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Kofanova O, Paul S, Pexaras A, Bellora C, Petersons A, Schmitt M, Baker Berjaoui M, Qaoud Y, Kenk M, Wagner H, Fleshner N, Betsou F. Biospecimen Qualification in a Clinical Biobank of Urological Diseases. Biopreserv Biobank 2024; 22:257-267. [PMID: 37878356 DOI: 10.1089/bio.2022.0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Development of novel biomarkers for diagnosis of disease and assessment of treatment efficacy utilizes a wide range of biospecimens for discovery research. The fitness of biospecimens for the purpose of biomarker development depends on the clinical characteristics of the donor and on a number of critical and potentially uncontrolled pre-analytical variables. Pre-analytical factors influence the reliability of the biomarkers to be analyzed and can seriously impact analytic outcomes. Sample quality stratification assays and tools can be utilized by biorepositories to minimize bias resulting from samples' inconsistent quality. In this study, we evaluated the quality of biobanked specimens by comparing analytical outcomes at 1, 5, and 10 years after collection. Our results demonstrate that currently available assays and tools can be used by biobank laboratories to support objective biospecimen qualification. We have established a workflow to monitor the quality of different types of biospecimens and, in this study, present the results of a qualification exercise applied to fluid samples and their derivatives in the context of urological diseases.
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Affiliation(s)
- Olga Kofanova
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Sangita Paul
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Achilleas Pexaras
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Camille Bellora
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Ala Petersons
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Margaux Schmitt
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Mohamad Baker Berjaoui
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Yazan Qaoud
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Miran Kenk
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Heidi Wagner
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Neil Fleshner
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
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Mateus Pereira de Souza N, Kimberli Abeg da Rosa D, de Moraes C, Caeran M, Bordin Hoffmann M, Pozzobon Aita E, Prochnow L, Lya Assmann da Motta A, Antonio Corbellini V, Rieger A. Structural characterization of DNA amplicons by ATR-FTIR spectroscopy as a guide for screening metainflammatory disorders in blood plasma. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123897. [PMID: 38266599 DOI: 10.1016/j.saa.2024.123897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy is a promising rapid, reagent-free, and low-cost technique considered for clinical translation. It allows to characterize biofluids proteome, lipidome, and metabolome at once. Metainflammatory disorders share a constellation of chronic systemic inflammation, oxidative stress, aberrant adipogenesis, and hypoxia, that significantly increased cardiovascular and cancer risk. As a result, these patients have elevated concentration of cfDNA in the bloodstream. Considering this, DNA amplicons were analyzed by ATR-FTIR at 3 concentrations with 1:100 dilution: (IU/mL): 718, 7.18, and 0.0718. The generated IR spectrum was used as a guide for variable selection. The main peaks in the biofingerprint (1800-900 cm-1) give important information about the base, base-sugar, phosphate, and sugar-phosphate transitions of DNA. To validate our method of selecting variables in blood plasma, 38 control subjects and 12 with metabolic syndrome were used. Using the wavenumbers of the peaks in the biofingerprint of the DNA amplicons, was generated a discriminant analysis model with Mahalanobis distance in blood plasma, and 100 % discrimination accuracy was obtained. In addition, the interval 1475-1188 cm-1 showed the greatest sensitivity to variation in the concentration of DNA amplicons, so curve fitting with Gaussian funcion was performed, obtaining adjusted-R2 of 0.993. PCA with Mahalanobis distance in the interval 1475-1188 cm-1 obtained an accuracy of 96 % and PLS-DA modeling in the interval 1475-1088 cm-1 obtained AUC = 0.991 with sensitivity of 95 % and specificity of 100 %. Therefore, ATR-FTIR spectroscopy with variable selection guided by DNA IR peaks is a promising and efficient method to be applied in metainflammatory disorders.
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Affiliation(s)
| | - Dhuli Kimberli Abeg da Rosa
- Bioprocess Engineering and Biotechnology, State University of Rio Grande do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Caroline de Moraes
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Mariana Caeran
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Mairim Bordin Hoffmann
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Eduardo Pozzobon Aita
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Laura Prochnow
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Anna Lya Assmann da Motta
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Valeriano Antonio Corbellini
- Department of Sciences, Humanities, and Education, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, Rio Grande do Sul, Brazil.
| | - Alexandre Rieger
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, Rio Grande do Sul, Brazil.
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Potter E, Dolgova E, Proskurina A, Ruzanova V, Efremov Y, Kirikovich S, Oshikhmina S, Mamaev A, Taranov O, Bryukhovetskiy A, Grivtsova L, Kolchanov N, Ostanin A, Chernykh E, Bogachev S. Stimulation of mouse hematopoietic stem cells by angiogenin and DNA preparations. Braz J Med Biol Res 2024; 57:e13072. [PMID: 38451606 PMCID: PMC10913394 DOI: 10.1590/1414-431x2024e13072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/24/2024] [Indexed: 03/08/2024] Open
Abstract
Immature hematopoietic progenitors are a constant source for renewal of hemocyte populations and the basic component of the tissue and cell repair apparatus. A unique property of these cells of internalizing extracellular double-stranded DNA has been previously shown. The leukostimulatory effect demonstrated in our pioneering studies was considered to be due to the feature of this cell. In the present research, we have analyzed the effects of DNA genome reconstructor preparation (DNAgr), DNAmix, and human recombinant angiogenin on both hematopoietic stem cells and multipotent progenitors. Treatment with bone marrow cells of experimental mice with these preparations stimulates colony formation by hematopoietic stem cells and proliferation of multipotent descendants. The main lineage responsible for this is the granulocyte-macrophage hematopoietic lineage. Using fluorescent microscopy as well as FACS assay, co-localization of primitive c-Kit- and Sca-1-positive progenitors and the TAMRA-labeled double-stranded DNA has been shown. Human recombinant angiogenin was used as a reference agent. Cells with specific markers were quantified in intact bone marrow and colonies grown in the presence of inducers. Quantitative analysis revealed that a total of 14,000 fragment copies of 500 bp, which is 0.2% of the haploid genome, can be delivered into early progenitors. Extracellular double-stranded DNA fragments stimulated the colony formation in early hematopoietic progenitors from the bone marrow, which assumed their effect on cells in G0. The observed number of Sca1+/c-Kit+ cells in colonies testifies to the possibility of both symmetrical and asymmetrical division of the initial hematopoietic stem cell and its progeny.
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Affiliation(s)
- E.A. Potter
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E.V. Dolgova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A.S. Proskurina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V.S. Ruzanova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Y.R. Efremov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk National Research State University, Novosibirsk, Russia
| | - S.S. Kirikovich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S.G. Oshikhmina
- Department of Natural Sciences, Novosibirsk National Research State University, Novosibirsk, Russia
| | - A.L. Mamaev
- LLC “Angiopharm Laboratory”, Novosibirsk, Russia
| | - O.S. Taranov
- State Research Center of Virology and Biotechnology “Vector”, Novosibirsk, Russia
| | | | - L.U. Grivtsova
- Department of Clinical Immunology, National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Obninsk, Russia
| | - N.A. Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A.A. Ostanin
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - E.R. Chernykh
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - S.S. Bogachev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Milecki T, Kluzek K, Pstrąg N, Antczak A, Cieślikowski WA, Wichtowski M, Kuncman Ł, Kwias Z, Wesoły J. Preoperative cell-free DNA concentration in plasma as a diagnostic and prognostic biomarker of clear cell renal cell carcinoma. Contemp Oncol (Pozn) 2024; 27:284-291. [PMID: 38405214 PMCID: PMC10883193 DOI: 10.5114/wo.2023.135366] [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: 08/06/2023] [Accepted: 01/02/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Assessment of renal tumour masses is based on conventional imaging studies (computer tomography or magnetic resonance), which does not allow characterisation of the histopathological type. Moreover, the prediction of prognosis in localised and metastatic renal cell carcinoma requires improvement as well. Analysis of circulating free DNA (cfDNA) in blood is one of the variants of liquid biopsy that may improve diagnostics and prognosis issues of patients with renal tumour masses suspected to be renal cell carcinoma. The aim of the study was to assess the diagnostic and prognostic role of preoperative cfDNA concentration in the plasma samples of clear cell renal cell carcinoma (ccRCC) patients. Material and methods The preoperative plasma cfDNA concentration was assessed in ccRCC patients (n = 46) and healthy individuals (control group) (n = 17). The circulating free DNA concentration was reflected by the 90 bp DNA fragments determined by real-time polymerase chain reaction. Results The median cfDNA concentration was significantly higher in ccRCC patients (n = 46) compared to the control g roup (n = 17) (2588 ±2554 copies/ml vs. 960 ±490 copies/ml, p < 0.01). In multivariate analysis, the preoperative plasma cfDNA concentration was the significant factor increasing the probability of ccRCC detection (OR: 1.003; 95% CI: 1.001-1.005). The median cfDNA concentration depended on the stage of ccRCC; it was higher in metastatic ccRCC patients (n = 11) compared to non-metastatic ccRCC patients (n = 35) (3619 ±4059 copies/ml vs. 2473 ±1378 copies/ml, p < 0.03). Kaplan-Meier survival analysis demon-strated that patients with high cfDNA values (above 2913 copies/ml) had significantly worse cancer-specific survival (HR: 4.5; 95% CI: 1.3-16.9, log-rank Mantel-Cox test p = 0.015). Conclusions Preoperative plasma cfDNA concentration has diagnostic and prognostic potential in ccRCC pa-tients.
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Affiliation(s)
- Tomasz Milecki
- Department of Urology, Poznań University of Medical Sciences, Poznań, Poland
| | - Katarzyna Kluzek
- Human Molecular Genetics Research Unit, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Poznań University of Medical Sciences, Poznań, Poland
| | - Natalia Pstrąg
- High Throughput Technologies Laboratory, Faculty of Biology, Poznań University of Medical Sciences, Poznań, Poland
| | - Andrzej Antczak
- Department of Urology, Poznań University of Medical Sciences, Poznań, Poland
| | | | - Mateusz Wichtowski
- Surgical Oncology Clinic, Poznań University of Medical Sciences, Poznań, Poland
| | - Łukasz Kuncman
- Department of Radiotherapy, Medical University of Łódź, Łódź, Poland
| | - Zbigniew Kwias
- Department of Urology, Poznań University of Medical Sciences, Poznań, Poland
| | - Joanna Wesoły
- High Throughput Technologies Laboratory, Faculty of Biology, Poznań University of Medical Sciences, Poznań, Poland
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Temilola DO, Wium M, Paccez J, Salukazana AS, Rotimi SO, Otu HH, Carbone GM, Kaestner L, Cacciatore S, Zerbini LF. Detection of Cancer-Associated Gene Mutations in Urinary Cell-Free DNA among Prostate Cancer Patients in South Africa. Genes (Basel) 2023; 14:1884. [PMID: 37895233 PMCID: PMC10606409 DOI: 10.3390/genes14101884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Prostate cancer (PCa) is the most common cause of cancer death among African men. The presence of tumor-specific variations in cell-free DNA (cfDNA), such as mutations, microsatellite instability, and DNA methylation, has been explored as a source of biomarkers for cancer diagnosis. In this study, we investigated the diagnostic role of cfDNA among South African PCa patients. We performed whole exome sequencing (WES) of urinary cfDNA. We identified a novel panel of 31 significantly deregulated somatic mutated genes between PCa and benign prostatic hyperplasia (BPH). Additionally, we performed whole-genome sequencing (WGS) on matching PCa and normal prostate tissue in an independent PCa cohort from South Africa. Our results suggest that the mutations are of germline origin as they were also found in the normal prostate tissue. In conclusion, our study contributes to the knowledge of cfDNA as a biomarker for diagnosing PCa in the South African population.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Juliano Paccez
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Azola Samkele Salukazana
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town 7925, South Africa; (A.S.S.); (L.K.)
| | | | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Giuseppina M. Carbone
- Institute of Oncology Research (IOR), Università della Svizzera italiana, 6900 Bellinzona, Switzerland;
| | - Lisa Kaestner
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town 7925, South Africa; (A.S.S.); (L.K.)
| | - Stefano Cacciatore
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa; (D.O.T.); (M.W.); (J.P.); (S.C.)
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Thakku SG, Lirette J, Murugesan K, Chen J, Theron G, Banaei N, Blainey PC, Gomez J, Wong SY, Hung DT. Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13. Nat Commun 2023; 14:1803. [PMID: 37002219 PMCID: PMC10064635 DOI: 10.1038/s41467-023-37183-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
Detection of microbial cell-free DNA (cfDNA) circulating in the bloodstream has emerged as a promising new approach for diagnosing infection. Microbial diagnostics based on cfDNA require assays that can detect rare and highly fragmented pathogen nucleic acids. We now report WATSON (Whole-genome Assay using Tiled Surveillance Of Nucleic acids), a method to detect low amounts of pathogen cfDNA that couples pooled amplification of genomic targets tiled across the genome with pooled CRISPR/Cas13-based detection of these targets. We demonstrate that this strategy of tiling improves cfDNA detection compared to amplification and detection of a single targeted locus. WATSON can detect cfDNA from Mycobacterium tuberculosis in plasma of patients with active pulmonary tuberculosis, a disease that urgently needs accurate, minimally-invasive, field-deployable diagnostics. We thus demonstrate the potential for translating WATSON to a lateral flow platform. WATSON demonstrates the ability to capitalize on the strengths of targeting microbial cfDNA to address the need for point-of-care diagnostic tests for infectious diseases.
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Affiliation(s)
| | | | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julie Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Clinical Microbiology Laboratory, Stanford Health Care, Palo Alto, CA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - James Gomez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sharon Y Wong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
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Downs BM, Hoang TM, Cope L. Increasing the Capture Rate of Circulating Tumor DNA in Unaltered Plasma Using Passive Microfluidic Mixer Flow Cells. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:3225-3234. [PMID: 36811956 DOI: 10.1021/acs.langmuir.2c02919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A limiting factor in using blood-based liquid biopsies for cancer detection is the volume of extracted blood required to capture a measurable number of circulating tumor DNA (ctDNA). To overcome this limitation, we developed a technology named the dCas9 capture system to capture ctDNA from unaltered flowing plasma, removing the need to extract the plasma from the body. This technology has provided the first opportunity to investigate whether microfluidic flow cell design can affect the capture of ctDNA in unaltered plasma. With inspiration from microfluidic mixer flow cells designed to capture circulating tumor cells and exosomes, we constructed four microfluidic mixer flow cells. Next, we investigated the effects of these flow cell designs and the flow rate on the rate of captured spiked-in BRAF T1799A (BRAFMut) ctDNA in unaltered flowing plasma using surface-immobilized dCas9. Once the optimal mass transfer rate of ctDNA, identified by the optimal ctDNA capture rate, was determined, we investigated whether the design of the microfluidic device, flow rate, flow time, and the number of spiked-in mutant DNA copies affected the rate of capture by the dCas9 capture system. We found that size modifications to the flow channel had no effect on the flow rate required to achieve the optimal capture rate of ctDNA. However, decreasing the size of the capture chamber decreased the flow rate required to achieve the optimal capture rate. Finally, we showed that, at the optimal capture rate, different microfluidic designs using different flow rates could capture DNA copies at a similar rate over time. In this study, the optimal capture rate of ctDNA in unaltered plasma was identified by adjusting the flow rate in each of the passive microfluidic mixer flow cells. However, further validation and optimization of the dCas9 capture system are required before it is ready to be used clinically.
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Affiliation(s)
- Bradley M Downs
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Tra-My Hoang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Leslie Cope
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
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Hadipour M, Fasihi Harandi M, Mirhendi H, Yousofi Darani H. Diagnosis of echinococcosis by detecting circulating cell-free DNA and miRNA. Expert Rev Mol Diagn 2023; 23:133-142. [PMID: 36756744 DOI: 10.1080/14737159.2023.2178903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
INTRODUCTION Diagnosis of echinococcosis is difficult and usually performed based on clinical findings, imaging, and serological test. However, all of them have limitations, especially in follow-up approaches. AREAS COVERED Detection of cell-free DNA (cfDNA) and micro-RNA (miRNA) is currently a hot topic for diagnosis of echinococcosis diseases. For detecting cell-free DNA in echinococcosis patient's samples such as sera, some techniques are based on next-generation sequencing (NGS), DNA-deep sequencing, some are based on PCR-based methods, and a few works related to the detection of miRNA for the diagnosis of human echinococcosis. EXPERT OPINION In the detection of cell-free DNA in echinococcosis patient' samples, NGS and DNA-deep sequencing have shown high level of sensitivity, but are not suitable for routine clinical examination as they are expensive and inaccessible in the majority of endemic areas. However, PCR-based methods have shown a sensitivity of about 20-25%. To improve the sensitivity of these tests, improving the DNA extraction method, designing appropriate primers for detecting short-length fragments of circulating DNA, using a higher volume of a serum sample, and application of more sensitive PCR methods are recommended. In the field of miRNA detection, further works are recommended.
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Affiliation(s)
- Mahboubeh Hadipour
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
| | - Majid Fasihi Harandi
- Research center for Hydatid disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Mirhendi
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
| | - Hossein Yousofi Darani
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
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Bitenc M, Grebstad Tune B, Melheim M, Atneosen-Åsegg M, Lai X, Rajar P, Solberg R, Baumbusch LO. Assessing nuclear versus mitochondrial cell-free DNA (cfDNA) by qRT-PCR and droplet digital PCR using a piglet model of perinatal asphyxia. Mol Biol Rep 2023; 50:1533-1544. [PMID: 36512170 PMCID: PMC9889441 DOI: 10.1007/s11033-022-08135-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Since the discovery more than half a century ago, cell-free DNA (cfDNA) has become an attractive objective in multiple diagnostic, prognostic, and monitoring settings. However, despite the increasing number of cfDNA applications in liquid biopsies, we still lack a comprehensive understanding of the nature of cfDNA including optimal assessment. In the presented study, we continued testing and validation of common techniques for cfDNA extraction and quantification (qRT-PCR or droplet digital PCR) of nuclear- and mitochondrial cfDNA (ncfDNA and mtcfDNA) in blood, using a piglet model of perinatal asphyxia to determine potential temporal and quantitative changes at the levels of cfDNA. METHODS AND RESULTS Newborn piglets (n = 19) were either exposed to hypoxia (n = 11) or were part of the sham-operated control group (n = 8). Blood samples were collected at baseline (= start) and at the end of hypoxia or at 40-45 min for the sham-operated control group. Applying the qRT-PCR method, ncfDNA concentrations in piglets exposed to hypoxia revealed an increasing trend from 7.1 ng/ml to 9.5 ng/ml for HK2 (hexokinase 2) and from 4.6 ng/ml to 7.9 ng/ml for β-globulin, respectively, whereas the control animals showed a more balanced profile. Furthermore, median levels of mtcfDNA were much higher in comparison to ncfDNA, but without significant differences between intervention versus the control group. CONCLUSIONS Both, qRT-PCR and the droplet digital PCR technique identified overall similar patterns for the concentration changes of cfDNA; but, the more sensitive digital PCR methodology might be required to identify minimal responses.
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Affiliation(s)
- Marie Bitenc
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway
| | - Benedicte Grebstad Tune
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maria Melheim
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway
| | | | - Xiaoran Lai
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Polona Rajar
- Department of Neonatal Intensive Care, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Ullevål, Oslo, Norway
- Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Rønnaug Solberg
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway
- Department of Pediatrics, Vestfold Hospital Trust, Tønsberg, Norway
| | - Lars Oliver Baumbusch
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway.
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Kwan EM, Wyatt AW, Chi KN. Towards clinical implementation of circulating tumor DNA in metastatic prostate cancer: Opportunities for integration and pitfalls to interpretation. Front Oncol 2022; 12:1054497. [PMID: 36439451 PMCID: PMC9685669 DOI: 10.3389/fonc.2022.1054497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Plasma circulating tumor DNA (ctDNA) represents short fragments of tumor-derived DNA released into the bloodstream primarily from cancer cells undergoing apoptosis. In metastatic castration-resistant prostate cancer (mCRPC), characterizing genomic alterations in ctDNA identifies mutations, copy number alterations, and structural rearrangements with predictive and prognostic biomarker utility. These associations with clinical outcomes have resulted in ctDNA increasingly incorporated into routine clinical care. In this review, we summarize current and emerging applications for ctDNA analysis in metastatic prostate cancer, including outcome prediction, treatment selection, and characterization of treatment resistance. We also discuss potential pitfalls with interpreting ctDNA findings, namely false negatives arising from low tumor content and optimal assay design, including correction for clonal hematopoiesis of indeterminate potential and germline variants. Understanding the influence of these limitations on interpretation of ctDNA results is necessary to overcome barriers to clinical implementation. Nevertheless, as assay availability and technology continue to improve, recognizing both opportunities and shortcomings of ctDNA analysis will retain relevance with informing the implementation of precision-oncology initiatives for metastatic prostate cancer.
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Affiliation(s)
- Edmond M. Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver Centre, Vancouver, BC, Canada
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Kim N. Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver Centre, Vancouver, BC, Canada
- Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
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11
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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12
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Briggs GD, Gelzinnis S, Meakes S, King KL, Balogh ZJ. NOT ALL CELL-FREE MITOCHONDRIAL DNA IS EQUAL IN TRAUMA PATIENTS. Shock 2022; 58:231-235. [PMID: 36125357 PMCID: PMC9512242 DOI: 10.1097/shk.0000000000001969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/20/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
ABSTRACT Mitochondrial DNA (mtDNA) acts as a proinflammatory damage-associated molecular pattern that stimulates innate immune activation via Toll-like receptor 9, similarly to bacterial DNA. A number of clinical studies have measured elevated cell-free mtDNA in the plasma of trauma patients, thought to originate from tissue injury and inflammatory processes; however, the magnitude of this increase, the absolute concentration, and the association with poor outcomes varies considerably across studies. Measurements of cell-free mtDNA in healthy individuals have shown that the majority of "cell-free" mtDNA (>95%) can be centrifuged/filtered from plasma in the size range of 0.45 to 5 μm, suggesting that there are larger forms of mtDNA-containing complexes in the plasma that could be considered cell-free. Whether this is true for trauma patients (and other relevant disease states) and the clinical relevance of the larger forms of mtDNA is unknown. These findings from healthy individuals also suggest that the centrifugation speeds used to generate cell-free plasma (which are rarely consistent among studies) could result in mixed populations of cell-free mtDNA that could confound associations with outcomes. We demonstrate in this study of 25 major trauma patients that the majority of the cell-free mtDNA in trauma patient plasma (>95%) is removed after centrifugation at 16,000g. Despite the larger forms of mtDNA being predominant, they do not correlate with outcomes or expected parameters such as injury/shock severity, multiple organ failure, and markers of inflammation, whereas low-molecular-weight cell-free mtDNA correlates strongly with these variables.
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Affiliation(s)
- Gabrielle D. Briggs
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Scott Gelzinnis
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Simone Meakes
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Kate L. King
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Zsolt J. Balogh
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
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13
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Igari F, Tanaka H, Giuliano AE. The applications of plasma cell-free DNA in cancer detection: Implications in the management of breast cancer patients. Crit Rev Oncol Hematol 2022; 175:103725. [PMID: 35618229 DOI: 10.1016/j.critrevonc.2022.103725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Liquid biopsy probes DNA, RNA, and proteins in body fluids for cancer detection and is one of the most rapidly developing areas in oncology. Tumor-derived DNA (circulating tumor DNA, ctDNA) in the context of cell-free DNA (cfDNA) in blood has been the main target for its potential utilities in cancer detection. Liquid biopsy can report tumor burden in real-time without invasive interventions, and would be feasible for screening tumor types that lack standard-of-care screening approaches. Two major approaches to interrogating ctDNA are genetic mutation and DNA methylation profiling. Mutation profiling can identify tumor driver mutations and guide precision therapy. Targeted genomic profiling of DNA methylation has become the main approach for cancer screening in the general population. Here we review the recent technological development and ongoing efforts in clinical applications. For clinical applications, we focus on breast cancer, in which subtype-specific biology demarcates the applications of ctDNA.
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Affiliation(s)
- Fumie Igari
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Department of Breast Oncology, Juntendo University, Tokyo, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA.
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
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14
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Downs BM, Sukumar S. Capturing ctDNA from Unaltered Stationary and Flowing Plasma with dCas9. ACS APPLIED MATERIALS & INTERFACES 2022; 14:24113-24121. [PMID: 35603357 DOI: 10.1021/acsami.2c03186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many studies have established that blood-based liquid biopsies can be used to detect cancer in its early stages. However, the limiting factor for early cancer detection is the volume of blood required to capture the small amount of circulating tumor DNA (ctDNA). An apheresis machine is a device that can draw whole blood, separate the blood components, and infuse the blood components back into the individual. This device provides the opportunity to screen large volumes of plasma without extracting it from the body. However, current DNA capture technologies require the plasma to be altered before the ctDNA can be captured. Our goal was to develop the first technology that can capture ctDNA from flowing unaltered plasma. To simulate cancer patient plasma, we spiked BRAF T1799A (BRAFMut) DNA into plasma from healthy individuals. We used catalytically dead Cas9 (dCas9), guide RNA, and allele-specific quantitative polymerase chain reaction (qPCR) to capture and measure the number of captured BRAFMut DNA copies. We found that dCas9 captured BRAFMut alleles with equal efficiency at room temperature (25 °C) and body temperature (37 °C). Next, we showed that, in stationary unaltered plasma, dCas9 was as efficient in capturing BRAFMut as a commercial cell-free DNA (cfDNA) capture kit. However, in contrast to the cfDNA capture kit, dCas9 enriched BRAFMut by 1.8-3.3-fold. We then characterized the dCas9 capture system in laminar and turbulent flowing plasma. We showed that the capture rate using turbulent flow was greater than that in laminar flow and stationary plasma. With turbulent flow, the number of captured BRAFMut copies doubles with time (slope = -1.035 Ct) and is highly linear (R2 = 0.874). While we showed that the dCas9 capture system can capture ctDNA from unaltered flowing plasma, further optimization and validation of this technology is required before its clinical utility can be determined.
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Affiliation(s)
- Bradley M Downs
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Saraswati Sukumar
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
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15
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Yuwono NL, Boyd MAA, Henry CE, Werner B, Ford CE, Warton K. Circulating cell-free DNA undergoes significant decline in yield after prolonged storage time in both plasma and purified form. Clin Chem Lab Med 2022; 60:1287-1298. [DOI: 10.1515/cclm-2021-1152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/16/2022] [Indexed: 11/15/2022]
Abstract
Abstract
Objectives
Circulating DNA (cirDNA) is generally purified from plasma that has been biobanked for variable lengths of time. In long-term experiments or clinical trials, the plasma can be stored frozen for up to several years. Therefore, it is crucial to determine the stability of cirDNA to ensure confidence in sample quality upon analysis. Our main objective was to determine the effect of storage for up to 2 years on cirDNA yield and fragmentation.
Methods
We stored frozen EDTA plasma and purified cirDNA from 10 healthy female donors, then quantified cirDNA yield at baseline, and at regular intervals for up to 2 years, by qPCR and Qubit. We also compared cirDNA levels in non-haemolysed and haemolysed blood samples after 16 months of storage and tested the effect of varying DNA extraction protocol parameters.
Results
Storage up to two years caused an annual cirDNA yield decline of 25.5% when stored as plasma and 23% when stored as purified DNA, with short fragments lost more rapidly than long fragments. Additionally, cirDNA yield was impacted by plasma input and cirDNA elution volumes, but not by haemolysis.
Conclusions
The design of long-term cirDNA-based studies and clinical trials should factor in the deterioration of cirDNA during storage.
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Affiliation(s)
- Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Mollie Ailie Acheson Boyd
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Claire Elizabeth Henry
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Bonnita Werner
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
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16
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Verhoeven JGHP, Hesselink DA, Peeters AMA, de Jonge E, von der Thüsen JH, van Schaik RHN, Matic M, Baan CC, Manintveld OC, Boer K. Donor-Derived Cell-Free DNA for the Detection of Heart Allograft Injury: The Impact of the Timing of the Liquid Biopsy. Transpl Int 2022; 35:10122. [PMID: 35387397 PMCID: PMC8977404 DOI: 10.3389/ti.2022.10122] [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: 10/18/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022]
Abstract
Background: In heart transplant recipients, donor-derived cell-free DNA (ddcfDNA) is a potential biomarker for acute rejection (AR), in that increased values may indicate rejection. For the assessment of ddcfDNA as new biomarker for rejection, blood plasma sampling around the endomyocardial biopsy (EMB) seems a practical approach. To evaluate the effect of the EMB procedure on ddcfDNA values, ddcfDNA values before the EMB were pairwise compared to ddcfDNA values after the EMB. We aimed at evaluating whether it matters whether the ddcfDNA sampling is done before or after the EMB-procedure. Methods: Plasma samples from heart transplant recipients were obtained pre-EMB and post-EMB. A droplet digital PCR method was used for measuring ddcfDNA, making use of single-nucleotide polymorphisms that allowed both relative quantification, as well as absolute quantification of ddcfDNA. Results: Pairwise comparison of ddcfDNA values pre-EMB with post-EMB samples (n = 113) showed significantly increased ddcfDNA concentrations and ddcfDNA% in post-EMB samples: an average 1.28-fold increase in ddcfDNA concentrations and a 1.31-fold increase in ddcfDNA% was observed (p = 0.007 and p = 0.03, respectively). Conclusion: The EMB procedure causes iatrogenic injury to the allograft that results in an increase in ddcfDNA% and ddcfDNA concentrations. For the assessment of ddcfDNA as marker for AR, collection of plasma samples before the EMB procedure is therefore essential.
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Affiliation(s)
- Jeroen G H P Verhoeven
- Division of Nephrology and Transplantation, Department of Internal Medicine, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Dennis A Hesselink
- Division of Nephrology and Transplantation, Department of Internal Medicine, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Annemiek M A Peeters
- Division of Nephrology and Transplantation, Department of Internal Medicine, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Evert de Jonge
- Department of Clinical Chemistry, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Maja Matic
- Department of Clinical Chemistry, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Carla C Baan
- Division of Nephrology and Transplantation, Department of Internal Medicine, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - O C Manintveld
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Karin Boer
- Division of Nephrology and Transplantation, Department of Internal Medicine, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
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17
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Damodara S, Arora J, Liaw PC, Fox-Robichaud AE, Selvaganapathy PR. Single-step measurement of cell-free DNA for sepsis prognosis using a thread-based microfluidic device. Mikrochim Acta 2022; 189:146. [PMID: 35298718 DOI: 10.1007/s00604-022-05245-1] [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: 11/05/2021] [Accepted: 02/22/2022] [Indexed: 10/18/2022]
Abstract
Cell-free DNA (cfDNA) content in plasma has been studied as a biomarker for sepsis. Recent publications show that the cfDNA content in sepsis patients entering intensive care unit who were likely to survive had a total cfDNA concentration of 1.16 ± 0.13 μg/mL compared to 4.65 ± 0.48 μg/mL of non-survivors. Current methods for measuring cfDNA content in plasma were designed to amplify and measure low concentrations of specific DNA, making them unsuitable for low-cost measurement of total cfDNA content in plasma. Here, we have developed a point of care (POC) device that uses a thread silicone device as a medium to store a fluorescent dye which eliminates the need for preparatory steps, external aliquoting and dispensing of reagents, preconcentration, and external mixing while reducing the detection cost. The device was paired with a portable imaging system with an excitation filter at 472 ± 10 nm and an emission filter of 520 ± 10 nm that can be operated with just 100 mA current supply. The device was demonstrated for use in the quantification of buffered cfDNA samples in a range 1-6 μg/mL with a sensitivity of 5.72 AU/μg/mL and with cfDNA spiked in plasma with a range of 1-3 μg/mL and a sensitivity of 5.43 AU/μg/mL. The results showed that the device could be used as a low-cost, rapid, and portable POC device for differentiating between survivors and non-survivors of sepsis within 20 min.
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Affiliation(s)
- Sreekant Damodara
- Department of Mechanical Engineering, McMaster University, Hamilton, Canada
| | - Jaskirat Arora
- Department of Medicine, McMaster University, Hamilton, Canada
| | - Patricia C Liaw
- Department of Medicine, McMaster University, Hamilton, Canada
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18
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Ochmann DT, Philippi KFA, Zeier P, Sandner M, Hillen B, Neuberger EWI, Ruiz de Azua I, Lieb K, Wessa M, Lutz B, Simon P, Brahmer A. Association of Innate and Acquired Aerobic Capacity With Resilience in Healthy Adults: Protocol for a Randomized Controlled Trial of an 8-Week Web-Based Physical Exercise Intervention. JMIR Res Protoc 2021; 10:e29712. [PMID: 34847062 PMCID: PMC8669579 DOI: 10.2196/29712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/10/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Physical activity alleviates chronic stress. The latest research suggests a relationship between resilience and physical fitness. Beneficial adaptations of the hypothalamic-pituitary-adrenal axis, sympathetic nervous system, endocannabinoid system, and tryptophan pathway, which are induced by an active lifestyle, are considered to be conducive to resilience. However, detailed knowledge on the molecular link between the effects of acute and chronic physical exercise and improved resilience to stress in humans is missing. Moreover, the relationship between innate and acquired aerobic capacity and resilience is poorly understood. OBJECTIVE The aim of this study is to implement a human exercise intervention trial addressing the following main hypotheses: a high innate aerobic capacity is associated with high resilience to stress, and web-based physical exercise training improves aerobic capacity of physically inactive adults, which is accompanied by improved resilience. In this setting, we will analyze the relationship between resilience parameters and innate and acquired aerobic capacity as well as circulating signaling molecules. METHODS A total of 70 healthy, physically inactive (<150 minutes/week of physical activity) adults (aged 18-45 years) will be randomly assigned to an intervention or control group. Participants in the intervention group will receive weekly training using progressive endurance and interval running adapted individually to their remotely supervised home training performance via web-based coach support. A standardized incremental treadmill exercise test will be performed before and after the intervention period of 8 weeks to determine the innate and acquired aerobic capacity (peak oxygen uptake). Before and after the intervention, psychological tests and questionnaires that characterize parameters implicated in resilience will be applied. Blood and saliva will be sampled for the analysis of cortisol, lactate, endocannabinoids, catecholamines, kynurenic acid, and further circulating signal transducers. Statistical analysis will provide comprehensive knowledge on the relationship between aerobic capacity and resilience, as well as the capacity of peripheral factors to mediate the promoting effects of exercise on resilience. RESULTS The study was registered in October 2019, and enrollment began in September 2019. Of the 161 participants who were initially screened via a telephone survey, 43 (26.7%) fulfilled the inclusion criteria and were included in the study. Among the 55% (17/31) of participants in the intervention group and 45% (14/31) of participants in the control group who completed the study, no serious adverse incidents were reported. Of 43 participants, 4 (9%) withdrew during the program (for individual reasons) and 8 (19%) have not yet participated in the program; moreover, further study recruitment was paused for an indeterminate amount of time because of the COVID-19 pandemic. CONCLUSIONS Our study aims to further define the physiological characteristics of human resilience, and it may offer novel approaches for the prevention and therapy of mental disorders via an exercise prescription. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/29712.
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Affiliation(s)
- David T Ochmann
- Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Keito F A Philippi
- Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Peter Zeier
- Clinical Psychology and Neuropsychology, Institute for Psychology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Magdalena Sandner
- Clinical Psychology and Neuropsychology, Institute for Psychology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Barlo Hillen
- Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Elmo W I Neuberger
- Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Inigo Ruiz de Azua
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Klaus Lieb
- Department of Psychiatry and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michèle Wessa
- Clinical Psychology and Neuropsychology, Institute for Psychology, Johannes Gutenberg-University Mainz, Mainz, Germany
- Leibniz Institute for Resilience Research, Mainz, Germany
| | - Beat Lutz
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Leibniz Institute for Resilience Research, Mainz, Germany
| | - Perikles Simon
- Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Alexandra Brahmer
- Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
- Extracellular Vesicles Research Group, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, Mainz, Germany
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19
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Uhe I, Hagen ME, Ris F, Meyer J, Toso C, Douissard J. Cell-free DNA liquid biopsy for early detection of gastrointestinal cancers: A systematic review. World J Gastrointest Oncol 2021; 13:1799-1812. [PMID: 34853652 PMCID: PMC8603462 DOI: 10.4251/wjgo.v13.i11.1799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/06/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gastrointestinal tumors are among the most common cancer types, and early detection is paramount to improve their management. Cell-free DNA (cfDNA) liquid biopsy raises significant hopes for non-invasive early detection.
AIM To describe current applications of this technology for gastrointestinal cancer detection and screening.
METHODS A systematic review of the literature was performed across the PubMed database. Articles reporting the use of cfDNA liquid biopsy in the screening or diagnosis of gastrointestinal cancers were included in the analysis.
RESULTS A total of 263 articles were screened for eligibility, of which 13 articles were included. Studies investigated colorectal cancer (5 studies), pancreatic cancer (2 studies), hepatocellular carcinoma (3 studies), and multi-cancer detection (3 studies), including gastric, oesophageal, or bile duct cancer, representing a total of 4824 patients. Test sensitivities ranged from 71% to 100%, and specificities ranged from 67.4% to 100%. Pre-cancerous lesions detection was less performant with a sensitivity of 16.9% and a 100% specificity in one study. Another study using a large biobank demonstrated a 94.9% sensitivity in detecting cancer up to 4 years before clinical symptoms, with a 61% accuracy in tissue-of-origin identification.
CONCLUSION cfDNA liquid biopsy seems capable of detecting gastrointestinal cancers at an early stage of development in a non-invasive and repeatable manner and screening simultaneously for multiple cancer types in a single blood sample. Further trials in clinically relevant settings are required to determine the exact place of this technology in gastrointestinal cancer screening and diagnosis strategies.
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Affiliation(s)
- Isabelle Uhe
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
| | | | - Frédéric Ris
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
| | - Jeremy Meyer
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
| | - Christian Toso
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
| | - Jonathan Douissard
- Abdominal Surgery Division, Geneva University Hospitals, Geneva 1211, Switzerland
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20
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Yuwono NL, Warton K, Ford CE. The influence of biological and lifestyle factors on circulating cell-free DNA in blood plasma. eLife 2021; 10:e69679. [PMID: 34752217 PMCID: PMC8577835 DOI: 10.7554/elife.69679] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/23/2021] [Indexed: 01/02/2023] Open
Abstract
Research and clinical use of circulating cell-free DNA (cirDNA) is expanding rapidly; however, there remain large gaps in our understanding of the influence of lifestyle and biological factors on the amount of cirDNA present in blood. Here, we review 66 individual studies of cirDNA levels and lifestyle and biological factors, including exercise (acute and chronic), alcohol consumption, occupational hazard exposure, smoking, body mass index, menstruation, hypertension, circadian rhythm, stress, biological sex and age. Despite technical and methodological inconsistences across studies, we identify acute exercise as a significant influence on cirDNA levels. Given the large increase in cirDNA induced by acute exercise, we recommend that controlling for physical activity prior to blood collection is routinely incorporated into study design when total cirDNA levels are of interest. We also highlight appropriate selection and complete reporting of laboratory protocols as important for improving the reproducibility cirDNA studies and ability to critically evaluate the results.
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Affiliation(s)
- Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
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21
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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22
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Huckriede J, de Vries F, Hultström M, Wichapong K, Reutelingsperger C, Lipcsey M, Garcia de Frutos P, Frithiof R, Nicolaes GAF. Histone H3 Cleavage in Severe COVID-19 ICU Patients. Front Cell Infect Microbiol 2021; 11:694186. [PMID: 34568088 PMCID: PMC8461091 DOI: 10.3389/fcimb.2021.694186] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/19/2021] [Indexed: 12/26/2022] Open
Abstract
The severity of coronavirus disease 19 (COVID-19) is associated with neutrophil extracellular trap (NET) formation. During NET formation, cytotoxic extracellular histones are released, the presence of which is linked to the initiation and progression of several acute inflammatory diseases. Here we study the presence and evolution of extracellular histone H3 and several other neutrophil-related molecules and damage-associated molecular patterns (DAMPs) in the plasma of 117 COVID-19-positive ICU patients. We demonstrate that at ICU admission the levels of histone H3, MPO, and DNA-MPO complex were all significantly increased in COVID-19-positive patients compared to control samples. Furthermore, in a subset of 54 patients, the levels of each marker remained increased after 4+ days compared to admission. Histone H3 was found in 28% of the patients on admission to the ICU and in 50% of the patients during their stay at the ICU. Notably, in 47% of histone-positive patients, we observed proteolysis of histone in their plasma. The overall presence of histone H3 during ICU stay was associated with thromboembolic events and secondary infection, and non-cleaved histone H3 was associated with the need for vasoactive treatment, invasive ventilation, and the development of acute kidney injury. Our data support the validity of treatments that aim to reduce NET formation and additionally underscore that more targeted therapies focused on the neutralization of histones should be considered as treatment options for severe COVID-19 patients.
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Affiliation(s)
- Joram Huckriede
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Femke de Vries
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Michael Hultström
- Department of Surgical Sciences, Section for Anaesthesia & Intensive Care, Uppsala University, Uppsala, Sweden.,Department of Medical Cell Biology, Integrative Physiology, Uppsala University, Uppsala, Sweden
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Chris Reutelingsperger
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Miklos Lipcsey
- Department of Surgical Sciences, Section for Anaesthesia & Intensive Care, Uppsala University, Uppsala, Sweden.,Hedenstierna Laboratory, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Pablo Garcia de Frutos
- Department of Cell Death and Proliferation, IIBB-CSIC, IDIBAPS and CIBERCV, Barcelona, Spain
| | - Robert Frithiof
- Department of Surgical Sciences, Section for Anaesthesia & Intensive Care, Uppsala University, Uppsala, Sweden
| | - Gerry A F Nicolaes
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
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23
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An electrochemiluminescence resonance energy transfer biosensor for the detection of circulating tumor DNA from blood plasma. iScience 2021; 24:103019. [PMID: 34522862 PMCID: PMC8426273 DOI: 10.1016/j.isci.2021.103019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/02/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
A liquid biopsy is a noninvasive approach for detecting double-stranded circulating tumor DNA (ctDNA) of 90–320 nucleotides in blood plasma from patients with cancer. Most techniques employed for ctDNA detection are time consuming and require expensive DNA purification kits. Electrochemiluminescence resonance energy transfer (ECL-RET) biosensors exhibit high sensitivity, a wide response range, and are promising for straightforward sensing applications. Until now, ECL-RET biosensors have been designed for sensing short single-stranded oligonucleotides of less than 45 nucleotides. In this work, an ECL-RET biosensor comprising graphitic carbon nitride quantum dots was assessed for the amplification-free detection in the blood plasma of DNA molecules coding for the EGFR L858R mutation, which is associated with non-small-cell lung cancer. Following a low-cost pre-treatment, the highly specific ECL-RET biosensor quantified double-stranded EGFR L858R DNA of 159 nucleotides diluted into the blood within a linear range of 0.01 fM to 1 pM, demonstrating its potential for noninvasive biopsies. An ECL-RET biosensor with g-CNQDs was developed for liquid biopsies of ctDNA The biosensor detected DNA molecules coding for the lung cancer EGFR L858R mutation EGFR L858R DNA molecules of 18 and 159 nucleotides activated the biosensor The biosensor detected ctDNA-like EGFR L858R molecules diluted in blood plasma
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24
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Huebner H, Lubrich H, Blum S, Antoniadis S, Lermann J, Ekici A, Fasching PA, Beckmann MW, Ruebner M, Burghaus S. Comparison of methods for isolation and quantification of circulating cell-free DNA from patients with endometriosis. Reprod Biomed Online 2021; 43:788-798. [PMID: 34493460 DOI: 10.1016/j.rbmo.2021.08.004] [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: 03/01/2021] [Revised: 07/13/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
RESEARCH QUESTION Which is the optimal extraction method for isolating and quantifying circulating cell-free DNA (ccfDNA) from patients with endometriosis? Endometriosis is a common benign disease, associated with pain, infertility and reduced quality of life. Endometriosis is also a known risk factor for various cancers. Robust biomarkers for early detection and prediction of prognosis, however, are lacking. CcfDNA is an easy to obtain biomarker associated with prognosis of cancer patients and enables non-invasive analysis of somatic mutations. Recently, elevated levels of ccfDNA were detected in patients with endometriosis. DESIGN Two different ccfDNA extraction methods were compared: Maxwell RSC ccfDNA plasma kit (Maxwell) and QiAamp minElute ccfDNA mini kit (QIAamp). The ccfDNA and circulating mitochondrial DNA (mtDNA) quantities from 34 patients diagnosed with endometriosis were analysed. Fluorometric measurement and quantitative reverse transcription polymerase chain reaction (qRT-PCR) of short and long ALU and mtDNA fragments were used to quantiy ccfDNA. RESULTS The yield of ccfDNA isolated with the Maxwell method was significantly higher compared with the QIAamp method (P < 0.0001). Integrity of ccfDNA was significantly higher in the QIAamp isolate (P < 0.0001). Recovered mtDNA was not significantly different between both extraction methods used. CONCLUSIONS The choice of extraction method can significantly influence the ccfDNA output and integrity. Both methods, however, enabled isolation of sufficient ccfDNA for further downstream applications. With this approach, isolation of ccfDNA could enable the non-invasive detection and analysis of somatic mutation within endometriosis tissue.
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Affiliation(s)
- Hanna Huebner
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Hannah Lubrich
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Simon Blum
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Sophia Antoniadis
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Johannes Lermann
- Department of Obstetrics and Gynecology, Klinikum Klagenfurt am Wörthersee, Austria
| | - Arif Ekici
- Institute of Human Genetics, Erlangen University Hospital, Friedrich-Alexander University, Erlangen-Nürnberg, Erlangen, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Matthias Ruebner
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Stefanie Burghaus
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany.
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25
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de Miranda FS, Barauna VG, dos Santos L, Costa G, Vassallo PF, Campos LCG. Properties and Application of Cell-Free DNA as a Clinical Biomarker. Int J Mol Sci 2021; 22:9110. [PMID: 34502023 PMCID: PMC8431421 DOI: 10.3390/ijms22179110] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022] Open
Abstract
Biomarkers are valuable tools in clinical practice. In 2001, the National Institutes of Health (NIH) standardized the definition of a biomarker as a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. A biomarker has clinical relevance when it presents precision, standardization and reproducibility, suitability to the patient, straightforward interpretation by clinicians, and high sensitivity and/or specificity by the parameter it proposes to identify. Thus, serum biomarkers should have advantages related to the simplicity of the procedures and to the fact that venous blood collection is commonplace in clinical practice. We described the potentiality of cfDNA as a general clinical biomarker and focused on endothelial dysfunction. Circulating cell-free DNA (cfDNA) refers to extracellular DNA present in body fluid that may be derived from both normal and diseased cells. An increasing number of studies demonstrate the potential use of cfDNA as a noninvasive biomarker to determine physiologic and pathologic conditions. However, although still scarce, increasing evidence has been reported regarding using cfDNA in cardiovascular diseases. Here, we have reviewed the history of cfDNA, its source, molecular features, and release mechanism. We also show recent studies that have investigated cfDNA as a possible marker of endothelial damage in clinical settings. In the cardiovascular system, the studies are quite new, and although interesting, stronger evidence is still needed. However, some drawbacks in cfDNA methodologies should be overcome before its recommendation as a biomarker in the clinical setting.
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Affiliation(s)
- Felipe Silva de Miranda
- Post Graduation Program in Biology and Biotechnology of Microorganisms, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Department of Biological Science, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Valério Garrone Barauna
- Post Graduation Program in Health Sciences, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Molecular Physiology Laboratory of Exercise Science, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
| | - Leandro dos Santos
- Academic Unit of Serra Talhada, Rural Federal University of Pernambuco, Serra Talhada 56909-535, Pernambuco, Brazil;
| | - Gustavo Costa
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
| | - Paula Frizera Vassallo
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
- Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Luciene Cristina Gastalho Campos
- Post Graduation Program in Biology and Biotechnology of Microorganisms, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Department of Biological Science, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Post Graduation Program in Health Sciences, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
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26
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Huckriede J, Anderberg SB, Morales A, de Vries F, Hultström M, Bergqvist A, Ortiz-Pérez JT, Sels JW, Wichapong K, Lipcsey M, van de Poll M, Larsson A, Luther T, Reutelingsperger C, de Frutos PG, Frithiof R, Nicolaes GAF. Evolution of NETosis markers and DAMPs have prognostic value in critically ill COVID-19 patients. Sci Rep 2021; 11:15701. [PMID: 34344929 PMCID: PMC8333321 DOI: 10.1038/s41598-021-95209-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022] Open
Abstract
Coronavirus disease 19 (COVID-19) presents with disease severities of varying degree. In its most severe form, infection may lead to respiratory failure and multi-organ dysfunction. Here we study the levels and evolution of the damage associated molecular patterns (DAMPS) cell free DNA (cfDNA), extracellular histone H3 (H3) and neutrophil elastase (NE), and the immune modulators GAS6 and AXL in relation to clinical parameters, ICU scoring systems and mortality in patients (n = 100) with severe COVID-19. cfDNA, H3, NE, GAS6 and AXL were increased in COVID-19 patients compared to controls. These measures associated with occurrence of clinical events and intensive care unit acquired weakness (ICUAW). cfDNA and GAS6 decreased in time in patients surviving to 30 days post ICU admission. A decrease of 27.2 ng/mL cfDNA during ICU stay associated with patient survival, whereas levels of GAS6 decreasing more than 4.0 ng/mL associated with survival. The presence of H3 in plasma was a common feature of COVID-19 patients, detected in 38% of the patients at ICU admission. NETosis markers cfDNA, H3 and NE correlated well with parameters of tissue damage and neutrophil counts. Furthermore, cfDNA correlated with lowest p/f ratio and a lowering in cfDNA was observed in patients with ventilator-free days.
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Affiliation(s)
- Joram Huckriede
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
| | - Sara Bülow Anderberg
- Department of Surgical Sciences, Section for Anaesthesia & Intensive Care, Uppsala University, Uppsala, Sweden
| | - Albert Morales
- Department of Cell Death and Proliferation, IIBB-CSIC, IDIBAPS, and BCLC, CIBEREHD, Barcelona, Spain
| | - Femke de Vries
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
| | - Michael Hultström
- Department of Surgical Sciences, Section for Anaesthesia & Intensive Care, Uppsala University, Uppsala, Sweden
- Department of Medical Cell Biology, Integrative Physiology, Uppsala University, Uppsala, Sweden
| | - Anders Bergqvist
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden
| | - José T Ortiz-Pérez
- Cardiology Department, Hospital Clinic Barcelona and CIBERCV, Barcelona, Spain
| | - Jan Willem Sels
- Department of Intensive Care Medicine, Maastricht University Medical Centre MUMC+), Maastricht, the Netherlands
- Department of Cardiology, Maastricht University Medical Centre, MUMC+), Maastricht, the Netherlands
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
| | - Miklos Lipcsey
- Department of Surgical Sciences, Section for Anaesthesia & Intensive Care, Uppsala University, Uppsala, Sweden
- Hedenstierna Laboratory, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Marcel van de Poll
- Department of Intensive Care Medicine, Maastricht University Medical Centre MUMC+), Maastricht, the Netherlands
- Department of Surgery, Maastricht University Medical Centre (MUMC+), School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, the Netherlands
| | - Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Tomas Luther
- Department of Surgical Sciences, Section for Anaesthesia & Intensive Care, Uppsala University, Uppsala, Sweden
| | - Chris Reutelingsperger
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
| | - Pablo Garcia de Frutos
- Department of Cell Death and Proliferation, IIBB-CSIC, IDIBAPS and CIBERCV, Barcelona, Spain
| | - Robert Frithiof
- Department of Surgical Sciences, Section for Anaesthesia & Intensive Care, Uppsala University, Uppsala, Sweden
| | - Gerry A F Nicolaes
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands.
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27
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Neuberger EWI, Brahmer A, Ehlert T, Kluge K, Philippi KFA, Boedecker SC, Weinmann-Menke J, Simon P. Validating quantitative PCR assays for cfDNA detection without DNA extraction in exercising SLE patients. Sci Rep 2021; 11:13581. [PMID: 34193884 PMCID: PMC8245561 DOI: 10.1038/s41598-021-92826-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 06/07/2021] [Indexed: 01/10/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has been investigated as a screening tool for many diseases. To avoid expensive and time-consuming DNA isolation, direct quantification PCR assays can be established. However, rigorous validation is required to provide reliable data in the clinical and non-clinical context. Considering the International Organization for Standardization, as well as bioanalytical method validation guidelines, we provide a comprehensive procedure to validate assays for cfDNA quantification from blood plasma without DNA isolation. A 90 and 222 bp assay was validated to study the kinetics of cfDNA after exercise in patients with systemic lupus erythematosus (SLE). The assays showed ultra-low limit of quantification (LOQ) with 0.47 and 0.69 ng/ml, repeatability ≤ 11.6% (95% CI 8.1-20.3), and intermediate precision ≤ 12.1% (95% CI 9.2-17.7). Incurred sample reanalysis confirmed the precision of the procedure. The additional consideration of pre-analytical factors shows that centrifugation speed and temperature do not change cfDNA concentrations. In SLE patients cfDNA increases ~ twofold after a walking exercise, normalizing after 60 min of rest. The established assays allow reliable and cost-efficient quantification of cfDNA in minute amounts of plasma in the clinical setting. Additionally, the assay can be used as a tool to determine the impact of pre-analytical factors and validate cfDNA quantity and quality of isolated samples.
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Affiliation(s)
- Elmo W I Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Alexandra Brahmer
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Tobias Ehlert
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Katrin Kluge
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Keito F A Philippi
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Simone C Boedecker
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Julia Weinmann-Menke
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany.
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28
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Wang J, Yang L, Diao Y, Liu J, Li J, Li R, Zheng L, Zhang K, Ma Y, Hao X. Circulating tumour DNA methylation in hepatocellular carcinoma diagnosis using digital droplet PCR. J Int Med Res 2021; 49:300060521992962. [PMID: 33750234 PMCID: PMC7989135 DOI: 10.1177/0300060521992962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objective To evaluate the performance of a DNA methylation-based digital droplet polymerase chain reaction (ddPCR) assay to detect aberrant DNA methylation in cell-free DNA (cfDNA) and to determine its application in the detection of hepatocellular carcinoma (HCC). Methods The present study recruited patients with liver-related diseases and healthy control subjects. Blood samples were used for the extraction of cfDNA, which was then bisulfite converted and the extent of DNA methylation quantified using a ddPCR platform. Results A total of 97 patients with HCC, 80 healthy control subjects and 46 patients with chronic hepatitis B/C virus infection were enrolled in the study. The level of cfDNA in the HCC group was significantly higher than that in the healthy control group. For the detection of HCC, based on a cut-off value of 15.7% for the cfDNA methylation ratio, the sensitivity and specificity were 78.57% and 89.38%, respectively. The diagnostic accuracy was 85.27%, the positive predictive value was 81.91% and the negative predictive value was 87.20%. The positive likelihood ratio of 15.7% in HCC diagnosis was 7.40, while the negative likelihood ratio was 0.24. Conclusions A sensitive methylation-based assay might serve as a liquid biopsy test for diagnosing HCC.
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Affiliation(s)
- Juan Wang
- Department of Clinical Laboratory Medicine, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, China
| | - Liu Yang
- Department of Clinical Laboratory Medicine, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, China
| | - Yanjun Diao
- Department of Clinical Laboratory Medicine, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, China
| | - Jiayun Liu
- Department of Clinical Laboratory Medicine, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, China
| | - Jinjie Li
- Department of Clinical Laboratory Medicine, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, China
| | - Rui Li
- Department of Clinical Laboratory Medicine, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, China
| | - Lianghong Zheng
- Guangzhou Youze Biological Pharmaceutical Technology Company Ltd., Guangzhou, Guangdong Province, China
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Yueyun Ma
- Department of Clinical Laboratory, Air Force Medical Centre, Air Force Medical University, Beijing, China
| | - Xiaoke Hao
- Department of Clinical Laboratory Medicine, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, China
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29
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Yu F, Leong KW, Makrigiorgos A, Adalsteinsson VA, Ladas I, Ng K, Mamon H, Makrigiorgos GM. NGS-based identification and tracing of microsatellite instability from minute amounts DNA using inter-Alu-PCR. Nucleic Acids Res 2021; 49:e24. [PMID: 33290560 PMCID: PMC7913684 DOI: 10.1093/nar/gkaa1175] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/13/2020] [Accepted: 11/20/2020] [Indexed: 12/20/2022] Open
Abstract
Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new approach to detect MSI using inter-Alu-PCR followed by targeted NGS, that combines the practical advantages of multiplexed-PCR with the breadth of information provided by NGS. Inter-Alu-PCR employs poly-adenine repeats of variable length present in every Alu element and provides a massively-parallel, rapid approach to capture poly-A-rich genomic fractions within short 80–150bp amplicons generated from adjacent Alu-sequences. A custom-made software analysis tool, MSI-tracer, enables Alu-associated MSI detection from tissue biopsies or MSI-tracing at low-levels in circulating-DNA. MSI-associated indels at somatic-indel frequencies of 0.05–1.5% can be detected depending on the availability of matching normal tissue and the extent of instability. Due to the high Alu copy-number in human genomes, a single inter-Alu-PCR retrieves enough information for identification of MSI-associated-indels from ∼100 pg circulating-DNA, reducing current limits by ∼2-orders of magnitude and equivalent to circulating-DNA obtained from finger-sticks. The combined practical and informational advantages of inter-Alu-PCR make it a powerful tool for identifying tissue-MSI-status or tracing MSI-associated-indels in liquid biopsies.
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Affiliation(s)
- Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medicine School, Boston, MA, USA
| | - Harvey Mamon
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Andersson D, Kristiansson H, Kubista M, Ståhlberg A. Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations. Expert Rev Mol Diagn 2021; 21:299-310. [PMID: 33683971 DOI: 10.1080/14737159.2021.1889371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation.Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications.Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Helena Kristiansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Kubista
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.,TATAA Biocenter, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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Martins VF, Dobson CR, Begur M, Parekh J, Ball ST, Gonzalez F, Hughes-Austin JM, Schenk S. Surgical site peptidylarginine deaminase 4 (PAD4), a biomarker of NETosis, correlates with insulin resistance in total joint arthroplasty patients: A preliminary report. PLoS One 2021; 16:e0245594. [PMID: 33481860 PMCID: PMC7822240 DOI: 10.1371/journal.pone.0245594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/04/2021] [Indexed: 01/12/2023] Open
Abstract
While obesity and insulin resistance are known risk factors for wound complications after total joint arthroplasty (TJA), the biologic causes remain to be elucidated. Recently, neutrophil extracellular trap formation (NETosis) was identified as a mediator of delayed wound healing in insulin resistant states. Herein, we explored the relationship between obesity, insulin resistance and biomarkers of NET formation in TJA subjects. We enrolled 14 obese (body mass index [BMI]≥30 kg/m2), and 15 lean (BMI<30 kg/m2) subjects undergoing primary knee or hip TJA. On the day of surgery, skeletal muscle proximal to the operated joint and plasma were collected. Protein abundance of NETosis biomarkers, peptidylarginine deaminase 4 (PAD4) and neutrophil elastase (NE) were assessed in skeletal muscle by immunoblotting and metabolic parameters (glucose, insulin, triglycerides, free fatty acids) and cell-free double-stranded DNA (cf-dsDNA) were assessed in plasma and were correlated with obesity and insulin resistance (as measured by the homeostatic model assessment for insulin resistance). When comparing lean and obese subjects, there were no significant differences in plasma cf-dsDNA or skeletal muscle NE or PAD4 abundance. In contrast, skeletal muscle PAD4 abundance, but not NE or plasma cf-dsDNA, was positively correlated with insulin resistance. Compared to insulin sensitive subjects, insulin resistant TJA subjects have higher expression of PAD4 at the surgical site and therefore may have higher rates of NET formation, which may lead to delayed surgical site wound healing.
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Affiliation(s)
- Vitor F. Martins
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States of America
| | - Christopher R. Dobson
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Maedha Begur
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Jesal Parekh
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Scott T. Ball
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Francis Gonzalez
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Jan M. Hughes-Austin
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States of America
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Hagstrom AD, Yuwono N, Warton K, Ford CE. Sex Bias in Cohorts Included in Sports Medicine Research. Sports Med 2021; 51:1799-1804. [PMID: 33400219 DOI: 10.1007/s40279-020-01405-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2020] [Indexed: 10/22/2022]
Affiliation(s)
- Amanda D Hagstrom
- Department of Exercise Physiology, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Nicole Yuwono
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, A/Prof Caroline Ford, Sydney, NSW, 2052, Australia
| | - Kristina Warton
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, A/Prof Caroline Ford, Sydney, NSW, 2052, Australia
| | - Caroline E Ford
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, A/Prof Caroline Ford, Sydney, NSW, 2052, Australia.
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Boedecker SC, Philippi KFA, Neuberger E, Schmidt S, Pfirrmann D, Haller N, Schwarting A, Simon P, Weinmann-Menke J. Twelve-Week Internet-Based Individualized Exercise Program in Adults With Systemic Lupus Erythematosus: Protocol for a Randomized Controlled Trial. JMIR Res Protoc 2020; 9:e18291. [PMID: 33141101 PMCID: PMC7671835 DOI: 10.2196/18291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 01/17/2023] Open
Abstract
Background Systemic lupus erythematosus is a systemic autoimmune disease, which is associated with high cardiovascular risk, a predisposition to metabolic disorders, muscle wasting, and fatigue. Exercise therapy has become an important part of the long-term treatment of comorbidities in systemic lupus erythematosus. Exercise can lead to various benefits in patients with systemic lupus erythematosus such as increased aerobic capacity and exercise tolerance, resulting in an increased quality of life, decreased depression, and decreased fatigue. At the moment, no evidence-based treatment guidelines that recommend exercise for patients with systemic lupus erythematosus exist. Also, the efficacy of different training programs requires further investigation. Objective This study focuses on the feasibility, efficacy, and safety of an internet-based exercise program in patients with systemic lupus erythematosus. Furthermore, we investigate the feasibility and efficiency of anaerobic training compared to aerobic training. Methods Overall, patients with systemic lupus erythematosus from the Division of Nephrology, Rheumatology, and Immunology outpatient clinic of the University Medical Center Mainz who are clinically stable status are included and randomized in an aerobic exercise group (n=10), anaerobic exercise group (n=10), or treatment as usual group (n=10). After completing initial clinical testing and physical fitness tests, patients undergo supervised 12-week online exercise programs, receiving weekly individualized training plans adapted to their physical performance. The primary outcome is change in physical fitness (VO2 peak) after 12 weeks compared to baseline. Secondary outcomes are disease activity measured via laboratory results (complement, autoantibodies) and questionnaires, as well as changes in muscle mass (anaerobic exercise group), results of the Chair-Stand test, and measurements of circulating cell-free DNA and extracellular vesicles. Results The study was registered in May 2019. Enrollment began in May 2019. Of 40 patients who were initially screened, 30 patients fulfilled the inclusion criteria and were included in the study; 1 participant withdrew prior to the start of the exercise program. Among the 25 patients who completed the study, no serious adverse events have been reported; 3 participants withdrew during the program (due to frequent colds, n=1; Crohn relapse, n=1; physical strain, n=1), and 1 participant has not yet completed the program. Data analysis is ongoing, and results are expected to be submitted for publication in January 2021. Conclusions We expect the online exercise intervention to be a feasible and efficient tool to provide regular individualized exercise for patients with systemic lupus erythematosus. Trial Registration ClinicalTrials.gov NCT03942718; http://clinicaltrials.gov/ct2/show/NCT03942718. International Registered Report Identifier (IRRID) DERR1-10.2196/18291
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Affiliation(s)
| | - Keito Finn Akanby Philippi
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Elmo Neuberger
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Schmidt
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Daniel Pfirrmann
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nils Haller
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Schwarting
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Julia Weinmann-Menke
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Mainz, Germany
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Schmitz TC, Dede Eren A, Spierings J, de Boer J, Ito K, Foolen J. Solid-phase silica-based extraction leads to underestimation of residual DNA in decellularized tissues. Xenotransplantation 2020; 28:e12643. [PMID: 32935355 PMCID: PMC9286341 DOI: 10.1111/xen.12643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/05/2020] [Accepted: 08/24/2020] [Indexed: 01/08/2023]
Abstract
Decellularization of animal tissues is a novel route to obtain biomaterials for use in tissue engineering and organ transplantation. Successful decellularization is required as animal DNA causes inflammatory reactions and contains endogenous retroviruses, which could be transmitted to the patient. One of the criteria for successful decellularization is digestion (fragmentation) and elimination (residual quantity) of DNA from the tissue. Quantification of DNA can be done in many ways, but it has recently been shown that silica‐based solid‐phase extraction methods often do not completely purify in particular small DNA fragments. In the context of decellularization, this means that the measured DNA amount is underestimated, which could compromise safety of the processed tissue for in‐patient use. In this article, we review DNA quantification methods used by researchers and assess their influence on the reported DNA contents after decellularization. We find that underestimation of residual DNA amount after silica‐based solid‐phase extraction may be as large as a factor of ten. We therefore recommend a direct assessment of DNA amount in tissue lysate using dsDNA‐specific binding dyes, such as Picogreen, due to their higher accuracy for small fragment detection as well as ease of use and widespread availability.
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Affiliation(s)
- Tara C Schmitz
- Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Aysegul Dede Eren
- BioInterface Science, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Janne Spierings
- Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,BioInterface Science, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jan de Boer
- BioInterface Science, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Keita Ito
- Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jasper Foolen
- Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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NIPT Technique Based on the Use of Long Chimeric DNA Reads. Genes (Basel) 2020; 11:genes11060590. [PMID: 32466452 PMCID: PMC7349339 DOI: 10.3390/genes11060590] [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: 04/21/2020] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still relatively expensive. At the same time, there is an increasing trend in the length of reads yielded by sequencers. Since extracellular DNA is short, in the order of 140–160 bp, it is not possible to effectively use long reads. The authors used high-performance sequencing of cell-free DNA (cfDNA) libraries that went through additional stages of enzymatic fragmentation and random ligation of the resulting products to create long chimeric reads. The authors used a controlled set of samples to analyze a set of cfDNA samples from pregnant women with a high risk of fetus aneuploidy according to the results of the first trimester screening and confirmed by invasive karyotyping of the fetus using laboratory and analytical approaches developed by the authors. They evaluated the sensitivity, specificity, PPV (positive predictive value), and NPV (negative predictive value) of the results. The authors developed a technique for constructing long chimeric reads from short cfDNA fragments and validated the test using a control set of extracellular DNA samples obtained from pregnant women. The obtained sensitivity and specificity parameters of the NIPT developed by the authors corresponded to the approaches proposed earlier (99.93% and 99.14% for T21; 100% and 98.34% for T18; 100% and 99.17% for T13, respectively).
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Krenzien F, Katou S, Papa A, Sinn B, Benzing C, Feldbrügge L, Kamali C, Brunnbauer P, Splith K, Lorenz RR, Ritschl P, Wiering L, Öllinger R, Schöning W, Pratschke J, Schmelzle M. Increased Cell-Free DNA Plasma Concentration Following Liver Transplantation Is Linked to Portal Hepatitis and Inferior Survival. J Clin Med 2020; 9:jcm9051543. [PMID: 32443763 PMCID: PMC7291032 DOI: 10.3390/jcm9051543] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 12/15/2022] Open
Abstract
Donor organ quality is crucial for transplant survival and long-term survival of patients after liver transplantation. Besides bacterial and viral infections, endogenous damage-associated molecular patterns (DAMPs) can stimulate immune responses. Cell-free DNA (cfDNA) is one such DAMP that exhibits highly proinflammatory effects via DNA sensors. Herein, we measured cfDNA after liver transplantation and found elevated levels when organs from resuscitated donors were transplanted. High levels of cfDNA were associated with high C-reactive protein, leukocytosis as well as granulocytosis in the recipient. In addition to increased systemic immune responses, portal hepatitis was observed, which was associated with increased interface activity and a higher numbers of infiltrating neutrophils and eosinophils in the graft. In fact, the cfDNA was an independent significant factor in multivariate analysis and increased concentration of cfDNA was associated with inferior 1-year survival. Moreover, cfDNA levels were found to be decreased significantly during the postoperative course when patients underwent continuous veno-venous haemofiltration. In conclusion, patients receiving livers from resuscitated donors were characterised by high postoperative cfDNA levels. Those patients showed pronounced portal hepatitis and systemic inflammatory responses in the short term leading to a high mortality. Further studies are needed to evaluate the clinical relevance of cfDNA clearance by haemoadsorption and haemofiltration in vitro and in vivo.
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Affiliation(s)
- Felix Krenzien
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Shadi Katou
- Department of General, Visceral and Transplantation Surgery, Universitätsklinikum Münster, 48149 Münster, Germany;
| | - Alba Papa
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Bruno Sinn
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
- Institute of Pathology, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Christian Benzing
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Linda Feldbrügge
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Can Kamali
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Philipp Brunnbauer
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Katrin Splith
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Ralf Roland Lorenz
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Paul Ritschl
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Leke Wiering
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Robert Öllinger
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Wenzel Schöning
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Johann Pratschke
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Moritz Schmelzle
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
- Correspondence:
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Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
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Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Comparison of methods for the isolation of cell-free DNA from cell culture supernatant. Tumour Biol 2020; 42:1010428320916314. [PMID: 32338581 DOI: 10.1177/1010428320916314] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In vitro characterization of cell-free DNA using two-dimensional cell culture models is emerging as an important step toward an improved understanding of the physical and biological characteristics of cell-free DNA in human biology. However, precise measurement of the cell-free DNA in cell culture medium is highly dependent on the efficacy of the method used for DNA purification, and is often a juncture of experimental confusion. Therefore, in this study, we compared six commercially available cell-free DNA isolation kits for the recovery of cell-free DNA from the cell culture supernatant of a human bone cancer cell line (143B), including two magnetic bead-based manual kits, one automated magnetic bead-based extraction method, and three manual spin-column kits. Based on cell-free DNA quantitation and sizing, using the Qubit dsDNA HS assay and Bioanalyzer HS DNA assay, respectively, the different methods showed significant variability concerning recovery, reproducibility, and size discrimination. These findings highlight the importance of selecting a cell-free DNA extraction method that is appropriate for the aims of a study. For example, mutational analysis of cell-free DNA may be enhanced by a method that favors a high yield or is biased toward the isolation of short cell-free DNA fragments. In contrast, quantitative analysis of cell-free DNA in a comparative setting (e.g. measuring the fluctuation of cell-free DNA levels over time) may require the selection of a cell-free DNA isolation method that forgoes a high recovery for high reproducibility and minimal size bias.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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Wan Z, Peng X, Ma L, Tian Q, Wu S, Li J, Ling J, Lv W, Ding B, Tan J, Zhang Z. Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA. PLoS Negl Trop Dis 2020; 14:e0008147. [PMID: 32155159 PMCID: PMC7083330 DOI: 10.1371/journal.pntd.0008147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/20/2020] [Accepted: 02/18/2020] [Indexed: 11/20/2022] Open
Abstract
Background Echinococcosis is a chronic zoonosis caused by tapeworms of the genus Echinococcus. Treatment of the disease is often expensive and complicated, sometimes requiring extensive surgery. Ultrasonographic imaging is currently the main technique for diagnosis, while immunological analysis provides additional information. Confirmation still needs pathological analysis. However, these diagnostic techniques generally detect infection in late stages of the disease. An accurate, early and non-invasive molecular diagnostic method is still unavailable. Methodology/Principal findings We sequenced the cell-free DNA (cfDNA) from plasma of echinococcosis patients and confirmed the presence of Echinococcus DNA. To improve detection sensitivity, we developed a method based on targeted next-generation sequencing of repeat regions. Simulation experiments demonstrate that the targeted sequencing is sensitive enough to detect as little as 0.1% of an Echinococcus genome in 1 mL of plasma. Results obtained using patient plasma shows that the Area Under the Curve (AUC) of the method is 0.862, with a detection sensitivity of 62.50% and specificity of 100%, corresponding to a Youden-index of 0.625. Conclusions/Significance This study provides evidence that hydatid cysts release cfDNA fragments into patient plasma. Using the repeat region targeted sequencing method, highly specific detection of Echinococcus infection was achieved. This study paves a new avenue for potential non-invasive screening and diagnosis of echinococcosis. Echinococcosis is a severe chronic parasitic disease caused by tapeworms of the genus Echinococcus. According to the World Health Organization, there are more than 1 million people living with echinococcosis worldwide. For decades, little progress has been made to develop a molecular diagnosis and specific treatment for the disease. Although imaging and immunological detection are used for diagnosis, these technologies are either only effective for late stages of the disease or hardly conclusive. The detection of cell-free DNA has been a powerful tool for precise diagnosis. In this study, we showed the presence of Echinococcus-derived cell-free DNA in plasma of echinococcosis patients. We further established an assay to detect parasite DNA in blood samples based on amplification of Echinococcus specific repeat regions followed by targeted next-generation sequencing. This technique provides a new method for potential extensive screening and precision diagnosis of echinococcosis with high specificity.
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Affiliation(s)
- Zhengqing Wan
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Xiaoqing Peng
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Qingshan Tian
- Center for Prevention and Treatment of Echinococcosis, Qinghai Provincial People's Hospital, Xining, Qinghai, China
| | - Shizheng Wu
- Department of Neurology, Qinghai Provincial People's Hospital, Xining, Qinghai, China
| | - Junqi Li
- Sunrain Biotechnology Corporation, Changsha, Hunan, China
| | - Jie Ling
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
| | - Weigang Lv
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Binrong Ding
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Jieqiong Tan
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
- Department of Neurosciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- * E-mail:
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Conde AJ, Keraite I, Ongaro AE, Kersaudy-Kerhoas M. Versatile hybrid acoustic micromixer with demonstration of circulating cell-free DNA extraction from sub-ml plasma samples. LAB ON A CHIP 2020; 20:741-748. [PMID: 31960868 DOI: 10.1039/c9lc01130g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Acoustic micromixers have attracted considerable attention in the last years since they can deliver high mixing efficiencies without the need for movable components. However, their adoption in the academic and industrial microfluidics community has been limited, possibly due to the reduced flexibility and accessibility of previous designs since most of them are application-specific and fabricated with techniques that are expensive, not widely available and difficult to integrate with other manufacturing technologies. In this work, we describe a simple, yet highly versatile, bubble-based micromixer module fabricated with a combination of low-cost rapid prototyping techniques. The hybrid approach enables the integration of the module into practically any substrate and the individual control of multiple micromixers embedded within the same monolithic chip. The module can operate under static and continuous flow conditions showing enhanced mixing capabilities compared to similar devices. We show that the system is capable of performing cell-free DNA extractions from small volumes of blood plasma (≤500 μl) with up to a ten-fold increase in capture efficiency when compared to control methods.
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Affiliation(s)
- Alvaro J Conde
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, UK. and Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ieva Keraite
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, UK. and Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| | - Alfredo E Ongaro
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, UK. and Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK and Department of Civil, Environmental, Aerospace and Materials Engineering (DICAM), University of Palermo, Palermo, Italy
| | - Maïwenn Kersaudy-Kerhoas
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, UK. and Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
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Noninvasive prenatal diagnosis of hemophilia A by a haplotype-based approach using cell-free fetal DNA. Biotechniques 2020; 68:117-121. [PMID: 31996009 DOI: 10.2144/btn-2019-0113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aim: We aimed to demonstrate noninvasive prenatal diagnosis (NIPD) of hemophilia A (HA) using a haplotype-based approach. Methods: Two families at risk for HA were recruited for this study. First, maternal haplotypes associated with pathogenic variants were constructed using the genotypes of the mothers and probands. Then, fetal haplotypes were deduced using a maternal haplotype-assisted hidden Markov model. Finally, the NIPD results were further confirmed by invasive prenatal diagnosis. Results: Two fetal genotypes were successfully inferred, with one normal fetus and one carrier fetus. The NIPD results were confirmed by invasive prenatal diagnosis, with a 100% consistency rate. Conclusion: Our test has been shown to be accurate and reliable. With further validation in a large patient cohort, this haplotype-based approach could be feasible for the NIPD of HA and other X-linked single-gene disorders.
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Cell free DNA as a diagnostic and prognostic marker for cardiovascular diseases. Clin Chim Acta 2020; 503:145-150. [PMID: 31978408 DOI: 10.1016/j.cca.2020.01.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/14/2022]
Abstract
Release of cell free DNA (cfDNA) from damaged or dead cells routinely occurs in normal physiology. Recently, cfDNA has emerged as an essential biomarker in cardiovascular disease (CVD) of potential prognostic and diagnostic significance. Within the last decade, significant research efforts have been devoted to uncovering the mechanisms mediating cfDNA release and its outcome-predicting ability. The current review focuses on the pathways for cfDNA release in myocardial infarction, heart failure and hypertension, and discusses implementation of cfDNA monitoring to assess the overall development of these disease states and predict future complications.
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44
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Brodbeck K, Schick S, Bayer B, Anslinger K, Krüger K, Mayer Z, Holdenrieder S, Peldschus S. Biological variability of cell-free DNA in healthy females at rest within a short time course. Int J Legal Med 2020; 134:911-919. [DOI: 10.1007/s00414-019-02240-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022]
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Abstract
ctDNA provided by liquid biopsy offers a promising alternative to tumor biopsy as it gives a non-invasive and «real-time» access to the cancer genome and reflects tumor intra and extra heterogeneity. ctDNA has shown growing clinical interest for cancer diagnosis, prognosis, theragnostics, therapeutic monitoring, and clonal evolution tracking. A major technical limit for ctDNA analysis from body fluids is the extremely low proportion of ctDNA compared to non-malignant cell-free DNA, underscoring the need for highly sensitive and specific detection techniques. The control of pre-analytical procedures appears essential for optimal ctDNA analysis and need to be standardized for clinical research applications. This chapter provides insights into major current technologies for ctDNA detection. Overall, PCR-based techniques are able to detect limited molecular alterations and have a high sensitivity suitable for monitoring purposes while NGS-based approaches are broad range molecular screening assays more specifically indicated for treatment selection. We briefly reviewed new technical innovations that are now available for ctDNA detection.
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Affiliation(s)
- Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, 54000, Nancy, France.
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46
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Rajar P, Åsegg-Atneosen M, Saugstad OD, Solberg R, Baumbusch LO. Quantification of circulating cell-free DNA (cfDNA) in urine using a newborn piglet model of asphyxia. PLoS One 2020; 14:e0227066. [PMID: 31891615 PMCID: PMC6938324 DOI: 10.1371/journal.pone.0227066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/10/2019] [Indexed: 12/03/2022] Open
Abstract
Cell free DNA (cfDNA) in plasma has been described as a potential diagnostic indicator for a variety of clinical conditions, including neonatal hypoxia. Neonatal hypoxia or perinatal asphyxia is a severe medical condition caused by a temporary interruption in oxygen availability during birth. Previously, we have reported temporal changes of cfDNA detected in blood in a newborn piglet model of perinatal asphyxia. However, cfDNA can also be found in other body liquids, opening for a less invasive diagnostic prospective. The objective of this study was to test and establish a reliable method for the isolation and quantification of cfDNA from urine and to explore changes in the quantities of cfDNA using a newborn piglet model of asphyxia. Animals were exposed to hypoxia-reoxygenation (n = 6), hypoxia-reoxygenation + hypothermia (n = 6) or were part of the sham-operated control group (n = 6) and urine samples (n = 18) were collected at 570 minutes post-intervention. Two alternative applications of cfDNA measurement were tested, an indirect method comprising a centrifugation step together with DNA extraction with magnetic beads versus a direct assessment based on two centrifugation steps. CfDNA concentrations were determined by a fluorescent assay using PicoGreen and by qRT-PCR. Genomic (gDNA) and mitochondrial DNA (mtDNA) cfDNA were determined in parallel, taking into account potential differences in the rates of damages caused by oxidative stress. In contrast to previous publications, our results indicate that the direct method is insufficient. Application of the indirect method obtained with the fluorescence assay revealed mean cfDNA levels (SD) of 1.23 (1.76) ng/ml for the hypoxia samples, 4.47 (6.15) ng/ml for the samples exposed to hypoxia + hypothermia and 2.75 (3.62) ng/ml for the control animals. The mean cfDNA levels in piglets exposed to hypoxia + hypothermia revealed significantly higher cfDNA amounts compared to mean cfDNA levels in the samples purely exposed to hypoxia (p < 0.05); however, no significant difference could be determined when compared to the control group (p = 0.09). Application of the indirect method by qRT-PCR revealed mean cfDNA levels of mtDNA and gDNA at the detection limit of the technique and thus no reliable statistics could be performed between the observed cfDNA levels in the investigated groups. The methodology for detection and monitoring of cfDNA in urine has to be further optimized before it can be applied in a clinical setting in the future.
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Affiliation(s)
- Polona Rajar
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Monica Åsegg-Atneosen
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Ola Didrik Saugstad
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Rønnaug Solberg
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Pediatrics, Vestfold Hospital Trust, Tønsberg, Norway
| | - Lars Oliver Baumbusch
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
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Kerachian MA, Poudineh A, Thiery JP. Cell free circulating tumor nucleic acids, a revolution in personalized cancer medicine. Crit Rev Oncol Hematol 2019; 144:102827. [DOI: 10.1016/j.critrevonc.2019.102827] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/13/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
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Stawski R, Walczak K, Perdas E, Wlodarczyk A, Sarniak A, Kosielski P, Meissner P, Budlewski T, Padula G, Nowak D. Decreased integrity of exercise-induced plasma cell free nuclear DNA - negative association with the increased oxidants production by circulating phagocytes. Sci Rep 2019; 9:15970. [PMID: 31685910 PMCID: PMC6828751 DOI: 10.1038/s41598-019-52409-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/12/2019] [Indexed: 12/21/2022] Open
Abstract
Strenuous exercise increases circulating cell free DNA (cfDNA) and stimulates blood phagocytes to generate reactive oxygen species (ROS) which may induce DNA strand breaks. We tested whether: (A) elevated cfDNA in response to three repeated bouts of exhaustive exercise has decreased integrity; (B) each bout of exercise increases luminol enhanced whole blood chemiluminescence (LBCL) as a measure of ROS production by polymorphonuclear leukocytes. Eleven men performed three treadmill exercise tests to exhaustion separated by 72 hours of resting. Pre- and post-exercise concentrations and integrity of cf nuclear and mitochondrial DNA (cf n-DNA, cf mt-DNA) and resting (r) and fMLP (n-formyl-methionyl-leucyl-phenylalanine)-stimulated LBCL were determined. Each bout increased concentrations of cf n-DNA by more than 10-times which was accompanied by about 2-times elevated post-exercise rLBCL and fMLP-LBCL. Post-exercise cf n-DNA integrity (integrity index, I229/97) decreased after the first (0.59 ± 0.19 vs. 0.48 ± 0.18) and second (0.53 ± 0.14 vs. 0.44 ± 0.17) bout of exercise. There were negative correlations between I229/97 and rLBCL (ƍ = –0.37), and I229/97 and fMLP-LBCL (ƍ = –0.40) – analysis of pooled pre- and post-exercise data (n = 66). cf mt- DNA integrity (I218/78) did not alter in response to exercise. This suggests an involvement of phagocyte ROS in cf n-DNA strand breaks in response to exhaustive exercise.
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Affiliation(s)
- Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, Lodz, Poland
| | - Konrad Walczak
- Department of Internal Medicine and Nephrodiabetology, Medical University of Lodz, Lodz, Poland
| | - Ewelina Perdas
- Department of Cardiovascular Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Anna Wlodarczyk
- Department of Sleep Medicine and Metabolic Disorders, Medical University of Lodz, Lodz, Poland
| | - Agata Sarniak
- Department of General Physiology, Medical University of Lodz, Lodz, Poland
| | - Piotr Kosielski
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Pawel Meissner
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Tomasz Budlewski
- Department of Rheumatology, Medical University of Lodz, University Hospital name of the Military Medical Academy-Central Hospital Veterans of Lodz Ul. Pieniny 30, 92-115, Łódź, Poland
| | - Gianluca Padula
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, Lodz, Poland.
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Canale M, Pasini L, Bronte G, Delmonte A, Cravero P, Crinò L, Ulivi P. Role of liquid biopsy in oncogene-addicted non-small cell lung cancer. Transl Lung Cancer Res 2019; 8:S265-S279. [PMID: 31857950 DOI: 10.21037/tlcr.2019.09.15] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery of actionable oncogene in non-small cell lung cancer (NSCLC) allowed the identification of a subgroup of patients who benefit from targeted tyrosine kinase inhibitors more than others. Mutations in the epidermal growth factor receptor (EGFR), translocations in the anaplastic lymphoma kinase (ALK) and rearrangements in the ROS proto-oncogene 1 (ROS1) must be identified in tumor tissue to guide the proper treatment choice. Liquid biopsy is based on the analysis of tumor materials released in the circulation. Liquid biopsy can be complementary to tissue biopsy, both at baseline and at progression, especially in the detection of somatic gene alterations emerging during the treatment with tyrosine kinase inhibitors (TKIs). Particularly, circulating DNA is used to find mutations in driver oncogenes, while circulating tumor cells, extracellular vesicles (EVs) and cell-free microRNAs (cfmiRNAs) are still under investigation. To help the unbiased use of liquid biopsy in the choice of the appropriate therapy, some recommendations were delivered by expert panels. Currently, analysis of EGFR mutations in cell-free DNA (cfDNA) is recommended at baseline when tissue biopsy harbors scarce tumor cells, and at progression before performing tissue biopsy; liquid biopsy analysis for other oncogenic drivers is not indicated in the clinical practice.
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Affiliation(s)
- Matteo Canale
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Luigi Pasini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giuseppe Bronte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Angelo Delmonte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Paola Cravero
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Lucio Crinò
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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50
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Progress in quantitative technique of circulating cell free DNA and its role in cancer diagnosis and prognosis. Cancer Genet 2019; 239:75-84. [PMID: 31639530 DOI: 10.1016/j.cancergen.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/24/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023]
Abstract
The interest in the potential application value of circulating cell free DNA (ccfDNA) has increased rapidly in recent years, as numerous researchers have demonstrated that the change of its level in the blood is associated with many diseases. Its potential role in cancer management is of particular concern. In comparison with traditional invasive tissue biopsy, quantitative analysis of ccfDNA level for the detection of cancer is advantageous due to the non-invasiveness of blood collection. Moreover, its clinical significance in prognosis prediction and dynamic monitoring of disease progression in cancer patients is equally worthy of attention. At the same time, quantitative detection of ccfDNA is being improved to pursue higher sensitivity due to its low concentration in the blood sample. In this review, we will summarize the progress in quantitative technology of ccfDNA and describe the possible relationship between ccfDNA level and cancer diagnosis and prognosis prediction.
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