktionov P. Cell-surface-bound circulating DNA in the blood: Biology and clinical application. IUBMB Life 2019; 71:1201-1210. [PMID: 31091350 DOI: 10.1002/iub.2070] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/17/2019] [Indexed: 01/04/2023]
Abstract
Cell-surface-bound extracellular DNA (csbDNA) is present on the outer membrane of blood cells, including both red blood cells and leukocytes. Although less well characterized than cell-free DNA (cfDNA) in plasma and serum, leukocyte and red blood cell csbDNA form a considerable fraction of the blood extracellular nucleic acids pool, with typically at least comparable amount of DNA occurring bound to the outer surface of cells as compared with circulating free DNA in plasma. The cellular origin of csbDNA is not clear; however, as with cfDNA, in patients with cancer a proportion is derived from the tumor, thus making it potentially a useful source of DNA for cancer diagnosis, prognosis, and monitoring. © 2019 IUBMB Life, 71(9):1201-1210, 2019.
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Affiliation(s)
- Svetlana Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk National Research State University, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
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Kustanovich A, Schwartz R, Peretz T, Grinshpun A. Life and death of circulating cell-free DNA. Cancer Biol Ther 2019; 20:1057-1067. [PMID: 30990132 PMCID: PMC6606043 DOI: 10.1080/15384047.2019.1598759] [Citation(s) in RCA: 302] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/24/2019] [Accepted: 03/12/2019] [Indexed: 12/18/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA in liquid biopsies is a promising source of biomarkers for minimally invasive serial monitoring of treatment responses in cancer management. We will review the current understanding of the origin of circulating cell-free DNA and different forms of DNA release (including various types of cell death and active secretion processes) and clearance routes. The dynamics of extracellular DNA in blood during therapy and the role of circulating DNA in pathophysiological processes (tumor-associated inflammation, NETosis, and pre-metastatic niche development) provide insights into the mechanisms that contribute to tumor development and metastases formation. Better knowledge of circulating tumor-specific cell-free DNA could facilitate the development of new therapeutic and diagnostic options for cancer management.
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Affiliation(s)
- Anatoli Kustanovich
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ruth Schwartz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Albert Grinshpun
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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25
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Koessler T, Addeo A, Nouspikel T. Implementing circulating tumor DNA analysis in a clinical laboratory: A user manual. Adv Clin Chem 2019; 89:131-188. [PMID: 30797468 DOI: 10.1016/bs.acc.2018.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Liquid biopsy, the analysis of cell-free circulating tumor DNA (ctDNA), is becoming one of the most promising tools in oncology. It has already shown its usefulness in selecting and modulating therapy via remote analysis of the tumor genome and holds important promises in cancer therapy and management, such as assessing the success of key therapeutic steps, monitoring residual disease, early detection of relapses, and establishing prognosis. Yet, ctDNA analysis is technically challenging and its implementation in the laboratory raises multiple strategic and practical issues. As for oncology clinics, integration of this novel test in well-established therapeutic protocols can also pose numerous questions. The current review is intended as a field guide for (1) diagnostic laboratories wishing to implement, validate and possibly accredit ctDNA testing and (2) clinical oncologists interested in integrating the various applications of liquid biopsies in their daily practice. We provide advice and practical recommendations based on our own experience with the technical validations of these methods and on a review of the current literature, with a focus toward gastro-intestinal, lung and breast cancers.
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Affiliation(s)
- Thibaud Koessler
- Department of Oncology, Geneva University Hospital, Geneva, Switzerland
| | - Alfredo Addeo
- Department of Oncology, Geneva University Hospital, Geneva, Switzerland
| | - Thierry Nouspikel
- Service of Medical Genetics, Diagnostics Department, Geneva University Hospital, Geneva, Switzerland.
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Fettke H, Kwan EM, Azad AA. Cell-free DNA in cancer: current insights. Cell Oncol (Dordr) 2018; 42:13-28. [PMID: 30367445 DOI: 10.1007/s13402-018-0413-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The field of liquid biopsies in oncology is rapidly expanding, with the application of cell-free circulating tumour DNA (ctDNA) showing promise in this era of precision medicine. Compared with traditional clinical and radiographic tumour monitoring methods, the analysis of ctDNA provides a minimally-invasive and technically feasible approach to assess temporal and spatial molecular evolutions of the tumour landscape. The constantly advancing technological platforms available for ctDNA extraction and analysis allow greater analytical sensitivities than ever before. The potential translational impact of ctDNA as a blood-based biomarker for the identification, characterization and monitoring of cancer has been demonstrated in numerous proof-of-concept studies, with ctDNA analysis beginning to be applied clinically across multiple facets of oncology. CONCLUSIONS In this review we discuss the biology, recent advancements, technical considerations and clinical implications of ctDNA in the context of cancer, and highlight important challenges and future directions for the integration of ctDNA into standardised patient care.
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Affiliation(s)
- Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
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Grölz D, Hauch S, Schlumpberger M, Guenther K, Voss T, Sprenger-Haussels M, Oelmüller U. Liquid Biopsy Preservation Solutions for Standardized Pre-Analytical Workflows-Venous Whole Blood and Plasma. CURRENT PATHOBIOLOGY REPORTS 2018; 6:275-286. [PMID: 30595972 PMCID: PMC6290703 DOI: 10.1007/s40139-018-0180-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsy analyses based on circulating cell-free nucleic acids, circulating tumor cells or other diseased cells from organs, and exosomes or other microvesicles in blood offer new means for non-invasive diagnostic applications. The main goal of this review is to explain the importance of preserving whole blood specimens after blood draw for use as liquid biopsies, and to summarize preservation solutions that are currently available. RECENT FINDINGS Despite the great potential of liquid biopsies for diagnostics and disease management, besides non-invasive prenatal testing (NIPT), only a few liquid biopsy applications are fully implemented for routine in vitro diagnostic testing. One major barrier is the lack of standardized pre-analytical workflows, including the collection of consistent quality blood specimens and the generation of good-quality plasma samples therefrom. Broader use of liquid biopsies in clinical routine applications therefore requires improved pre-analytical procedures to enable high-quality specimens to obtain unbiased analyte profiles (DNA, RNA, proteins, etc.) as they are in the patient's body. SUMMARY A growing number of stabilizing reagents and dedicated blood collection tubes are available for the post-collection preservation of circulating cell-free DNA (ccfDNA) profiles in whole blood. In contrast, solutions for the preservation of circulating tumor cells (CTC) that enable both, enumeration and molecular analyses are rare. Solutions for extracellular vesicle (EV) populations, including exosomes, do not yet exist.
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Affiliation(s)
- Daniel Grölz
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Siegfried Hauch
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Kalle Guenther
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Thorsten Voss
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Uwe Oelmüller
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
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Marrugo-Ramírez J, Mir M, Samitier J. Blood-Based Cancer Biomarkers in Liquid Biopsy: A Promising Non-Invasive Alternative to Tissue Biopsy. Int J Mol Sci 2018; 19:E2877. [PMID: 30248975 PMCID: PMC6213360 DOI: 10.3390/ijms19102877] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/13/2018] [Accepted: 09/17/2018] [Indexed: 12/18/2022] Open
Abstract
Cancer is one of the greatest threats facing our society, being the second leading cause of death globally. Currents strategies for cancer diagnosis consist of the extraction of a solid tissue from the affected area. This sample enables the study of specific biomarkers and the genetic nature of the tumor. However, the tissue extraction is risky and painful for the patient and in some cases is unavailable in inaccessible tumors. Moreover, a solid biopsy is expensive and time consuming and cannot be applied repeatedly. New alternatives that overcome these drawbacks are rising up nowadays, such as liquid biopsy. A liquid biopsy is the analysis of biomarkers in a non-solid biological tissue, mainly blood, which has remarkable advantages over the traditional method; it has no risk, it is non-invasive and painless, it does not require surgery and reduces cost and diagnosis time. The most studied cancer non-invasive biomarkers are circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosomes. These circulating biomarkers play a key role in the understanding of metastasis and tumorigenesis, which could provide a better insight into the evolution of the tumor dynamics during treatment and disease progression. Improvements in isolation technologies, based on a higher grade of purification of CTCs, exosomes, and ctDNA, will provide a better characterization of biomarkers and give rise to a wide range of clinical applications, such as early detection of diseases, and the prediction of treatment responses due to the discovery of personalized tumor-related biomarkers.
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Affiliation(s)
- José Marrugo-Ramírez
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC) Barcelona Institute of Science and Technology (BIST), 12 Baldiri Reixac 15-21, 08028 Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain.
| | - Mònica Mir
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC) Barcelona Institute of Science and Technology (BIST), 12 Baldiri Reixac 15-21, 08028 Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain.
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.
| | - Josep Samitier
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC) Barcelona Institute of Science and Technology (BIST), 12 Baldiri Reixac 15-21, 08028 Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain.
- Department of Electronics and Biomedical Engineering, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.
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Wang W, Kong P, Ma G, Li L, Zhu J, Xia T, Xie H, Zhou W, Wang S. Characterization of the release and biological significance of cell-free DNA from breast cancer cell lines. Oncotarget 2018; 8:43180-43191. [PMID: 28574818 PMCID: PMC5522137 DOI: 10.18632/oncotarget.17858] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/14/2017] [Indexed: 12/26/2022] Open
Abstract
In breast cancer, cell-free DNA (cfDNA) has been proven to be a diagnostic and prognostic biomarker. However, there have been few studies on the origin and biological significance of cfDNA. In this study, we assessed the release pattern of cfDNA from breast cancer cell lines under different culture conditions and investigated the biological significance of cfDNA. The cfDNA concentration increased rapidly (6 h) after passage, decreased gradually, and was then maintained at a relatively stable level after 24 h. In addition, the cfDNA concentration did not correlate with the amount of apoptotic and necrotic cells. Interestingly, if more cells were in the G1 phase, more cfDNA was detected (p < 0.01) and the cfDNA concentration correlated positively with the percent of cells in the G1 phase (p < 0.05). We observed that cells could release cfDNA actively, but not exclusively, via exosomes. Furthermore, we showed that cfDNA could stimulate hormone receptor-positive breast cancer cell proliferation by activating the TLR9-NF-κB-cyclin D1 pathway. In conclusion, cfDNA is released from breast cancer mainly by active secretion, and cfDNA could stimulate proliferation of breast cancer cells.
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Affiliation(s)
- Wei Wang
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Peng Kong
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Ge Ma
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Li Li
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Jin Zhu
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Tiansong Xia
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Hui Xie
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Wenbin Zhou
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Shui Wang
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. The diverse origins of circulating cell-free DNA in the human body: a critical re-evaluation of the literature. Biol Rev Camb Philos Soc 2018; 93:1649-1683. [PMID: 29654714 DOI: 10.1111/brv.12413] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 12/13/2022]
Abstract
Since the detection of cell-free DNA (cfDNA) in human plasma in 1948, it has been investigated as a non-invasive screening tool for many diseases, especially solid tumours and foetal genetic abnormalities. However, to date our lack of knowledge regarding the origin and purpose of cfDNA in a physiological environment has limited its use to more obvious diagnostics, neglecting, for example, its potential utility in the identification of predisposition to disease, earlier detection of cancers, and lifestyle-induced epigenetic changes. Moreover, the concept or mechanism of cfDNA could also have potential therapeutic uses such as in immuno- or gene therapy. This review presents an extensive compilation of the putative origins of cfDNA and then contrasts the contributions of cellular breakdown processes with active mechanisms for the release of cfDNA into the extracellular environment. The involvement of cfDNA derived from both cellular breakdown and active release in lateral information transfer is also discussed. We hope to encourage researchers to adopt a more holistic view of cfDNA research, taking into account all the biological pathways in which cfDNA is involved, and to give serious consideration to the integration of in vitro and in vivo research. We also wish to encourage researchers not to limit their focus to the apoptotic or necrotic fraction of cfDNA, but to investigate the intercellular messaging capabilities of the actively released fraction of cfDNA and to study the role of cfDNA in pathogenesis.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
| | - Abel J Bronkhorst
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
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Vizza E, Corrado G, De Angeli M, Carosi M, Mancini E, Baiocco E, Chiofalo B, Patrizi L, Zampa A, Piaggio G, Cicchillitti L. Serum DNA integrity index as a potential molecular biomarker in endometrial cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:16. [PMID: 29382392 PMCID: PMC5791183 DOI: 10.1186/s13046-018-0688-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 01/23/2018] [Indexed: 12/18/2022]
Abstract
Background Circulating cell-free DNA (cfDNA) and its integrity index may represent a rapid and noninvasive “liquid biopsy” biomarker, which gives important complementary information for diagnosis, prognosis, and treatment stratification in cancer patients. The aim of our study was to evaluate the possible role of cfDNA and its integrity index as a complementary tool for endometrial cancer (EC) management. Methods Alu-quantitative real-time PCR (qPCR) analysis wasprformed on 60 serum samples from preoperative EC patients randomly recruited. Both cfDNA content and DNA integrity index were measured by qPCR-Alu115 (representing total cfDNA) and qPCR-Alu247 (corresponding to high molecular weight DNA) and correlated with clinicopathologic characteristics. Lymphovascular space invasion (LVSI) was detected by hematoxylin and eosin staining. In case of doubt, LVSI status was further evaluate by immunohistochemistry using anti-CD31 and anti-CD34 antibodies. Results Total cfDNA content significantly increases in high grade EC. A significant decrease of DNA integrity index was detected in the subset of hypertensive and obese high grade EC. Serum DNA integrity was higher in samples with LVSI. The ordinal regression analysis predicted a significant correlation between decreased integrity index values and hypertension specifically in tumors presenting LVSI. Conclusions Our study supports the utility of serum DNA integrity index as a noninvasive molecular biomarker in EC. We show that a correlation analysis between cfDNA quantitative and qualitative content and clinicopathologic features, such as blood pressure level, body mass index (BMI) and LVSI status, could represent a potential predictive signature to help stratification approaches in EC. Electronic supplementary material The online version of this article (doi:10.1186/s13046-018-0688-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enrico Vizza
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giacomo Corrado
- Department of Health of Woman and Child, Gynecologic Oncology Unit, Catholic University of the Sacred Heart, Rome, Italy.
| | - Martina De Angeli
- Department of Biomedicine and Prevention, Obstetrics and Gynecology Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Mariantonia Carosi
- Department of Research, Advanced Diagnostics and Technological Innovation, Anatomy Pathology Unit Regina Elena National Cancer Institute, Rome, Italy
| | - Emanuela Mancini
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Ermelinda Baiocco
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Benito Chiofalo
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Lodovico Patrizi
- Department of Biomedicine and Prevention, Obstetrics and Gynecology Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Ashanti Zampa
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Piaggio
- Department of Research, Advanced Diagnostics and Technological Innovation, Area of Translational Research, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
| | - Lucia Cicchillitti
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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Glebova KV, Veiko NN, Nikonov AA, Porokhovnik LN, Kostuyk SV. Cell-free DNA as a biomarker in stroke: Current status, problems and perspectives. Crit Rev Clin Lab Sci 2018; 55:55-70. [PMID: 29303618 DOI: 10.1080/10408363.2017.1420032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
There is currently no proposed stroke biomarker with consistent application in clinical practice. A number of studies have examined cell-free DNA (cfDNA), which circulates in biological fluids during stroke, as a potential biomarker of this disease. The data available suggest that dynamically-determined levels of blood cfDNA may provide new prognostic information for assessment of stroke severity and outcome. However, such an approach has its own difficulties and limitations. This review covers the potential role of cfDNA as a biomarker in stroke, and includes evidence from both animal models and clinical studies, protocols used to analyze cfDNA, and hypotheses on the origin of cfDNA.
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Affiliation(s)
- Kristina V Glebova
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Natalya N Veiko
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Aleksey A Nikonov
- b Department of Neurology, Neurosurgery and Medical Genetics , Pirogov Russian National Research Medical University , Moscow , Russia
| | - Lev N Porokhovnik
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Svetlana V Kostuyk
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
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Cicchillitti L, Corrado G, De Angeli M, Mancini E, Baiocco E, Patrizi L, Zampa A, Merola R, Martayan A, Conti L, Piaggio G, Vizza E. Circulating cell-free DNA content as blood based biomarker in endometrial cancer. Oncotarget 2017; 8:115230-115243. [PMID: 29383155 PMCID: PMC5777767 DOI: 10.18632/oncotarget.23247] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/01/2017] [Indexed: 12/15/2022] Open
Abstract
Background Altered circulating cell-free DNA (cfDNA) levels are related to cancer development and aggressiveness. Up to now, very few studies have been performed for evaluating cfDNA content in endometrial cancer (EC). Methods First, we measured cfDNA release in blood serum of EC cancer patients collected before surgery and before the beginning of any treatment by SYBR Gold assay and correlated it with tumor aggressiveness. We also assessed the relative mitochondrial cell-free DNA (cfmtDNA) content by qRT-PCR. Next, we correlated cfDNA levels with BMI, age, hypertension and inflammation markers. Results CfDNA levels are higher in G2 and G3 compared with G1 EC sera. A significant modulation of cfDNA content was detected in sera from patients with BMI>30 compared with those with BMI<30. We observed a further and significant alteration in cfDNA level in hypertensive patients with G2-G3, but not in G1 EC. Analysis of preoperative neutrophil-to-lymphocyte (NLR) and monocyte-to-lymphocyte (MLR) ratios suggests a contribution of the host response in the altered cfDNA levels in EC. Conclusions Our data indicate that assessment of total and mitochondrial cfDNA levels in blood sera and the relative NLR and MLR in blood obtained from preoperative patients may help clinical management and prognosis in EC.
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Affiliation(s)
- Lucia Cicchillitti
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giacomo Corrado
- Department of Obstetrics and Gynecology, Gynecologic Oncology Unit, Catholic University of Sacred Heart, Rome, Italy
| | - Martina De Angeli
- Department of Biomedicine and Prevention, Obstetrics and Gynecology Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Emanuela Mancini
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Ermelinda Baiocco
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Lodovico Patrizi
- Department of Biomedicine and Prevention, Obstetrics and Gynecology Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Ashanti Zampa
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Roberta Merola
- Clinical Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Aline Martayan
- Clinical Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Laura Conti
- Clinical Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Piaggio
- Department of Research, Advanced Diagnostics and Technological Innovation, Area of Translational Research, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Enrico Vizza
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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Macías M, Alegre E, Díaz-Lagares A, Patiño A, Pérez-Gracia JL, Sanmamed M, López-López R, Varo N, González A. Liquid Biopsy: From Basic Research to Clinical Practice. Adv Clin Chem 2017; 83:73-119. [PMID: 29304904 DOI: 10.1016/bs.acc.2017.10.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the molecular analysis in biological fluids of nucleic acids, subcellular structures, especially exosomes, and, in the context of cancer, circulating tumor cells. In the last 10 years, there has been an intensive research in liquid biopsy to achieve a less invasive and more precise personalized medicine. Molecular assessment of these circulating biomarkers can complement or even surrogate tissue biopsy. Because of this research, liquid biopsy has been introduced in clinical practice, especially in oncology, prenatal screening, and transplantation. Here we review the biology, methodological approaches, and clinical applications of the main biomarkers involved in liquid biopsy.
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Affiliation(s)
| | - Estibaliz Alegre
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Angel Díaz-Lagares
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Ana Patiño
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Jose L Pérez-Gracia
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Miguel Sanmamed
- Yale University School of Medicine, New Haven, CT, United States
| | - Rafael López-López
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Nerea Varo
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Alvaro González
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain.
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Aucamp J, Calitz C, Bronkhorst AJ, Wrzesinski K, Hamman S, Gouws C, Pretorius PJ. Cell-free DNA in a three-dimensional spheroid cell culture model: A preliminary study. Int J Biochem Cell Biol 2017; 89:182-192. [DOI: 10.1016/j.biocel.2017.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/07/2017] [Accepted: 06/22/2017] [Indexed: 02/07/2023]
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Aucamp J, Bronkhorst AJ, Peters DL, Van Dyk HC, Van der Westhuizen FH, Pretorius PJ. Kinetic analysis, size profiling, and bioenergetic association of DNA released by selected cell lines in vitro. Cell Mol Life Sci 2017; 74:2689-2707. [PMID: 28315952 PMCID: PMC11107759 DOI: 10.1007/s00018-017-2495-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/19/2017] [Accepted: 02/22/2017] [Indexed: 01/09/2023]
Abstract
Although circulating DNA (cirDNA) analysis shows great promise as a screening tool for a wide range of pathologies, numerous stumbling blocks hinder the rapid translation of research to clinical practice. This is related directly to the inherent complexity of the in vivo setting, wherein the influence of complex systems of interconnected cellular responses and putative DNA sources creates a seemingly arbitrary representation of the quantitative and qualitative properties of the cirDNA in the blood of any individual. Therefore, to evaluate the potential of in vitro cell cultures to circumvent the difficulties encountered in in vivo investigations, the purpose of this work was to elucidate the characteristics of the DNA released [cell-free DNA (cfDNA)] by eight different cell lines. This revealed three different forms of cfDNA release patterns and the presence of nucleosomal fragments as well as actively released forms of DNA, which are not only consistently observed in every tested cell line, but also in plasma samples. Correlations between cfDNA release and cellular origin, growth rate, and cancer status were also investigated by screening and comparing bioenergetics flux parameters. These results show statistically significant correlations between cfDNA levels and glycolysis, while no correlations between cfDNA levels and oxidative phosphorylation were observed. Furthermore, several correlations between growth rate, cancer status, and dependency on aerobic glycolysis were observed. Cell cultures can, therefore, successfully serve as closed-circuit models to either replace or be used in conjunction with biofluid samples, which will enable sharper focus on specific cell types or DNA origins.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Dimetrie L Peters
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Hayley C Van Dyk
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | | | - Piet J Pretorius
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
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Aucamp J, Van Dyk HC, Bronkhorst AJ, Pretorius PJ. Valproic acid alters the content and function of the cell-free DNA released by hepatocellular carcinoma (HepG2) cells in vitro. Biochimie 2017; 140:93-105. [PMID: 28668269 DOI: 10.1016/j.biochi.2017.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 06/27/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND It has long been believed that cell-free DNA (cfDNA) actively released into circulation can serve as intercellular messengers, and their involvement in processes such as the bystander effect strongly support this. However, this intercellular messaging function of cfDNA may have clinical implications that have not yet been considered. METHODS CfDNA was isolated from the growth medium of HepG2 cells treated with valproic acid (VPA). This cfDNA was then administered to untreated cells and cellular metabolic activity was measured. RESULTS VPA altered the characteristics of cfDNA released by treated HepG2 cells in vitro. When administered to untreated cells, the cfDNA from cells treated with VPA resulted in the dose-dependent induction of glycolytic activity within 36 min of administration, but little to no alterations in oxidative phosphorylation. The glycolytic activity lasted for 4-6 h, whereas changes in subsequent cfDNA release and characteristics were found to remain persistent after two 24 h treatments. Fragmented genomic DNA from VPA-treated cells did not induce the effects observed for cfDNA obtained VPA-treated cells. CONCLUSIONS It is possible for cfDNA to, under in vitro conditions, transfer pharmaceutically-induced effects to untreated recipient cells. Further investigation regarding this occurrence under in vivo conditions is, therefore, strongly encouraged. GENERAL SIGNIFICANCE The intercellular messaging functions of cfDNA present in donated biological fluids has potential clinical implications that require urgent attention. These implications may, however, also have potential as new forms of treatment that can circumvent pharmacological barriers.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa.
| | - Hayley C Van Dyk
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Abel J Bronkhorst
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Piet J Pretorius
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
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Cai S, Cheng X, Pan X, Li J. Emerging role of exosomes in liver physiology and pathology. Hepatol Res 2017; 47:194-203. [PMID: 27539153 DOI: 10.1111/hepr.12794] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/21/2016] [Accepted: 08/10/2016] [Indexed: 12/13/2022]
Abstract
Exosomes can mediate intercellular communication by conveying various bioactive molecules. Plentiful evidence suggests that exosomes are involved in many liver diseases including hepatitis C virus infection, hepatitis B virus infection, hepatocellular carcinoma, liver fibrosis, cirrhosis, non-alcoholic fatty liver disease, and alcoholic liver disease. Moreover, exosomes are present in nearly all human body fluids. Therefore, exosomal miRNA or proteins have the potential to be novel biomarkers of liver diseases. In the treatment of liver diseases, exosomes could participate in adaptive immune response and mesenchymal stem cell-based therapy. Exosomes can also be used as vehicles for genetic materials and drug delivery.
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Affiliation(s)
- Shuangpeng Cai
- School of Pharmacy, Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei, China
| | - Xiaoyu Cheng
- School of Pharmacy, Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei, China
| | - Xueyin Pan
- School of Pharmacy, Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei, China
| | - Jun Li
- School of Pharmacy, Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei, China
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles. Cell Mol Life Sci 2016; 73:4355-4381. [PMID: 27652382 PMCID: PMC11108302 DOI: 10.1007/s00018-016-2370-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/20/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.
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Affiliation(s)
- Janine Aucamp
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
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Hocking J, Mithraprabhu S, Kalff A, Spencer A. Liquid biopsies for liquid tumors: emerging potential of circulating free nucleic acid evaluation for the management of hematologic malignancies. Cancer Biol Med 2016; 13:215-25. [PMID: 27458529 PMCID: PMC4944540 DOI: 10.20892/j.issn.2095-3941.2016.0025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circulating free nucleic acids; cell free DNA and circulating micro-RNA, are found in the
plasma of patients with hematologic and solid malignancies at levels higher than that of
healthy individuals. In patients with hematologic malignancy cell free DNA reflects the
underlying tumor mutational profile, whilst micro-RNAs reflect genetic interference
mechanisms within a tumor and potentially the surrounding microenvironment and immune
effector cells. These circulating nucleic acids offer a potentially simple, non-invasive,
repeatable analysis that can aid in diagnosis, prognosis and therapeutic decisions in
cancer treatment.
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Affiliation(s)
- Jay Hocking
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne 3004, Australia; Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne 3004, Australia
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne 3004, Australia
| | - Anna Kalff
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne 3004, Australia
| | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne 3004, Australia; Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne 3004, Australia
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42
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Yao W, Mei C, Nan X, Hui L. Evaluation and comparison of in vitro degradation kinetics of DNA in serum, urine and saliva: A qualitative study. Gene 2016; 590:142-8. [PMID: 27317895 DOI: 10.1016/j.gene.2016.06.033] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/12/2016] [Accepted: 06/14/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Cell-free DNA is naturally degraded in various bodily fluids. The aim of this study was to determine the degradation kinetics of DNA, with and without protein, in serum, urine and saliva. METHODS Naked DNA and DNA-protein complex were prepared, added to the samples to be analysed and incubated at 37°C and room temperature for various lengths of time. Alleles of 20 short tandem repeat loci were amplified from the incubated samples, and clearance models were generated from the mean peak areas. RESULTS Plotting the natural logarithm of DNA concentration against the incubation time produced a linear relationship. The half-lives of DNA with and without protein in serum were 157.6min and 30.8min at 37°C, 330.5min and 70.5min at room temperature, respectively. The half-lives of DNA with protein in saliva were 175.6min and 251.3min at 37°C and room temperature, respectively. However, the half-lives of DNA in urine (both with and without protein) were too short to detect. CONCLUSIONS The kinetics of DNA degradation in serum and saliva followed a first-order clearance model. Urine had the strongest effect on DNA degradation, and the half-lives of DNA with protein were relatively longer than those of naked DNA.
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Affiliation(s)
- Wang Yao
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University, 214002 Wuxi, Jiangsu, China
| | - Chen Mei
- Dalian Blood Centre, Dalian, China
| | - Xiao Nan
- Dalian Blood Centre, Dalian, China
| | - Liu Hui
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China.
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Abstract
INTRODUCTION As the U.S. population ages, the incidence of chronic disease will rise. Chronic diseases have been linked to chronic inflammation. The purpose of this review is to summarize the literature on cell-free DNA (cfDNA) in relation to inflammation. METHODS PubMed, EMBASE, and Web of Science were searched. Inclusion criteria were noninterventional studies on acute and chronic inflammation, autoimmunity, and infection published in English after 2000, conducted in humans using the fluorescence method of quantifying DNA. Of the 442 articles retrieved, 83 were identified for full-text review and 13 remained after application of inclusion criteria. RESULTS Of the reviewed studies, three involved acute inflammation, six involved chronic inflammation, and four involved infection. Healthy controls with interpretable results were included in six studies, three of which used the Quant-iT high-sensitivity DNA kit and found cfDNA quantities near 800 ng/ml, while the other three used other fluorescence methods and found quantities below 100 ng/ml. All 13 studies compared groups, and all but 1 found statistically significant differences between them. Among studies using the Quant-iT reagent, levels were higher in infection than in chronic inflammation. Among studies that used other reagents, levels increased from chronic to acute inflammation to severe infection. CfDNA levels were associated with mortality and with clinical outcomes in acute inflammation and infection. Most studies assessed cfDNA's correlation with other inflammation biomarkers and found inconclusive results. CONCLUSION There appears to be an association between inflammation and cfDNA. Further research is necessary before cfDNA can be used clinically as a measure of inflammation.
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Affiliation(s)
- Mayu O Frank
- College of Nursing, New York University, New York, NY, USA Rockefeller University, New York, NY, USA
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Aarthy R, Mani S, Velusami S, Sundarsingh S, Rajkumar T. Role of Circulating Cell-Free DNA in Cancers. Mol Diagn Ther 2015; 19:339-50. [PMID: 26400814 DOI: 10.1007/s40291-015-0167-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Liquid biopsy is a term used to describe non-invasive tests, which provide information about disease conditions through analysis of circulating cell-free DNA and circulating tumor cells from peripheral blood samples. In patients with cancer, the concentration of cell-free DNA increases, and structural, sequence, and epigenetic changes to DNA can be observed through the disease process and during therapy. Furthermore, cell-free DNA released by the tumor contains the same variants as those in the tumor cells. Therefore, cell-free DNA allows non-invasive assessment of cancer in real time. This review summarizes the origin of cell-free DNA, recent advancements in the detection of cell-free DNA, a possible role in metastasis, and its importance as a non-invasive diagnostic assay for cancer.
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Affiliation(s)
- Raghu Aarthy
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Sridevi Velusami
- Department of Surgical Oncology, Cancer Institute (WIA), Chennai, India
| | | | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India.
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45
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Bronkhorst AJ, Wentzel JF, Aucamp J, van Dyk E, du Plessis L, Pretorius PJ. Characterization of the cell-free DNA released by cultured cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:157-65. [PMID: 26529550 DOI: 10.1016/j.bbamcr.2015.10.022] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/22/2015] [Accepted: 10/30/2015] [Indexed: 01/08/2023]
Abstract
The most prominent factor that delays the translation of cell-free DNA (cfDNA) analyses to clinical practice is the lack of knowledge regarding its origin and composition. The elucidation of the former is complicated by the seemingly random fluctuation of quantitative and qualitative characteristics of cfDNA in the blood of healthy and diseased individuals. Besides methodological discrepancies, this could be ascribed to a web of cellular responses to various environmental cues and stressors. Since all cells release cfDNA, it follows that the cfDNA in the blood of cancer patients is not only representative of tumor derived DNA, but also of DNA released by healthy cells under different conditions. Additionally, cfDNA released by malignant cells is not necessarily just aberrant, but likely includes non-mutated chromosomal DNA fragments. This may cause false positive/negative results. Although many have acknowledged that this is a major problem, few have addressed it. We propose that many of the current stumbling blocks encountered in in vivo cfDNA studies can be partially circumvented by in vitro models. Accordingly, the purpose of this work was to evaluate the release of cfDNA from cultured cells and to gauge its potential use for elucidating the nature of cfDNA. Results suggest that the occurrence of cfDNA is not a consequence of apoptosis or necrosis, but primarily a result of actively secreted DNA, perhaps in association with a protein complex. This study demonstrates the potential of in vitro cell culture models to obtain useful information about the phenomenon of cfDNA.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa.
| | - Johannes F Wentzel
- Centre of Excellence for Pharmaceutical Sciences (PHARMACEN), North-West University, Potchefstroom 2520, South Africa
| | - Janine Aucamp
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | - Etresia van Dyk
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | - Lissinda du Plessis
- Centre of Excellence for Pharmaceutical Sciences (PHARMACEN), North-West University, Potchefstroom 2520, South Africa
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
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46
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Chandrananda D, Thorne NP, Bahlo M. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA. BMC Med Genomics 2015; 8:29. [PMID: 26081108 PMCID: PMC4469119 DOI: 10.1186/s12920-015-0107-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/04/2015] [Indexed: 12/13/2022] Open
Abstract
Background High-throughput sequencing of cell-free DNA fragments found in human plasma has been used to non-invasively detect fetal aneuploidy, monitor organ transplants and investigate tumor DNA. However, many biological properties of this extracellular genetic material remain unknown. Research that further characterizes circulating DNA could substantially increase its diagnostic value by allowing the application of more sophisticated bioinformatics tools that lead to an improved signal to noise ratio in the sequencing data. Methods In this study, we investigate various features of cell-free DNA in plasma using deep-sequencing data from two pregnant women (>70X, >50X) and compare them with matched cellular DNA. We utilize a descriptive approach to examine how the biological cleavage of cell-free DNA affects different sequence signatures such as fragment lengths, sequence motifs at fragment ends and the distribution of cleavage sites along the genome. Results We show that the size distributions of these cell-free DNA molecules are dependent on their autosomal and mitochondrial origin as well as the genomic location within chromosomes. DNA mapping to particular microsatellites and alpha repeat elements display unique size signatures. We show how cell-free fragments occur in clusters along the genome, localizing to nucleosomal arrays and are preferentially cleaved at linker regions by correlating the mapping locations of these fragments with ENCODE annotation of chromatin organization. Our work further demonstrates that cell-free autosomal DNA cleavage is sequence dependent. The region spanning up to 10 positions on either side of the DNA cleavage site show a consistent pattern of preference for specific nucleotides. This sequence motif is present in cleavage sites localized to nucleosomal cores and linker regions but is absent in nucleosome-free mitochondrial DNA. Conclusions These background signals in cell-free DNA sequencing data stem from the non-random biological cleavage of these fragments. This sequence structure can be harnessed to improve bioinformatics algorithms, in particular for CNV and structural variant detection. Descriptive measures for cell-free DNA features developed here could also be used in biomarker analysis to monitor the changes that occur during different pathological conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0107-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dineika Chandrananda
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Natalie P Thorne
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Melanie Bahlo
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia.
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Virzì GM, Milan Manani S, Brocca A, Cantaluppi V, de Cal M, Pastori S, Tantillo I, Zambon R, Crepaldi C, Ronco C. Peritoneal Cell-free DNA: an innovative method for determining acute cell damage in peritoneal membrane and for monitoring the recovery process after peritonitis. J Nephrol 2015; 29:111-8. [DOI: 10.1007/s40620-015-0212-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/18/2015] [Indexed: 02/07/2023]
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Borghini A, Mercuri A, Turchi S, Chiesa MR, Piccaluga E, Andreassi MG. Increased circulating cell-free DNA levels and mtDNA fragments in interventional cardiologists occupationally exposed to low levels of ionizing radiation. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:293-300. [PMID: 25327629 DOI: 10.1002/em.21917] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/30/2014] [Indexed: 06/04/2023]
Abstract
Circulating cell-free DNA (ccf-DNA) and mtDNA (ccf-mtDNA) have often been used as indicators of cell death and tissue damage in acute and chronic disorders, but little is known about changes in ccf-DNA and ccf-mtDNA concentrations following radiation exposure. The aim of the study was to investigate the impact of chronic low-dose radiation exposure on serum ccf-DNA levels and ccf-mtDNA fragments (mtDNA-79 and mtDNA-230) of interventional cardiologists working in high-volume cardiac catheterization laboratory to assess their possible role as useful radiation biomarkers. We enrolled 50 interventional cardiologists (26 males; age = 48.4 ± 10 years) and 50 age- and gender-matched unexposed controls (27 males; age = 47.6 ± 8.3 years). Quant-iT™ dsDNA High-Sensitivity assay was used to measure circulating ccf-DNA isolated from serum samples. Quantitative analysis of mtDNA fragments was performed by real-time PCR. No significant relationships were found between ccf-DNA and ccf-mtDNA, and age, gender, smoking, or other clinical parameters. Ccf-DNA levels (44.2 ± 31.1 vs. 30.6 ± 19.2 ng/ml, P = 0.013), ccf-mtDNA-79 (2.6 ± 2.1 vs. 1.1 ± 0.8, P < 0.01), and ccf-mtDNA-230 copies (2.0 ± 1.8 vs. 1.04 ± 0.9, P = 0.02) were significantly higher in interventional cardiologists compared with the non-exposed group. In a subset (n = 15) of interventional cardiologists with a reliable reconstruction of cumulative professional exposure (59.7 ± 48.4 mSv; range: 1.4-182 mS), ccf-DNA (53.2 ± 41.3 vs. 36.4 ± 22.9 and 32.2 ± 20.5, P = 0.08), mtDNA-79 (2.4 ± 2.1 vs. 2.03 ± 1.7 and 1.09 ± 0.82, P = 0.05), and mtDNA-230 (2.0 ± 2.2 vs. 1.5 ± 1.4 and 1.04 ± 0.9, P = 0.09) tended to be significantly increased in high-exposure subjects compared with both low-exposure interventional cardiologists and controls. Our results provide evidence for a possible role of circulating DNA as a relevant biomarker of cellular damage induced by exposure to chronic low-dose radiation.
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Affiliation(s)
- Andrea Borghini
- Genetics Research Unit, CNR Institute of Clinical Physiology, Pisa, Italy
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Penfornis P, Vallabhaneni KC, Whitt J, Pochampally R. Extracellular vesicles as carriers of microRNA, proteins and lipids in tumor microenvironment. Int J Cancer 2015; 138:14-21. [PMID: 25559768 DOI: 10.1002/ijc.29417] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/05/2014] [Accepted: 12/23/2014] [Indexed: 12/13/2022]
Abstract
In recent years, the knowledge about the control of tumor microenvironment has increased and emerged as an important player in tumorigenesis. The role of normal stromal cells in the tumor initiation and progression has brought our vision in to the forefront of cell-to-cell communication. In this review, we focus on the mechanism of communication between stromal and tumor cells, which is based on the exchange of extracellular vesicles (EVs). We describe several, evergrowing, pieces of evidence that EVs transfer messages through their miRNA, lipid, protein and nucleic acid contents. A better understanding of this sophisticated method of communication between normal cancer cells may lead to developing novel approaches for personalized diagnostics and therapeutics.
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Affiliation(s)
- Patrice Penfornis
- Department of Biochemistry and Cancer Institute, University of Mississippi Medical Center, Jackson, MS
| | - Krishna C Vallabhaneni
- Department of Biochemistry and Cancer Institute, University of Mississippi Medical Center, Jackson, MS
| | - Jason Whitt
- Department of Biochemistry and Cancer Institute, University of Mississippi Medical Center, Jackson, MS
| | - Radhika Pochampally
- Department of Biochemistry and Cancer Institute, University of Mississippi Medical Center, Jackson, MS
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50
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Bryzgunova O, Laktionov P. Generation of blood circulating DNA: the sources, peculiarities of circulation and structure. ACTA ACUST UNITED AC 2015; 61:409-26. [DOI: 10.18097/pbmc20156104409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Extracellular nucleic acids (exNA) were described in blood of both healthy and illness people as early as in 1948, but staied overlooked until middle 60-th. Starting from the beginning of new millennium and mainly in the last 5 years exNA are intensively studied. Main attention is directed to investigation of exNA as the source of diagnostic material whereas the mechanisms of their generation, as well as mechanisms to providing long-term circulation of exNA in the bloodstream are not established unambiguously. According to some authors, the main source of circulating nucleic acids in blood are the processes of apoptosis and necrosis, while others refer to the possible nucleic acid secretion by healthy and tumor cells. Circulating DNA were found to be stable in the blood for a long time, escaping from the action of DNA hydrolyzing enzymes and are apparently packed in different supramolecular complexes. This review presents the opinions of various authors and evidence in favor of all the theories describingappearance of extracellular DNA, the features of the circulation and structure of the extracellular DNA and factors affecting the time of DNA circulation in blood
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Affiliation(s)
- O.E. Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - P.P. Laktionov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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