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Shao S, Zou Y, Kennedy KG, Dimick MK, Andreazza AC, Young LT, Goncalves VF, MacIntosh BJ, Goldstein BI. Pilot study of circulating cell-free mitochondrial DNA in relation to brain structure in youth bipolar disorder. Int J Bipolar Disord 2024; 12:21. [PMID: 38874862 PMCID: PMC11178693 DOI: 10.1186/s40345-024-00334-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/08/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Mitochondrial dysfunction is implicated in the neuropathology of bipolar disorder (BD). Higher circulating cell-free mitochondrial DNA (ccf-mtDNA), generally reflecting poorer mitochondrial health, has been associated with greater symptoms severity in BD. The current study examines the association of serum ccf-mtDNA and brain structure in relation to youth BD. We hypothesized that higher ccf-mtDNA will be associated with measures of lower brain structure, particularly in the BD group. METHODS Participants included 40 youth (BD, n = 19; Control group [CG], n = 21; aged 13-20 years). Serum ccf-mtDNA levels were assayed. T1-weighted brain images were acquired using 3T-MRI. Region of interest (ROI) analyses examined prefrontal cortex (PFC) and whole brain gray matter, alongside exploratory vertex-wise analyses. Analyses examined ccf-mtDNA main-effects and ccf-mtDNA-by-diagnosis interaction effects controlling for age, sex, and intracranial volume. RESULTS There was no significant difference in ccf-mtDNA levels between BD and CG. In ROI analyses, higher ccf-mtDNA was associated with higher PFC surface area (SA) (β = 0.32 p < 0.001) and PFC volume (β = 0.32 p = 0.002) in the overall sample. In stratified analyses, higher ccf-mtDNA was associated with higher PFC SA within both subgroups (BD: β = 0.39 p = 0.02; CG: β = 0.24 p = 0.045). Higher ccf-mtDNA was associated with higher PFC volume within the BD group (β = 0.39 p = 0.046). In vertex-wise analyses, higher ccf-mtDNA was associated with higher SA and volume in frontal clusters within the overall sample and within the BD group. There were significant ccf-mtDNA-by-diagnosis interactions in three frontal and parietal clusters, whereby higher ccf-mtDNA was associated with higher neurostructural metrics in the BD group but lower neurostructural metrics in CG. CONCLUSIONS Contrasting our hypothesis, higher ccf-mtDNA was consistently associated with higher, rather than lower, regional neuralstructural metrics among youth with BD. While this finding may reflect a compensatory mechanism, future repeated-measures prospective studies evaluating the inter-relationship among ccf-mtDNA, mood, and brain structure across developmental epochs and illness stages are warranted.
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Affiliation(s)
- Suyi Shao
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Department of Pharmacology & Toxicology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Yi Zou
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Kody G Kennedy
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Mikaela K Dimick
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Ana C Andreazza
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Pharmacology & Toxicology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - L Trevor Young
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Vanessa F Goncalves
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Bradley J MacIntosh
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Heart and Stroke Foundation Canadian Partnership for Stroke Recovery, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Program, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Benjamin I Goldstein
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Department of Pharmacology & Toxicology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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Casas S, Tangprasertchai NS, Oikonomaki K, Mathers S, Sollet ZC, Samara S, Liu J, Burlinson ND, Constantoulakis P, Villard J, Viard T. Multi-centre analytical performance verification of an IVD assay to quantify donor-derived cell-free DNA in solid organ transplant recipients. HLA 2024; 103:e15518. [PMID: 38733247 DOI: 10.1111/tan.15518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Donor-derived cell-free DNA (dd-cfDNA) has been widely studied as biomarker for non-invasive allograft rejection monitoring. Earlier rejection detection enables more prompt diagnosis and intervention, ultimately improving patient treatment and outcomes. This multi-centre study aims to verify analytical performance of a next-generation sequencing-based dd-cfDNA assay at end-user environments. Three independent laboratories received the same experimental design and 16 blinded samples to perform cfDNA extraction and the dd-cfDNA assay workflow. dd-cfDNA results were compared between sites and against manufacturer validation to evaluate concordance, reproducibility, repeatability and verify analytical performance. A total of 247 sample libraries were generated across 18 runs, with completion time of <24 h. A 96.0% first pass rate highlighted minimal failures. Overall observed versus expected dd-cfDNA results demonstrated good concordance and a strong positive correlation with linear least squares regression r2 = 0.9989, and high repeatability and reproducibility within and between sites, respectively (p > 0.05). Manufacturer validation established limit of blank 0.18%, limit of detection 0.23% and limit of quantification 0.23%, and results from independent sites verified those limits. Parallel analyses illustrated no significant difference (p = 0.951) between dd-cfDNA results with or without recipient genotype. The dd-cfDNA assay evaluated here has been verified as a reliable method for efficient, reproducible dd-cfDNA quantification in plasma from solid organ transplant recipients without requiring genotyping. Implementation of onsite dd-cfDNA testing at clinical laboratories could facilitate earlier detection of allograft injury, bearing great potential for patient care.
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Affiliation(s)
| | | | | | - Simon Mathers
- Transplantation Laboratory, Manchester University NHS Foundation Trust, Manchester, UK
| | - Zuleika Calderin Sollet
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Geneva University Hospitals, Geneva, Switzerland
| | | | - June Liu
- CareDx, Brisbane, California, USA
| | | | | | - Jean Villard
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Geneva University Hospitals, Geneva, Switzerland
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Morisi N, Virzì GM, Ferrarini M, Alfano G, Zanella M, Ronco C, Donati G. Exploring the Role of Cell-Free Nucleic Acids and Peritoneal Dialysis: A Narrative Review. Genes (Basel) 2024; 15:553. [PMID: 38790182 PMCID: PMC11121405 DOI: 10.3390/genes15050553] [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: 03/30/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
INTRODUCTION Cell-free nucleic acids (cf-NAs) represent a promising biomarker of various pathological and physiological conditions. Since its discovery in 1948, cf-NAs gained prognostic value in oncology, immunology, and other relevant fields. In peritoneal dialysis (PD), blood purification is performed by exposing the peritoneal membrane. Relevant sections: Complications of PD such as acute peritonitis and peritoneal membrane aging are often critical in PD patient management. In this review, we focused on bacterial DNA, cell-free DNA, mitochondrial DNA (mtDNA), microRNA (miRNA), and their potential uses as biomarkers for monitoring PD and its complications. For instance, the isolation of bacterial DNA in early acute peritonitis allows bacterial identification and subsequent therapy implementation. Cell-free DNA in peritoneal dialysis effluent (PDE) represents a marker of stress of the peritoneal membrane in both acute and chronic PD complications. Moreover, miRNA are promising hallmarks of peritoneal membrane remodeling and aging, even before its manifestation. In this scenario, with multiple cytokines involved, mtDNA could be considered equally meaningful to determine tissue inflammation. CONCLUSIONS This review explores the relevance of cf-NAs in PD, demonstrating its promising role for both diagnosis and treatment. Further studies are necessary to implement the use of cf-NAs in PD clinical practice.
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Affiliation(s)
- Niccolò Morisi
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
| | - Grazia Maria Virzì
- Department of Nephrology, Dialysis and Transplant, St. Bortolo Hospital, 36100 Vicenza, Italy
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Marco Ferrarini
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
| | - Gaetano Alfano
- Nephrology Dialysis and Transplant Unit, University Hospital of Modena, 41124 Modena, Italy
| | - Monica Zanella
- Department of Nephrology, Dialysis and Transplant, St. Bortolo Hospital, 36100 Vicenza, Italy
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Claudio Ronco
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Gabriele Donati
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
- Nephrology Dialysis and Transplant Unit, University Hospital of Modena, 41124 Modena, Italy
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Dlouha D, Huckova P, Rohlova E, Vymetalova J, Novakova S, Hubacek JA. Monitoring of plasma circulating donor DNA reflects cardiac graft injury: Report of two cases. Biomed Rep 2024; 20:50. [PMID: 38357233 PMCID: PMC10865169 DOI: 10.3892/br.2024.1738] [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: 04/20/2023] [Accepted: 12/19/2023] [Indexed: 02/16/2024] Open
Abstract
The current standard for graft rejection surveillance is endomyocardial biopsy (EMB), an invasive procedure with rare but potentially serious complications. Detection of circulating donor-derived cell-free DNA (ddcfDNA) is an option for noninvasive monitoring of graft injury and rejection. A 63-year-old man and a 65-year-old woman were monitored by EMB for allograft rejection. A total of 48 single-nucleotide polymorphisms with a minor allele frequency range of 0.4-0.5 were screened to distinguish donor and recipient DNA based on homozygosity, and digital droplet PCR was used to analyze ddcfDNA concentrations. Both subjects suffered rejection within the first 6 months after transplantation. The maximal ddcfDNA level of 270 copies (cp)/ml during EMB-confirmed acute cellular rejection (ACR; mild grade 1R/2, patient 1), and the maximal concentration of 1,846 cp/ml in the case of EMB-confirmed antibody-mediated rejection (AMR; grade 1+; patient 2), was detected. Individual monitoring of ddcfDNA dynamics from the 1st to the 6th month posttransplant reflected cardiac graft injury in patients suffering ACR or AMR, meaning that ddcfDNA may serve as a noninvasive biomarker.
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Affiliation(s)
- Dana Dlouha
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic
| | - Pavlina Huckova
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic
| | - Eva Rohlova
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic
- Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, BIOCEV, 25250 Vestec, Czech Republic
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, 12808 Prague, Czech Republic
| | - Jevgenija Vymetalova
- Cardio Center, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic
| | - Sarka Novakova
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic
| | - Jaroslav A. Hubacek
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic
- Third Department of Internal Medicine, First Faculty of Medicine, Charles University, 12808 Prague, Czech Republic
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Gao Y, Zhou N, Liu J. Ovarian Cancer Diagnosis and Prognosis Based on Cell-Free DNA Methylation. Cancer Control 2024; 31:10732748241255548. [PMID: 38764160 PMCID: PMC11104031 DOI: 10.1177/10732748241255548] [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: 01/24/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Background: Ovarian cancer stands as the deadliest malignant tumor within the female reproductive tract. As a result of the absence of effective diagnostic and monitoring markers, 75% of ovarian cancer cases are diagnosed at a late stage, leading to a mere 50% survival rate within five years. The advancement of molecular biology is essential for accurate diagnosis and treatment of ovarian cancer. Methods: A review of several randomized clinical trials, focusing on the ovarian cancer, was undertaken. The advancement of molecular biology and diagnostic methods related to accurate diagnosis and treatment of ovarian cancer were examined. Results: Liquid biopsy is an innovative method of detecting malignant tumors that has gained increasing attention over the past few years. Cell-free DNA assay-based liquid biopsies show potential in delineating tumor status heterogeneity and tracking tumor recurrence. DNA methylation influences a multitude of biological functions and diseases, especially during the initial phases of cancer. The cell-free DNA methylation profiling system has emerged as a sensitive and non-invasive technique for identifying and detecting the biological origins of cancer. It holds promise as a biomarker, enabling early screening, recurrence monitoring, and prognostic evaluation of cancer. Conclusions: This review evaluates recent advancements and challenges associated with cell-free DNA methylation analysis for the diagnosis, prognosis monitoring, and assessment of therapeutic responses in the management of ovarian cancers, aiming to offer guidance for precise diagnosis and treatment of this disease.
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Affiliation(s)
- Yajuan Gao
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Nanyang Zhou
- Department of Traditional Chinese Medicine, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Jie Liu
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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Dao J, Conway PJ, Subramani B, Meyyappan D, Russell S, Mahadevan D. Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation. Int J Mol Sci 2023; 24:13219. [PMID: 37686024 PMCID: PMC10487653 DOI: 10.3390/ijms241713219] [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: 08/04/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, accuracy, and cost over solid biopsies and other oncological markers. The technology used to differentiate ctDNA and cell-free DNA (cfDNA) continues to improve with new tests and methodologies being able to detect down to mutant allele frequencies of 0.001% or 1/100,000 copies. Recognizing this development in technology, the FDA has recently given pre-market approval and breakthrough device designations to multiple companies. The purpose of this review is to look at the utility of measuring total cfDNA, techniques used to differentiate ctDNA from cfDNA, and the utility of different ctDNA-based liquid biopsy kits using relevant articles from PubMed, clinicaltrials.gov, FDA approvals, and company newsletters. Measuring total cfDNA could be a cost-effective, viable prognostic marker, but various factors do not favor it as a monitoring tool during chemotherapy. While there may be a place in the clinic for measuring total cfDNA in the future, the lack of standardization means that it is difficult to move forward with large-scale clinical validation studies currently. While the detection of ctDNA has promising standardized liquid biopsy kits from various companies with large clinical trials ongoing, their applications in screening and minimal residual disease can suffer from lower sensitivity. However, researchers are working towards solutions to these issues with innovations in technology, multi-omics, and sampling. With great promise, further research is needed before liquid biopsies can be recommended for everyday clinical management.
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Affiliation(s)
- Jonathan Dao
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick J. Conway
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Baskaran Subramani
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Devi Meyyappan
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
| | - Sammy Russell
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Daruka Mahadevan
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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7
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Coppedè F, Bhaduri U, Stoccoro A, Nicolì V, Di Venere E, Merla G. DNA Methylation in the Fields of Prenatal Diagnosis and Early Detection of Cancers. Int J Mol Sci 2023; 24:11715. [PMID: 37511475 PMCID: PMC10380460 DOI: 10.3390/ijms241411715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The central objective of the metamorphosis of discovery science into biomedical applications is to serve the purpose of patients and curtail the global disease burden. The journey from the discovery of DNA methylation (DNAm) as a biological process to its emergence as a diagnostic tool is one of the finest examples of such metamorphosis and has taken nearly a century. Particularly in the last decade, the application of DNA methylation studies in the clinic has been standardized more than ever before, with great potential to diagnose a multitude of diseases that are associated with a burgeoning number of genes with this epigenetic alteration. Fetal DNAm detection is becoming useful for noninvasive prenatal testing, whereas, in very preterm infants, DNAm is also shown to be a potential biological indicator of prenatal risk factors. In the context of cancer, liquid biopsy-based DNA-methylation profiling is offering valuable epigenetic biomarkers for noninvasive early-stage diagnosis. In this review, we focus on the applications of DNA methylation in prenatal diagnosis for delivering timely therapy before or after birth and in detecting early-stage cancers for better clinical outcomes. Furthermore, we also provide an up-to-date commercial landscape of DNAm biomarkers for cancer detection and screening of cancers of unknown origin.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
- Interdepartmental Research Center of Biology and Pathology of Aging, University of Pisa, 56126 Pisa, Italy
| | - Utsa Bhaduri
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Eleonora Di Venere
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
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Meriranta L, Pitkänen E, Leppä S. Blood has never been thicker: Cell-free DNA fragmentomics in the liquid biopsy toolbox of B-cell lymphomas. Semin Hematol 2023; 60:132-141. [PMID: 37455222 DOI: 10.1053/j.seminhematol.2023.06.006] [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: 03/20/2023] [Revised: 05/30/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Liquid biopsies utilizing plasma circulating tumor DNA (ctDNA) are anticipated to revolutionize decision-making in cancer care. In the field of lymphomas, ctDNA-based blood tests represent the forefront of clinically applicable tools to harness decades of genomic research for disease profiling, quantification, and detection. More recently, the discovery of nonrandom fragmentation patterns in cell-free DNA (cfDNA) has opened another avenue of liquid biopsy research beyond mutational interrogation of ctDNA. Through examination of structural features, nucleotide content, and genomic distribution of massive numbers of plasma cfDNA molecules, the study of fragmentomics aims at identifying new tools that augment existing ctDNA-based analyses and discover new ways to profile cancer from blood tests. Indeed, the characterization of aberrant lymphoma ctDNA fragment patterns and harnessing them with powerful machine-learning techniques are expected to unleash the potential of nonmutant molecules for liquid biopsy purposes. In this article, we review cfDNA fragmentomics as an emerging approach in the ctDNA research of B-cell lymphomas. We summarize the biology behind the formation of cfDNA fragment patterns and discuss the preanalytical and technical limitations faced with current methodologies. Then we go through the advances in the field of lymphomas and envision what other noninvasive tools based on fragment characteristics could be explored. Last, we place fragmentomics as one of the facets of ctDNA analyses in emerging multiview and multiomics liquid biopsies. We pay attention to the unknowns in the field of cfDNA fragmentation biology that warrant further mechanistic investigation to provide rational background for the development of these precision oncology tools and understanding of their limitations.
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Affiliation(s)
- Leo Meriranta
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Esa Pitkänen
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), HILIFE, Helsinki, Finland
| | - Sirpa Leppä
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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Viglianisi G, Santonocito S, Polizzi A, Troiano G, Amato M, Zhurakivska K, Pesce P, Isola G. Impact of Circulating Cell-Free DNA (cfDNA) as a Biomarker of the Development and Evolution of Periodontitis. Int J Mol Sci 2023; 24:9981. [PMID: 37373135 DOI: 10.3390/ijms24129981] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
In the last few decades, circulating cell-free DNA (cfDNA) has been shown to have an important role in cell apoptosis or necrosis, including in the development and evolution of several tumors and inflammatory diseases in humans. In this regard, periodontitis, a chronic inflammatory disease that can induce the destruction of supporting components of the teeth, could represent a chronic inflammatory stimulus linked to a various range of systemic inflammatory diseases. Recently, a possible correlation between periodontal disease and cfDNA has been shown, representing new important diagnostic-therapeutic perspectives. During the development of periodontitis, cfDNA is released in biological fluids such as blood, saliva, urine and other body fluids and represents an important index of inflammation. Due to the possibility of withdrawing some of these liquids in a non-invasive way, cfDNA could be used as a possible biomarker for periodontal disease. In addition, discovering a proportional relationship between cfDNA levels and the severity of periodontitis, expressed through the disease extent, could open the prospect of using cfDNA as a possible therapeutic target. The aim of this article is to report what researchers have discovered in recent years about circulating cfDNA in the development, evolution and therapy of periodontitis. The analyzed literature review shows that cfDNA has considerable potential as a diagnostic, therapeutic biomarker and therapeutic target in periodontal disease; however, further studies are needed for cfDNA to be used in clinical practice.
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Affiliation(s)
- Gaia Viglianisi
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Simona Santonocito
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Alessandro Polizzi
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Mariacristina Amato
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Khrystyna Zhurakivska
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Paolo Pesce
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Ospedale S. Martino, 16148 Genoa, Italy
| | - Gaetano Isola
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
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Abstract
The high fragmentation of nuclear circulating DNA (cirDNA) relies on chromatin organization and protection or packaging within mononucleosomes, the smallest and the most stabilized structure in the bloodstream. The detection of differing size patterns, termed fragmentomics, exploits information about the nucleosomal packing of DNA. Fragmentomics not only implies size pattern characterization but also considers the positioning and occupancy of nucleosomes, which result in cirDNA fragments being protected and persisting in the circulation. Fragmentomics can determine tissue of origin and distinguish cancer-derived cirDNA. The screening power of fragmentomics has been considerably strengthened in the omics era, as shown in the ongoing development of sophisticated technologies assisted by machine learning. Fragmentomics can thus be regarded as a strategy for characterizing cancer within individuals and offers an alternative or a synergistic supplement to mutation searches, methylation, or nucleosome positioning. As such, it offers potential for improving diagnostics and cancer screening.
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Affiliation(s)
- A.R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, and ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France,Corresponding author
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11
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Chen H, Xu C, Fang Z, Mao S. Cell-Free DNA, MicroRNAs, Proteins, and Peptides as Liquid Biopsy Biomarkers in Prostate Cancer and Bladder Cancer. Methods Mol Biol 2023; 2695:165-179. [PMID: 37450118 DOI: 10.1007/978-1-0716-3346-5_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Liquid biopsy, as a novel noninvasive tool for biomarker discovery, has gained a lot of attention and represents a significant innovation in precision medicine. Due to its minimally invasive nature, liquid biopsy has fewer complications and can be scheduled more frequently to provide individualized snapshots of the disease at successive time points. This is particularly valuable in providing simultaneous measurements of tumor burden during treatment and early detection of tumor recurrence or drug resistance. Blood-based liquid biopsy is an attractive, minimally invasive alternative, which has shown promise in diagnosis, risk stratification, disease monitoring, and more. Urine has gained popularity due to its less invasive sampling, the ability to easily repeat samples, and the ability to track tumor evolution in real time, making it a powerful tool for diagnosis and treatment monitoring, especially in urologic cancers. In this review, we provide a detailed discussion on the potential clinical applications of prostate cancer (PCa) and bladder cancer (BCa), with cell-free DNA (cfDNA), microRNAs (miRNAs), proteins, and peptides as liquid biopsy biomarkers.
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Affiliation(s)
- Haoran Chen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chenyang Xu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zujun Fang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Shanhua Mao
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
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12
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Tamkovich S, Tupikin A, Kozyakov A, Laktionov P. Size and Methylation Index of Cell-Free and Cell-Surface-Bound DNA in Blood of Breast Cancer Patients in the Contest of Liquid Biopsy. Int J Mol Sci 2022; 23:ijms23168919. [PMID: 36012175 PMCID: PMC9408721 DOI: 10.3390/ijms23168919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Aberrantly methylated circulating DNA (cirDNA) has proven to be a good cancer marker, but its detection is limited by low concentrations, fragmentation, and insufficiency. Since the methylated cirDNA was shown to be more stable in circulation than the unmethylated one and was shown to bind with the blood cell surface, we studied the concentration, representation, and fragmentation of tumor-derived methylated DNA in cell-free and cell-surface-associated DNA. We found that long DNA fragments (more than 10 kb) are mainly associated with the surface of blood cells. However, in plasma short DNA fragments (100–1000 bp) were also found along with long DNA fragments. Isolation of short fragments after separation of cirDNA in 6% PAGE followed by quantitative PCR (L1 element) has shown that short DNA fragments in healthy females represent 22% versus 0.5–4.4% in breast cancer patients. The methylated form of the RARβ2 gene was detected only in long DNA fragments by Real-time TaqMan PCR of bisulfite-converted DNA. The methylation index of cirDNA from healthy women was estimated at 0%, 9%, and 7% in plasma, PBS-EDTA, and trypsin eluates from the surface of blood cells, respectively. The methylation index of breast cancer patients’ DNA was found to be 33%, 15%, and 61% in the same fractions confirming the overrepresentation of methylated DNA in csbDNA.
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Affiliation(s)
- Svetlana Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Clinical Biochemistry, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Novosibirsk 630090, Russia
- Correspondence:
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anton Kozyakov
- Department of Mammology, Novosibirsk Regional Clinical Oncological Dispensary, Novosibirsk 630108, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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13
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Oberhofer A, Bronkhorst AJ, Uhlig C, Ungerer V, Holdenrieder S. Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures. Diagnostics (Basel) 2022; 12:diagnostics12081834. [PMID: 36010184 PMCID: PMC9406971 DOI: 10.3390/diagnostics12081834] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
All cell and tissue types constantly release DNA fragments into human body fluids by various mechanisms including programmed cell death, accidental cell degradation and active extrusion. Particularly, cell-free DNA (cfDNA) in plasma or serum has been utilized for minimally invasive molecular diagnostics. Disease onset or pathological conditions that lead to increased cell death alter the contribution of different tissues to the total pool of cfDNA. Because cfDNA molecules retain cell-type specific epigenetic features, it is possible to infer tissue-of-origin from epigenetic characteristics. Recent research efforts demonstrated that analysis of, e.g., methylation patterns, nucleosome occupancy, and fragmentomics determined the cell- or tissue-of-origin of individual cfDNA molecules. This novel tissue-of origin-analysis enables to estimate the contributions of different tissues to the total cfDNA pool in body fluids and find tissues with increased cell death (pathologic condition), expanding the portfolio of liquid biopsies towards a wide range of pathologies and early diagnosis. In this review, we summarize the currently available tissue-of-origin approaches and point out the next steps towards clinical implementation.
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14
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Ullah H, Arbab S, Li K, Khan MIU, Qadeer A, Muhammad N. Schistosomiasis related circulating cell-free DNA: A useful biomarker in diagnostics. Mol Biochem Parasitol 2022; 251:111495. [PMID: 35835258 DOI: 10.1016/j.molbiopara.2022.111495] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 12/26/2022]
Abstract
Schistosoma is a genus of trematodes causing schistosomiasis, a major neglected tropical disease infecting more than 240 million people and with 700 million people at the risk of infection in the tropical and subtropical regions of the world, especially low-income countries. For the elimination of the disease, accurate diagnostic tools are needed. Besides allowing early treatment, early detection prevents environmental contamination and in turn ensures safe water sources in the endemic areas. Cell-free DNA (cfDNA) biomarker detection is a relatively new tool, used for the diagnosis of schistosomiasis in the early stages of infection from non-invasive clinical or experimental samples. cfDNA can be detected in Schistosoma infected host body fluids such as urine, serum, saliva and tissues, mainly in blood offering significant benefits for accurate diagnosis. In the current review, we described different characteristics of cfDNA, evidencing and supporting its potential uses in Schistosoma diagnosis and the improvement of treatment effectiveness.
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Affiliation(s)
- Hanif Ullah
- West China School of Nursing, Sichuan University, Chengdu, China.
| | - Safia Arbab
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China; Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ka Li
- West China School of Nursing, Sichuan University, Chengdu, China.
| | - Muhammad Inayat Ullah Khan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Abdul Qadeer
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai 200241, China
| | - Nehaz Muhammad
- Department of Zoology, University of Swabi, Swabi 23561, Khyber Pakhtunkhwa, Pakistan
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15
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The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies. Diagnostics (Basel) 2022; 12:diagnostics12061363. [PMID: 35741173 PMCID: PMC9221655 DOI: 10.3390/diagnostics12061363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy is a broad term that refers to the testing of body fluids for biomarkers that correlate with a pathological condition. While a variety of body-fluid components (e.g., circulating tumor cells, extracellular vesicles, RNA, proteins, and metabolites) are studied as potential liquid biopsy biomarkers, cell-free DNA (cfDNA) has attracted the most attention in recent years. The total cfDNA population in a typical biospecimen represents an immensely rich source of biological and pathological information and has demonstrated significant potential as a versatile biomarker in oncology, non-invasive prenatal testing, and transplant monitoring. As a significant portion of cfDNA is composed of repeat DNA sequences and some families (e.g., pericentric satellites) were recently shown to be overrepresented in cfDNA populations vs their genomic abundance, it holds great potential for developing liquid biopsy-based biomarkers for the early detection and management of patients with cancer. By outlining research that employed cell-free repeat DNA sequences, in particular the ALU and LINE-1 elements, we highlight the clinical potential of the repeat-element content of cfDNA as an underappreciated marker in the cancer liquid biopsy repertoire.
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16
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Rapado-González Ó, López-Cedrún JL, Lago-Lestón RM, Abalo A, Rubin-Roger G, Salgado-Barreira Á, López-López R, Muinelo-Romay L, Suárez-Cunqueiro MM. Integrity and quantity of salivary cell-free DNA as a potential molecular biomarker in oral cancer: A preliminary study. J Oral Pathol Med 2022; 51:429-435. [PMID: 35416334 PMCID: PMC9322526 DOI: 10.1111/jop.13299] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Background Differences in cell‐free DNA (cfDNA) fragments have been described as a valuable tool to distinguish cancer patients from healthy individuals. We aim to investigate the concentration and integrity of cfDNA fragments in saliva from oral squamous cell carcinoma (OSCC) patients and healthy individuals in order to explore their value as diagnostic biomarkers. Methods Saliva samples were collected from a total of 34 subjects (19 OSCC patients and 15 healthy controls). The total concentration of salivary cfDNA (scfDNA) was determined using a fluorometry method and quantitative real‐time polymerase chain reaction (qPCR). To evaluate the scfDNA quantity and integrity, qPCR targeting Arthobacter luteus (ALU) sequences at three amplicons of different lengths (60, 115, and 247 bp, respectively) was carried out. ScfDNA integrity indexes (ALU115/ALU60 and ALU247/ALU60) were calculated as the ratio between the absolute concentration of the longer amplicons 115 bp and 247 bp and the total scfDNA amount (amplicon 60 bp). Results The total scfDNA concentration (ALU60) was higher in OSCC than in healthy donors, but this trend was not statistically significant. The medians of scfDNA integrity indexes, ALU115/ALU60 and ALU247/ALU60, were significantly higher in OSCC, showing area under the curve values of 0.8211 and 0.7018, respectively. Conclusion Our preliminary results suggest that scfDNA integrity indexes (ALU115/ALU60 and ALU247/ALU60) have potential as noninvasive diagnostic biomarkers for OSCC.
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Affiliation(s)
- Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis López-Cedrún
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña SERGAS, A Coruña, Spain
| | - Ramón Manuel Lago-Lestón
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Alicia Abalo
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Guillermo Rubin-Roger
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña SERGAS, A Coruña, Spain
| | - Ángel Salgado-Barreira
- Department of Preventive Medicine, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Epidemiology, Health Public and Health Technology Assessment, Health Research Institute of Santiago de Compostela (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Rafael López-López
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
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17
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Cell-Free DNA Fragmentomics in Liquid Biopsy. Diagnostics (Basel) 2022; 12:diagnostics12040978. [PMID: 35454026 PMCID: PMC9027801 DOI: 10.3390/diagnostics12040978] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Cell-free DNA (cfDNA) in bodily fluids has rapidly transformed the development of noninvasive prenatal testing, cancer liquid biopsy, and transplantation monitoring. Plasma cfDNA consists of a mixture of molecules originating from various bodily tissues. The study of the fragmentation patterns of cfDNA, also referred to as ‘fragmentomics’, is now an actively pursued area of biomarker research. Clues that cfDNA fragmentation patterns might carry information concerning the tissue of origin of cfDNA molecules have come from works demonstrating that circulating fetal, tumor-derived, and transplanted liver-derived cfDNA molecules have a shorter size distribution than the background mainly of hematopoietic origin. More recently, an improved understanding of cfDNA fragmentation has provided many emerging fragmentomic markers, including fragment sizes, preferred ends, end motifs, single-stranded jagged ends, and nucleosomal footprints. The intrinsic biological link between activities of various DNA nucleases and characteristic fragmentations has been demonstrated. In this review, we focus on the biological properties of cell-free DNA unveiled recently and their potential clinical applications.
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18
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At the dawn: cell-free DNA fragmentomics and gene regulation. Br J Cancer 2021; 126:379-390. [PMID: 34815523 PMCID: PMC8810841 DOI: 10.1038/s41416-021-01635-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms play instrumental roles in gene regulation during embryonic development and disease progression. However, it is challenging to non-invasively monitor the dynamics of epigenomes and related gene regulation at inaccessible human tissues, such as tumours, fetuses and transplanted organs. Circulating cell-free DNA (cfDNA) in peripheral blood provides a promising opportunity to non-invasively monitor the genomes from these inaccessible tissues. The fragmentation patterns of plasma cfDNA are unevenly distributed in the genome and reflect the in vivo gene-regulation status across multiple molecular layers, such as nucleosome positioning and gene expression. In this review, we revisited the computational and experimental approaches that have been recently developed to measure the cfDNA fragmentomics across different resolutions comprehensively. Moreover, cfDNA in peripheral blood is released following cell death, after apoptosis or necrosis, mainly from haematopoietic cells in healthy people and diseased tissues in patients. Several cfDNA-fragmentomics approaches showed the potential to identify the tissues-of-origin in cfDNA from cancer patients and healthy individuals. Overall, these studies paved the road for cfDNA fragmentomics to non-invasively monitor the in vivo gene-regulatory dynamics in both peripheral immune cells and diseased tissues.
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19
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Chopra B, Sureshkumar KK. Emerging role of cell-free DNA in kidney transplantation. World J Exp Med 2021; 11:55-65. [PMID: 34877265 PMCID: PMC8611196 DOI: 10.5493/wjem.v11.i5.55] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/01/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
Monitoring kidney transplants for rejection conventionally includes serum creatinine, immunosuppressive drug levels, proteinuria, and donor-specific antibody (DSA). Serum creatinine is a late marker of allograft injury, and the predictive ability of DSA regarding risk of rejection is variable. Histological analysis of an allograft biopsy is the standard method for diagnosing rejection but is invasive, inconvenient, and carries risk of complications. There has been a long quest to find a perfect biomarker that noninvasively predicts tissue injury caused by rejection at an early stage, so that diagnosis and treatment could be pursued without delay in order to minimize irreversible damage to the allograft. In this review, we discuss relatively novel research on identifying biomarkers of tissue injury, specifically elaborating on donor-derived cell-free DNA, and its clinical utility.
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Affiliation(s)
- Bhavna Chopra
- Nephrology and Hypertension, Allegheny General Hospital, Pittsburgh, PA 15212, United States
| | - Kalathil K Sureshkumar
- Division of Nephrology, Department of Medicine, Allegheny General Hospital, Allegheny Health Network, Pittsburgh, PA 15212, United State
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20
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Ehlayel A, Simms KJA, Ashoor IF. Emerging monitoring technologies in kidney transplantation. Pediatr Nephrol 2021; 36:3077-3087. [PMID: 33523298 DOI: 10.1007/s00467-021-04929-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/22/2020] [Accepted: 01/06/2021] [Indexed: 11/27/2022]
Abstract
Non-invasive technologies to monitor kidney allograft health utilizing high-throughput assays of blood and urine specimens are emerging out of the research realm and slowly becoming part of everyday clinical practice. HLA epitope analysis and eplet mismatch score determination promise a more refined approach to the pre-transplant recipient-donor HLA matching that may lead to reduced rejection risk. High-resolution HLA typing and multiplex single antigen bead assays are identifying potential new offending HLA antibody subtypes. There is increasing recognition of the deleterious role non-HLA antibodies play in post-transplant outcomes. Donor-derived cell-free DNA detected by next-generation sequencing is a promising biomarker for kidney transplant rejection. Multi-omics techniques are shedding light on discrete genomic, transcriptomic, proteomic, and metabolomic signatures that correlate with and predict allograft outcomes. Over the next decade, a comprehensive approach to optimize kidney matching and monitor transplant recipients for acute and chronic graft dysfunction will likely involve a combination of those emerging technologies summarized in this review.
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Affiliation(s)
- Abdulla Ehlayel
- Children's Hospital New Orleans, 200 Henry Clay Ave, New Orleans, LA, 70118, USA
| | - K'joy J A Simms
- Children's Hospital New Orleans, 200 Henry Clay Ave, New Orleans, LA, 70118, USA
| | - Isa F Ashoor
- Children's Hospital New Orleans, 200 Henry Clay Ave, New Orleans, LA, 70118, USA.
- Department of Pediatrics, LSU Health New Orleans, 200 Henry Clay Ave, New Orleans, LA, 70118, USA.
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21
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Zanini G, De Gaetano A, Selleri V, Savino G, Cossarizza A, Pinti M, Mattioli AV, Nasi M. Mitochondrial DNA and Exercise: Implications for Health and Injuries in Sports. Cells 2021; 10:cells10102575. [PMID: 34685555 PMCID: PMC8533813 DOI: 10.3390/cells10102575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/31/2022] Open
Abstract
Recently, several studies have highlighted the tight connection between mitochondria and physical activity. Mitochondrial functions are important in high-demanding metabolic activities, such as endurance sports. Moreover, regular training positively affects metabolic health by increasing mitochondrial oxidative capacity and regulating glucose metabolism. Exercise could have multiple effects, also on the mitochondrial DNA (mtDNA) and vice versa; some studies have investigated how mtDNA polymorphisms can affect the performance of general athletes and mtDNA haplogroups seem to be related to the performance of elite endurance athletes. Along with several stimuli, including pathogens, stress, trauma, and reactive oxygen species, acute and intense exercise also seem to be responsible for mtDNA release into the cytoplasm and extracellular space, leading to the activation of the innate immune response. In addition, several sports are characterized by a higher frequency of injuries, including cranial trauma, associated with neurological consequences. However, with regular exercise, circulating cell-free mtDNA levels are kept low, perhaps promoting cf-mtDNA removal, acting as a protective factor against inflammation.
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Affiliation(s)
- Giada Zanini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (G.Z.); (A.D.G.); (V.S.); (M.P.)
| | - Anna De Gaetano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (G.Z.); (A.D.G.); (V.S.); (M.P.)
- National Institute for Cardiovascular Research-INRC, 40126 Bologna, Italy; (A.C.); (A.V.M.)
| | - Valentina Selleri
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (G.Z.); (A.D.G.); (V.S.); (M.P.)
| | - Gustavo Savino
- Department of Public Healthcare, Sports Medicine Service, Azienda USL of Modena, 41121 Modena, Italy;
| | - Andrea Cossarizza
- National Institute for Cardiovascular Research-INRC, 40126 Bologna, Italy; (A.C.); (A.V.M.)
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (G.Z.); (A.D.G.); (V.S.); (M.P.)
| | - Anna Vittoria Mattioli
- National Institute for Cardiovascular Research-INRC, 40126 Bologna, Italy; (A.C.); (A.V.M.)
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Milena Nasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Correspondence: ; Tel.: +39-059-205-5422
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22
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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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Mitophagy: At the heart of mitochondrial quality control in cardiac aging and frailty. Exp Gerontol 2021; 153:111508. [PMID: 34358665 DOI: 10.1016/j.exger.2021.111508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 01/18/2023]
Abstract
Cardiovascular disease is highly prevalent among older adults and poses a huge burden on morbidity, disability, and mortality. The age-related increased vulnerability of the cardiovascular system towards stressors is a pathophysiological trait of cardiovascular disease. This has been associated with a progressive deterioration of blood vessels and decline in heart function during aging. Cardiomyocytes rely mostly on oxidative metabolism for deploying their activities and mitochondrial metabolism is crucial to this purpose. Dysmorphic, inefficient, and oxidant-producing mitochondria have been identified in aged cardiomyocytes in association with cardiac structural and functional alterations. These aberrant organelles are thought to arise from inefficient mitochondrial quality control, which has therefore been place in the spotlight as a relevant mechanism of cardiac aging. As a result of alterations in mitochondrial quality control and redox dyshomeostasis, mitochondrial damage accumulates and contributes to cardiac frailty. Herein, we discuss the contribution of defective mitochondrial quality control pathways to cardiac frailty. Emerging findings pointing towards the exploitation of these pathways as therapeutic targets against cardiac aging and cardiovascular disease will also be illustrated.
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Abstract
Cell-free DNA (cfDNA) exists in plasma and can be measured by several techniques. It is now possible to differentiate donor-derived cfDNA (ddcfDNA) from recipient cfDNA in the plasma or urine of solid organ transplant recipients in the absence of donor and recipient genotyping. The assessment of ddcfDNA is being increasingly studied as a noninvasive means of identifying acute rejection (AR) in solid organ transplants, including subclinical AR. We herein review the literature on the correlation of ddcfDNA with AR in kidney transplantation. There have been at least 15 observational studies that have assessed ddcfDNA in urine or plasma using various methodologies with various thresholds for abnormality. Overall, elevated ddcfDNA indicates allograft injury as may occur with AR, infection, or acute tubular injury but may also be found in clinically stable patients with normal histology. Sensitivity is greater for antibody-mediated AR than for cell-mediated AR, and normal levels do not preclude significant cell-mediated rejection. Measurement of ddcfDNA is not a replacement for biopsy that remains the gold standard for diagnosing AR. Serial monitoring of stable patients may allow earlier detection of subclinical AR, but the efficacy of this approach remains to be established. Normal levels should not preclude planned protocol biopsies. There may be roles for following ddcfDNA levels to assess the adequacy of treatment of AR and to guide the intensity of immunosuppression in the individual patient. Randomized controlled trials are necessary to validate the benefit and cost-effectiveness for these various uses. No firm recommendations can be made at this time.
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Trumpff C, Michelson J, Lagranha CJ, Taleon V, Karan KR, Sturm G, Lindqvist D, Fernström J, Moser D, Kaufman BA, Picard M. Stress and circulating cell-free mitochondrial DNA: A systematic review of human studies, physiological considerations, and technical recommendations. Mitochondrion 2021; 59:225-245. [PMID: 33839318 PMCID: PMC8418815 DOI: 10.1016/j.mito.2021.04.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/23/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
Cell-free mitochondrial DNA (cf-mtDNA) is a marker of inflammatory disease and a predictor of mortality, but little is known about cf-mtDNA in relation to psychobiology. A systematic review of the literature reveals that blood cf-mtDNA varies in response to common real-world stressors including psychopathology, acute psychological stress, and exercise. Moreover, cf-mtDNA is inducible within minutes and exhibits high intra-individual day-to-day variation, highlighting the dynamic regulation of cf-mtDNA levels. We discuss current knowledge on the mechanisms of cf-mtDNA release, its forms of transport ("cell-free" does not mean "membrane-free"), potential physiological functions, putative cellular and neuroendocrine triggers, and factors that may contribute to cf-mtDNA removal from the circulation. A review of in vitro, pre-clinical, and clinical studies shows conflicting results around the dogma that physiological forms of cf-mtDNA are pro-inflammatory, opening the possibility of other physiological functions, including the cell-to-cell transfer of whole mitochondria. Finally, to enhance the reproducibility and biological interpretation of human cf-mtDNA research, we propose guidelines for blood collection, cf-mtDNA isolation, quantification, and reporting standards, which can promote concerted advances by the community. Defining the mechanistic basis for cf-mtDNA signaling is an opportunity to elucidate the role of mitochondria in brain-body interactions and psychopathology.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Jeremy Michelson
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Claudia J Lagranha
- University of Pittsburgh, School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, United States
| | - Veronica Taleon
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Kalpita R Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Daniel Lindqvist
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden; Office of Psychiatry and Habilitation, Region Skåne, Sweden
| | - Johan Fernström
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden
| | - Dirk Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - Brett A Kaufman
- University of Pittsburgh, School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, United States
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, USA; New York State Psychiatric Institute, NY, USA.
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26
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Danesi R, Lo YMD, Oellerich M, Beck J, Galbiati S, Re MD, Lianidou E, Neumaier M, van Schaik RHN. What do we need to obtain high quality circulating tumor DNA (ctDNA) for routine diagnostic test in oncology? - Considerations on pre-analytical aspects by the IFCC workgroup cfDNA. Clin Chim Acta 2021; 520:168-171. [PMID: 34081934 DOI: 10.1016/j.cca.2021.05.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
The analysis of circulating cell free DNA is an important tool for the analysis of tumor resistance, tumor heterogeneity, detection of minimal residual disease and detection of allograft rejection in kidney or heart transplant patients. The proper use of this technique is important, and starts with considering pre-analytic aspects. The current paper addresses some important technical considerations to ensure the proper and harmonized use of cfDNA techniques.
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Affiliation(s)
- R Danesi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Y M D Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - M Oellerich
- Dept. Clinical Pharmacology, George-August University, University Medical Center Goettingen, Goettingen, Germany
| | - J Beck
- Chronix BioMedical GmbH, Goettingen, Germany
| | - S Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - M Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - E Lianidou
- Dept. Chemistry, University of Athens, Athens, Greece
| | - M Neumaier
- Institute for Clinical Chemistry, Mannheim, Germany
| | - R H N van Schaik
- Dept. Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands.
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27
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Lo YMD, Han DSC, Jiang P, Chiu RWK. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science 2021; 372:372/6538/eaaw3616. [PMID: 33833097 DOI: 10.1126/science.aaw3616] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze cell-free DNA in blood plasma are used for noninvasive prenatal testing, oncology, and monitoring of organ transplant recipients. DNA molecules are released into the plasma from various bodily tissues. Physical and molecular features of cell-free DNA fragments and their distribution over the genome bear information about their tissues of origin. Moreover, patterns of DNA methylation of these molecules reflect those of their tissue sources. The nucleosomal organization and nuclease content of the tissue of origin affect the fragmentation profile of plasma DNA molecules, such as fragment size and end motifs. Besides double-stranded linear fragments, other topological forms of cell-free DNA also exist-namely circular and single-stranded molecules. Enhanced by these features, liquid biopsies hold promise for the noninvasive detection of tissue-specific pathologies with a range of clinical applications.
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Affiliation(s)
- Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China. .,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory in Translational Oncology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Diana S C Han
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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28
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Myeloperoxidase has no effect on the low procoagulant activity of silica-free DNA. Thromb Res 2021; 203:36-45. [PMID: 33915354 DOI: 10.1016/j.thromres.2021.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/17/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022]
Abstract
Blood coagulation and innate immunity are closely interrelated. At sites of inflammation, DNA and myeloperoxidase (MPO) are released from polymorphonuclear leukocytes (PMNs) as an integral component of neutrophil extracellular traps (NETs). NETs exert pleiotropic thrombogenic effects, with DNA-mediated contact activation of factor XII (FXII) likely playing a role. We have previously shown that MPO, a highly cationic protein, regulates coagulation through heteromolecular interactions with various negatively charged structures, including membrane phospholipids and low-molecular-weight heparin. The aims of our current study were to confirm that DNA activates coagulation and to investigate whether its procoagulant activity (PCA) is regulated by PMN-derived MPO. To this end, we used thrombin generation and FXIIa amidolytic activity assays to analyze the PCA of cell-free DNA isolated with silica membrane-based (cfDNA) or silica-free procedures (PaxDNA). cfDNA potently activated FXII and promoted thrombin generation in a concentration-dependent manner, but its PCA was largely attributable to contaminating silica particles. In contrast, pure, i.e. silica-free, PaxDNA was markedly less procoagulant. Although PaxDNA amplified thrombin generation in plasma, it was devoid of any direct FXII activating activity. MPO supershifted both cfDNA and PaxDNA in gel electrophoresis, but only silica-associated PCA of cfDNA was neutralized by MPO independently of its catalytic properties. Moreover, pretreatment with DNase I abolished silica-induced thrombin generation. In summary, we show that pure DNA has rather weak PCA, which is not further inhibited by heteromolecular complex formation with exogenous MPO. Our study thus provides novel mechanistic insights into the regulation of coagulation by extracellular DNA under inflammatory conditions.
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29
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Can Circulating Cell-Free DNA or Circulating Tumor DNA Be a Promising Marker in Ovarian Cancer? JOURNAL OF ONCOLOGY 2021; 2021:6627241. [PMID: 33936202 PMCID: PMC8062166 DOI: 10.1155/2021/6627241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 12/29/2022]
Abstract
In recent years, the studies on ovarian cancer have made great progress, but the morbidity and mortality of patients with ovarian cancer are still very high. Due to the lack of effective early screening and detecting tools, 70% of ovarian cancer patients are diagnosed at an advanced stage. The overall survival rate of ovarian cancer patients treated with surgical combined with chemotherapy has not been significantly improved, and they usually relapse or resist chemotherapy. Therefore, a novel tumor marker is beneficial for the diagnosis and prognosis of patients with ovarian cancer. As the index of "liquid biopsy," circulating cell-free DNA/circulating tumor DNA (cfDNA/ctDNA) has attracted a lot of attention. It has more remarkable advantages than traditional methods and gives a wide range of clinical applications in kinds of solid tumors. This review attempts to illuminate the important value of cfDNA/ctDNA in ovarian cancer, including diagnosis, monitoring, and prognosis. Meanwhile, we will present future directions and challenges for detection of cfDNA/ctDNA.
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30
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Extracellular DNA in blood products and its potential effects on transfusion. Biosci Rep 2021; 40:222322. [PMID: 32150264 PMCID: PMC7098128 DOI: 10.1042/bsr20192770] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/18/2020] [Accepted: 03/03/2020] [Indexed: 02/05/2023] Open
Abstract
Blood transfusions are sometimes necessary after a high loss of blood due to injury or surgery. Some people need regular transfusions due to medical conditions such as haemophilia or cancer. Studies have suggested that extracellular DNA including mitochondrial DNA present in the extracellular milieu of transfused blood products has biological actions that are capable of activating the innate immune systems and potentially contribute to some adverse reactions in transfusion. From the present work, it becomes increasingly clear that extracellular DNA encompassed mitochondrial DNA is far from being biologically inert in blood products. It has been demonstrated to be present in eligible blood products and thus can be transfused to blood recipients. Although the presence of extracellular DNA in human plasma was initially detected in 1948, some aspects have not been fully elucidated. In this review, we summarize the potential origins, clearance mechanisms, relevant structures, and potential role of extracellular DNA in the innate immune responses and its relationship with individual adverse reactions in transfusion.
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31
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Sadeghan AA, Soltaninejad H, Dadmehr M, Hamidieh AA, Asadollahi MA, Hosseini M, Ganjali MR, Hosseinkhani S. Fluorimetric detection of methylated DNA of Sept9 promoter by silver nanoclusters at intrastrand 6C-loop. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119081. [PMID: 33128948 DOI: 10.1016/j.saa.2020.119081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Methylation of DNA at carbon 5 of cytosines is the most common epigenetic modification of human genome. Due to its critical role in many normal cell processes such as growth and development, any aberrant methylation pattern in a particular locus may lead to abnormal functions and diseases such as cancer. Development of methods to detect methylation state of DNA which may eliminate labor-intensive chemical or enzymatic treatments has received considerable attention in recent years. Herein, we report a DNA methylation detection procedure based on fluorescence turn-on strategy. Target sequence was selected from Sept9 promoter region that has been reported as one of the most frequently methylated sites in colorectal cancer. Probe DNA was designed to be complementary to this sequence with an additional six cytosines in the middle to form an internal loop to host silver nanoclusters. The fluorescence intensity of the synthesized silver nanoclusters with the duplexes of probe-non-methylated target was significantly different from that of probe-methylated target. The fluorescence enhanced with increasing the methylated DNA concentration with a linear relation in the range of 1.0 × 10-8 M to 5.0 × 10-7 M with the detection limit of 8.2 × 10-9 M, and quenched with non-methylated ones. The method was very specific in the presence of non-complementary sequences with maximum similarity of 40%. Circular dichroism spectra indicated that silver ions significantly affected the structure of methylated and non-methylated DNA into different extents which could further influence the nanocluster fluorescence. Finally, a method was introduced to meet the concerns in the applicability of the proposed method in real situation.
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Affiliation(s)
- Amir Amiri Sadeghan
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Soltaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran; Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | | | - Amir Ali Hamidieh
- Pediatric Cell Therapy Research Center, Tehran University of Medical Scienses, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, University of Tehran, Tehran, Iran; Biosensor Research Center, Endocrinology & Metabolism Molecular - Cellular Sciences Institute, Iran
| | - Saman Hosseinkhani
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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32
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Shabrish S, Mittra I. Cytokine Storm as a Cellular Response to dsDNA Breaks: A New Proposal. Front Immunol 2021; 12:622738. [PMID: 33597956 PMCID: PMC7882731 DOI: 10.3389/fimmu.2021.622738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/07/2021] [Indexed: 12/20/2022] Open
Abstract
Pathogenesis of cytokine storm is poorly understood. In this article we propose a new mechanism and suggest innovative therapeutic avenues for its prevention. We have reported that particles of cell-free chromatin (cfCh) that are released from the billions of cells that die in the body everyday can illegitimately integrate into genomes of healthy cells to trigger dsDNA breaks. The latter leads to apoptosis and/or intense activation of inflammatory cytokines in the affected cells. We hypothesise that a similar phenomenon of dsDNA breaks and inflammation is involved in cytokine storm. The abundant cfCh particles that are released from dying host cells following viral/microbial invasion initiate a cascading effect of more cell death resulting in a vicious cycle of further DNA damage, apoptosis and hyper-inflammation which culminate in cytokine storm. We propose that this unrelenting vicious cycle of cellular DNA damage and cytokine storm may be the underlying cause of high mortality from severe COVID-19. We discuss results of our preclinical studies wherein we have shown that endotoxin induced cytokine storm in mice can be reversed by three different agents that have the ability to inactivate cfCh. These agents may be worthy of investigation in clinical trials to reduce mortality from COVID-19.
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Affiliation(s)
- Snehal Shabrish
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, and Homi Bhabha National Institute, Mumbai, India
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, and Homi Bhabha National Institute, Mumbai, India
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33
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A New Perspective on the Origin of DNA Double-Strand Breaks and Its Implications for Ageing. Genes (Basel) 2021; 12:genes12020163. [PMID: 33530310 PMCID: PMC7912064 DOI: 10.3390/genes12020163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
It is estimated that 10-50 DNA double-strand breaks (DSBs) occur in a nucleated human cell per cell cycle. We reviewed the present state of knowledge and hypothesized that the currently accepted mechanisms cannot explain such high frequency of DSBs occurring daily under normal physiological conditions. We propose an alternative model that implicates illegitimate genomic integration into healthy cells of cell-free chromatin (cfCh) particles released from the billions of cells that die in the body every day. Repeated genomic integration of cfCh may have catastrophic consequences for the cell, such as DSBs, their faulty repair by nonhomologous end joining (NHEJ) followed by apoptosis with release of more cfCh which would integrate into genomes of surrounding cells. This can creates a vicious cycle of cfCh integration, DSBs, NHEJ, and more apoptosis, thereby providing a potential explanation as to why so many billions of cells die in the body on a daily basis. We also recount the recent observation that cfCh integration and the resulting DSBs activate inflammatory cytokines. This leads us to propose that concurrent DSBs and induction of inflammation occurring throughout life may be the underlying cause of ageing, degenerative disorders, and cancer. Finally, we discuss the prospect that agents that can inactivate/degrade cfCh may hold the key to making healthy ageing a realizable goal.
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34
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Bryzgunova OE, Konoshenko MY, Laktionov PP. Concentration of cell-free DNA in different tumor types. Expert Rev Mol Diagn 2020; 21:63-75. [PMID: 33270495 DOI: 10.1080/14737159.2020.1860021] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Cell-free DNA (cfDNA) circulates in the blood for a long time. The levels of cfDNA in the blood are assayed in cancer diagnostics because they are closely related to the tumor burden of patients.Areas covered: cfDNA escapes the action of DNA-hydrolyzing enzymes, being a part of supramolecular complexes or interacting with the plasma membrane of blood cells. cfDNA has heterogeneous size and composition, which impose various restrictions on both isolation methods and subsequent analysis. cfDNA concentration and structural changes with the development of diseases highlight the high potential of cfDNA as a diagnostic and prognostic marker. The concentration of cfDNA released in the blood by tumor cells determines the specificity of such diagnostics and the required blood volume. The present review aimed to synthesize the available data on cfDNA concentration in the cancer patient's blood as well as pre-analytical, analytical, and biological factors, which interfere with cfDNA concentration.Expert opinion: The concentration of cfDNA and tumor cell DNA (ctDNA), and the over-presentation of DNA loci in cfDNA must be considered when looking for tumor markers. Some inconsistent data on cfDNA concentrations (like those obtained by different methods) suggest that the study of cfDNA should be continued.
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Affiliation(s)
- O E Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
| | - M Yu Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
| | - P P Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
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35
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Shen J, Guo L, Yan P, Zhou J, Zhou Q, Lei W, Liu H, Liu G, Lv J, Liu F, Huang H, Dong W, Shu L, Wang H, Wu J, Chen J, Wang R. Prognostic value of the donor-derived cell-free DNA assay in acute renal rejection therapy: A prospective cohort study. Clin Transplant 2020; 34:e14053. [PMID: 32735352 DOI: 10.1111/ctr.14053] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/30/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022]
Abstract
Donor-derived cell-free DNA (dd-cfDNA) is a promising biomarker for monitoring allograft status. However, whether dd-cfDNA can reflect real-time anti-rejection treatment effects remains unclear. We prospectively recruited 28 patients with acute renal rejection, including 5 with ABMR, 12 with type IA or type IB rejection, and 11 with type IIA or IIB rejection. dd-cfDNA levels in peripheral blood were measured using human single nucleotide polymorphism (SNP) locus capture hybridization. The percentage of dd-cfDNA (dd-cfDNA%) declined significantly from 2.566 ± 0.549% to 0.773 ± 0.116% (P < .001) after anti-rejection therapy. The dd-cfDNA% decreased steadily over the course of 3 days with daily methylprednisolone injections, but no significant difference in the dd-cfDNA% was observed between the end of anti-rejection therapy and 2 weeks later. Changes in the dd-cfDNA% (∆dd-cfDNA%) demonstrated a positive correlation with estimated glomerular filtration rates at 1 month (ρ = 2.570, P = .022), 3 months (ρ = 3.210, P = .027), and 6 months (ρ = 2.860, P = .019) after therapy. Thus, the dd-cfDNA assay shows prognostic capabilities in therapy outcome and allograft recovery; however, its ability is inhibited by methylprednisolone regardless of the types of rejection. Additionally, a reassessment of frequency intervals for testing is required.
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Affiliation(s)
- Jia Shen
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Luying Guo
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Pengpeng Yan
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Jingyi Zhou
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Qin Zhou
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Wenhua Lei
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Haitao Liu
- AlloDx (Shanghai) biotech., Co., Ltd, Shanghai, China
| | - Guangjun Liu
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Junhao Lv
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Feng Liu
- AlloDx (Shanghai) biotech., Co., Ltd, Shanghai, China
| | - Hongfeng Huang
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Wenzhao Dong
- AlloDx (Shanghai) biotech., Co., Ltd, Shanghai, China
| | - Liping Shu
- AlloDx (Shanghai) biotech., Co., Ltd, Shanghai, China
| | - Huiping Wang
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Jianyong Wu
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Jianghua Chen
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China
| | - Rending Wang
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Key Clinical Department of Kidney Diseases, Zhejiang, China.,Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang, China.,Zhejiang University Institute of Nephrology, Hangzhou, China.,Organ Donation and Coordination Office, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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36
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Jiang P, Xie T, Ding SC, Zhou Z, Cheng SH, Chan RWY, Lee WS, Peng W, Wong J, Wong VWS, Chan HLY, Chan SL, Poon LCY, Leung TY, Chan KCA, Chiu RWK, Lo YMD. Detection and characterization of jagged ends of double-stranded DNA in plasma. Genome Res 2020; 30:1144-1153. [PMID: 32801148 PMCID: PMC7462074 DOI: 10.1101/gr.261396.120] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/22/2020] [Indexed: 01/06/2023]
Abstract
Cell-free DNA in plasma has been used for noninvasive prenatal testing and cancer liquid biopsy. The physical properties of cell-free DNA fragments in plasma, such as fragment sizes and ends, have attracted much recent interest, leading to the emerging field of cell-free DNA fragmentomics. However, one aspect of plasma DNA fragmentomics as to whether double-stranded plasma molecules might carry single-stranded ends, termed a jagged end in this study, remains underexplored. We have developed two approaches for investigating the presence of jagged ends in a plasma DNA pool. These approaches utilized DNA end repair to introduce differential methylation signals between the original sequence and the jagged ends, depending on whether unmethylated or methylated cytosines were used in the DNA end-repair procedure. The majority of plasma DNA molecules (87.8%) were found to bear jagged ends. The jaggedness varied according to plasma DNA fragment sizes and appeared to be in association with nucleosomal patterns. In the plasma of pregnant women, the jaggedness of fetal DNA molecules was higher than that of the maternal counterparts. The jaggedness of plasma DNA correlated with the fetal DNA fraction. Similarly, in the plasma of cancer patients, tumor-derived DNA molecules in patients with hepatocellular carcinoma showed an elevated jaggedness compared with nontumoral DNA. In mouse models, knocking out of the Dnase1 gene reduced jaggedness, whereas knocking out of the Dnase1l3 gene enhanced jaggedness. Hence, plasma DNA jagged ends represent an intrinsic property of plasma DNA and provide a link between nuclease activities and the fragmentation of plasma DNA.
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Affiliation(s)
- Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Tingting Xie
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Spencer C Ding
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Ze Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Suk Hang Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rebecca W Y Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wing-Shan Lee
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wenlei Peng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Vincent W S Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,Institute of Digestive Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Henry L Y Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,Institute of Digestive Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Stephen L Chan
- Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Liona C Y Poon
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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37
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Chen L, Chen Y, Feng YL, Zhu Y, Wang LQ, Hu S, Cheng P. Tumor circulome in the liquid biopsies for digestive tract cancer diagnosis and prognosis. World J Clin Cases 2020; 8:2066-2080. [PMID: 32548136 PMCID: PMC7281040 DOI: 10.12998/wjcc.v8.i11.2066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/10/2020] [Accepted: 04/28/2020] [Indexed: 02/05/2023] Open
Abstract
Digestive tract cancer is one of the main diseases that endanger human health. At present, the early diagnosis of digestive tract tumors mainly depends on serology, imaging, endoscopy, and so on. Although tissue specimens are the gold standard for cancer diagnosis, with the rapid development of precision medicine in cancer, the demand for dynamic monitoring of tumor molecular characteristics has increased. Liquid biopsy involves the collection of body fluids via non-invasive approaches, and analyzes biological markers such as circulating tumor cells, circulating tumor DNA, circulating cell-free DNA, microRNAs, and exosomes. In recent years, liquid biopsy has become more and more important in the diagnosis and prognosis of cancer in clinical practice due to its convenience, non-invasiveness, high specificity and it overcomes temporal-spatial heterogeneity. Therefore, this review summarizes the current evidence on liquid biopsies in digestive tract cancers in relation to diagnosis and prognosis.
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Affiliation(s)
- Long Chen
- Department of Radiotherapy, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, Zhejiang Province, China
| | - Yu Chen
- Department of Pediatric Surgery, Guangdong Women and Children Hospital, Guangzhou 511400, Guangdong Province, China
| | - Yuan-Ling Feng
- Department of Obstetrics, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310052, Zhejiang Province, China
| | - Yan Zhu
- Department of Respiratory, Shulan Hospital, Hangzhou 310004, Zhejiang Province, China
| | - Li-Quan Wang
- Department of Obstetrics, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310052, Zhejiang Province, China
| | - Shen Hu
- Department of Obstetrics, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310052, Zhejiang Province, China
| | - Pu Cheng
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310052, Zhejiang Province, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Hangzhou 310052, Zhejiang Province, China
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38
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Dengu F. Next-generation sequencing methods to detect donor-derived cell-free DNA after transplantation. Transplant Rev (Orlando) 2020; 34:100542. [PMID: 32265093 DOI: 10.1016/j.trre.2020.100542] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/30/2022]
Abstract
Following the initial technical challenge of implanting an organ, maintaining the organ against a vast array of pathologies for years to come, remains a colossal challenge for all clinicians working in transplantation. Drug toxicity, opportunistic infection, primary disease recurrence, and the constant battle against organ rejection are all differentials that are considered when graft dysfunction is observed, promoting a lifetime of laborious surveillance. Cell free DNA (cfDNA) since its discovery in 1948 has made an impactful change in transplantation. A growing body of evidence in transplantation (109 manuscripts from 55 studies) shows the promise of this tool as an early and accurate detection of allograft injury rejection as well the benefit to rule out injury as part of screening and routine monitoring. With next generation sequencing rapidly becoming the standard of care in quantifying DNA, understanding this science in the context of transplantation is critical to ensure studies, outcomes and care is improved.
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Affiliation(s)
- Fungai Dengu
- Nuffield Department of Surgical Sciences, University of Oxford, United Kingdom.
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39
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Lee H, Park C, Na W, Park KH, Shin S. Precision cell-free DNA extraction for liquid biopsy by integrated microfluidics. NPJ Precis Oncol 2020; 4:3. [PMID: 32133418 PMCID: PMC7039987 DOI: 10.1038/s41698-019-0107-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/20/2019] [Indexed: 01/05/2023] Open
Abstract
Cell-free DNA (cfDNA) has been implicated as an important biomarker in cancer management. Thus, efficient techniques for cfDNA extraction are necessary for precision medicine. We developed a centrifugation-free cfDNA extraction microfluidic chip capable of extracting cfDNA from plasma samples through microfluidic circuits within 15 min under vacuum pressure using an immiscible solvent. The microfluidic chip had excellent performance that was comparable to the most widely used commercial product (QIAamp kit) in terms of extraction efficiency, purity, and quality of DNA samples. The microfluidic chip was validated for the continuous monitoring of HER-2 type breast cancer and was able to successfully detect a point mutation in phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA) during severe liver metastasis. The chip effectively eliminates the repetitive centrifugation processes and dramatically shortened the sample preparation time. The proposed platform could facilitate the development of a sample-to-answer system for use in liquid biopsy of cancers.
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Affiliation(s)
- Hoyoon Lee
- 1School of Mechanical Engineering, Korea University, Seoul, 02841 Republic of Korea
| | - Chanhee Park
- 1School of Mechanical Engineering, Korea University, Seoul, 02841 Republic of Korea
| | - Wonhwi Na
- 2Nano-Biofluigonstic Research Center, Korea University, Seoul, 02841 Republic of Korea
| | - Kyong Hwa Park
- 3Division of Oncology/Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul, 02841 Republic of Korea
| | - Sehyun Shin
- 1School of Mechanical Engineering, Korea University, Seoul, 02841 Republic of Korea.,2Nano-Biofluigonstic Research Center, Korea University, Seoul, 02841 Republic of Korea
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40
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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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41
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Herbreteau G, Charpentier S, Vallée A, Denis MG. Use of circulating tumoral DNA to guide treatment for metastatic melanoma. Pharmacogenomics 2019; 20:1259-1270. [DOI: 10.2217/pgs-2019-0097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The management of metastatic cutaneous melanoma is conditioned by the identification of BRAF-activating mutations in tumor DNA. Tumor genotyping is usually performed on DNA extracted from tissue samples. However, these invasive samples are rarely repeated during follow-up, and their analysis requires a sample pre-treatment which may take several weeks. Circulating tumor DNA (ctDNA), released into blood by cancer cells, is a good alternative to tissue sampling. ctDNA is not subject to tumor heterogeneity, and can be analyzed rapidly, making possible the detection of mutations in emergency or in patients whose tumor cannot be sampled. ctDNA can also be analyzed repeatedly during follow-up, for postresection minimal residual disease assessment, for therapeutic response monitoring and for early relapse detection.
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Affiliation(s)
- Guillaume Herbreteau
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
- Centre de Recherche en Cancérologie et Immunologie, CRCINA, INSERM U1232, Nantes, France
| | - Sandrine Charpentier
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
- Centre de Recherche en Cancérologie et Immunologie, CRCINA, INSERM U1232, Nantes, France
| | - Audrey Vallée
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
- Centre de Recherche en Cancérologie et Immunologie, CRCINA, INSERM U1232, Nantes, France
| | - Marc G Denis
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
- Centre de Recherche en Cancérologie et Immunologie, CRCINA, INSERM U1232, Nantes, France
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42
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Jiang F, Yang X, He X, Yang M. Circulating DNA, a Potentially Sensitive and Specific Diagnostic Tool for Future Medicine. Dose Response 2019; 17:1559325819891010. [PMID: 31827416 PMCID: PMC6886285 DOI: 10.1177/1559325819891010] [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: 09/20/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 11/28/2022] Open
Abstract
Liquid biopsy has the great potential of detecting early diseases before deterioration and is valued for screening abnormalities at early stage. In oncology, circulating DNA derived from shed cancer cells reflects the tissue of origin, so it could be used to locate tissue sites during early screening. However, the heterogenous parameters of different types limit the clinical application, making it inaccessible to encompass all the cancer types. Instead, for reproducible scenario as pregnancy, fetal cell-free DNA has been well utilized for screening aneuploidies. Noninvasive and convenient as is, it would be of great value in the next decades far more than early diagnosis. This review recapitulates the discovery and development of tumor and fetal cell-free DNA. The common factors are also present that could be taken into consideration when collecting, transporting, and preserving samples. Meanwhile, several protocols used for purifying cell-free DNA, either classic ones or through commercial kits, are compared carefully. In addition, the development of technologies for analyzing cell-free DNA have been summarized and discussed in detail, especially some up-to-date approaches. At the end, the potential prospect of circulating DNA is bravely depicted. In summary, although there would be a lot of efforts before it’s prevalent, cell-free DNA remains a promising tool in point-of-care diagnostic medicine.
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Affiliation(s)
- Fan Jiang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiaoxiao Yang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiping He
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Mingming Yang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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43
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Pallares RM, Thanh NTK, Su X. Sensing of circulating cancer biomarkers with metal nanoparticles. NANOSCALE 2019; 11:22152-22171. [PMID: 31555790 DOI: 10.1039/c9nr03040a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The analysis of circulating cancer biomarkers, including cell-free and circulating tumor DNA, circulating tumor cells, microRNA and exosomes, holds promise in revolutionizing cancer diagnosis and prognosis using body fluid analysis, also known as liquid biopsy. To enable clinical application of these biomarkers, new analytical tools capable of detecting them in very low concentrations in complex sample matrixes are needed. Metal nanoparticles have emerged as extraordinary analytical scaffolds because of their unique optoelectronic properties and ease of functionalization. Hence, multiple analytical techniques have been developed based on these nanoparticles and their plasmonic properties. The aim of this review is to summarize and discuss the present development on the use of metal nanoparticles for the analysis of circulating cancer biomarkers. We examine how metal nanoparticles can be used as (1) analytical transducers in various sensing principles, such as aggregation induced colorimetric assays, plasmon resonance energy transfer, surface enhanced Raman spectroscopy, and refractive index sensing, and (2) signal amplification elements in surface plasmon resonance spectroscopy and electrochemical detection. We critically discuss the clinical relevance of each category of circulating biomarkers, followed by a thorough analysis of how these nanoparticle-based designs have overcome some of the main challenges that gold standard analytical techniques currently face, and what new directions the field may take in the future.
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Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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44
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Gall TMH, Belete S, Khanderia E, Frampton AE, Jiao LR. Circulating Tumor Cells and Cell-Free DNA in Pancreatic Ductal Adenocarcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:71-81. [PMID: 30558725 DOI: 10.1016/j.ajpath.2018.03.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/06/2018] [Accepted: 03/26/2018] [Indexed: 12/21/2022]
Abstract
Pancreatic cancer is detected late in the disease process and has an extremely poor prognosis. A blood-based biomarker that can enable early detection of disease, monitor response to treatment, and potentially allow for personalized treatment would be of great benefit. This review analyzes the literature regarding two potential biomarkers, circulating tumor cells (CTCs) and cell-free DNA (cfDNA), with regard to pancreatic ductal adenocarcinoma. The origin of CTCs and the methods of detection are discussed and a decade of research examining CTCs in pancreatic cancer is summarized, including both levels of CTCs and analyzing their molecular characteristics and how they may affect survival in both advanced and early disease and allow for treatment monitoring. The origin of cfDNA is discussed, and the literature over the past 15 years is summarized. This includes analyzing cfDNA for genetic mutations and methylation abnormalities, which have the potential to be used for the detection and prognosis of pancreatic ductal adenocarcinoma. However, the research certainly remains in the experimental stage, warranting future large trials in these areas.
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Affiliation(s)
- Tamara M H Gall
- Hepato-Pancreato-Biliary Surgical Unit, Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London, United Kingdom.
| | - Samuel Belete
- Hepato-Pancreato-Biliary Surgical Unit, Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London, United Kingdom
| | - Esha Khanderia
- Hepato-Pancreato-Biliary Surgical Unit, Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London, United Kingdom
| | - Adam E Frampton
- Hepato-Pancreato-Biliary Surgical Unit, Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London, United Kingdom
| | - Long R Jiao
- Hepato-Pancreato-Biliary Surgical Unit, Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London, United Kingdom
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45
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Advances in Directly Amplifying Nucleic Acids from Complex Samples. BIOSENSORS-BASEL 2019; 9:bios9040117. [PMID: 31574959 PMCID: PMC6955841 DOI: 10.3390/bios9040117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.
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46
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Rice A, Del Rio Hernandez A. The Mutational Landscape of Pancreatic and Liver Cancers, as Represented by Circulating Tumor DNA. Front Oncol 2019; 9:952. [PMID: 31608239 PMCID: PMC6769086 DOI: 10.3389/fonc.2019.00952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
The mutational landscapes of pancreatic and liver cancers share many common genetic alterations which drive cancer progression. However, these mutations do not occur in all cases of these diseases, and this tumoral heterogeneity impedes diagnosis, prognosis, and therapeutic development. One minimally invasive method for the evaluation of tumor mutations is the analysis of circulating tumor DNA (ctDNA), released through apoptosis, necrosis, and active secretion by tumor cells into various body fluids. By observing mutations in those genes which promote transformation by controlling the cell cycle and oncogenic signaling pathways, a representation of the mutational profile of the tumor is revealed. The analysis of ctDNA is a promising technique for investigating these two gastrointestinal cancers, as many studies have reported on the accuracy of ctDNA assessment for diagnosis and prognosis using a variety of techniques.
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Affiliation(s)
- Alistair Rice
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Armando Del Rio Hernandez
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
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47
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Nørøxe DS, Østrup O, Yde CW, Ahlborn LB, Nielsen FC, Michaelsen SR, Larsen VA, Skjøth-Rasmussen J, Brennum J, Hamerlik P, Poulsen HS, Lassen U. Cell-free DNA in newly diagnosed patients with glioblastoma - a clinical prospective feasibility study. Oncotarget 2019; 10:4397-4406. [PMID: 31320993 PMCID: PMC6633897 DOI: 10.18632/oncotarget.27030] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Glioblastoma (GB) is an incurable brain cancer with limited treatment options. The aim was to test the feasibility of using cell-free DNA (cfDNA) to support evaluation of treatment response, pseudo-progression and whether progression could be found before clinical and/or radiologic progression.
Results: CfDNA fluctuated during treatment with the highest levels before diagnostic surgery and at progression. An increase was seen in 3 out of 4 patients at the time of progression while no increase was seen in 3 out of 4 patients without progression. CfDNA levels could aid in 3 out of 3 questionable cases of pseudo-progression.
Methods: Eight newly diagnosed GB patients were included. Blood samples were collected prior to diagnosis, before start and during oncologic treatment until progression. Seven patients received concurrent radiotherapy/Temozolomide with adjuvant Temozolomide with one of the patients included in a clinical trial with either immunotherapy or placebo as add-on. One patient received radiation alone. CfDNA concentration was determined for each blood sample.
Conclusions: It was feasible to measure cfDNA concentration. Despite the limited cohort size, there was a good tendency between cfDNA and treatment course and -response, respectively with the highest levels at progression.
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Affiliation(s)
- Dorte Schou Nørøxe
- Department of Radiation Biology, Rigshospitalet, 2100 Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, 2100 Copenhagen, Denmark
| | | | | | | | | | | | | | - Jannick Brennum
- Department of Neurosurgery, Rigshospitalet, 2100 Copenhagen, Denmark
| | | | - Hans Skovgaard Poulsen
- Department of Radiation Biology, Rigshospitalet, 2100 Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Ulrik Lassen
- Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
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48
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Raghuram GV, Chaudhary S, Johari S, Mittra I. Illegitimate and Repeated Genomic Integration of Cell-Free Chromatin in the Aetiology of Somatic Mosaicism, Ageing, Chronic Diseases and Cancer. Genes (Basel) 2019; 10:genes10060407. [PMID: 31142004 PMCID: PMC6628102 DOI: 10.3390/genes10060407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence suggests that an individual is a complex mosaic of genetically divergent cells. Post-zygotic genomes of the same individual can differ from one another in the form of single nucleotide variations, copy number variations, insertions, deletions, inversions, translocations, other structural and chromosomal variations and footprints of transposable elements. High-throughput sequencing has led to increasing detection of mosaicism in healthy individuals which is related to ageing, neuro-degenerative disorders, diabetes mellitus, cardiovascular diseases and cancer. These age-related disorders are also known to be associated with significant increase in DNA damage and inflammation. Herein, we discuss a newly described phenomenon wherein the genome is under constant assault by illegitimate integration of cell-free chromatin (cfCh) particles that are released from the billions of cells that die in the body every day. We propose that such repeated genomic integration of cfCh followed by dsDNA breaks and repair by non-homologous-end-joining as well as physical damage to chromosomes occurring throughout life may lead to somatic/chromosomal mosaicism which would increase with age. We also discuss the recent finding that genomic integration of cfCh and the accompanying DNA damage is associated with marked activation of inflammatory cytokines. Thus, the triple pathologies of somatic mosaicism, DNA/chromosomal damage and inflammation brought about by a common mechanism of genomic integration of cfCh may help to provide an unifying model for the understanding of aetiologies of the inter-related conditions of ageing, degenerative disorders and cancer.
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Affiliation(s)
- Gorantla V Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Shahid Chaudhary
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Shweta Johari
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
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Increased Transfection of the Easily Oxidizable GC-Rich DNA Fragments into the MCF7 Breast Cancer Cell. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:2348165. [PMID: 30867888 PMCID: PMC6379852 DOI: 10.1155/2019/2348165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/16/2018] [Accepted: 11/14/2018] [Indexed: 01/15/2023]
Abstract
Objective Easily oxidizable GC-rich DNA (GC-DNA) fragments accumulate in the cell-free DNA (cfDNA) of patients with various diseases. The human oxidized DNA penetrates the MCF7 breast cancer cells and significantly changes their physiology. It can be assumed that readily oxidizable GC-DNA fragments can penetrate the cancer cells and be expressed. Methods MCF7 cells were cultured in the presence of two types of GC-DNA probes: (1) vectors pBR322 and pEGFP and (2) plasmids carrying inserted human rDNA (pBR322-rDNA and pEGFP-rDNA). pEGFP and pEGFP-rDNA contained a CMV promoter and a fluorescent protein gene EGFP. ROS generation rate, accumulation of the DNA probes in MCF7, 8-oxodG content, expression of EGFP and NOX4, and localization of EGFP, NOX4, and 8-oxodG in MCF7 were explored. The applied methods were qPCR, fluorescent microscopy (FM), immunoassay, and flow cytometry (FCA). Results When GC-DNA is added to the cell culture medium, it interacts with the cell surface. At the site of GC-DNA contact with the cell, NOX4 is expressed, and ROS level increases. The ROS oxidize the GC-DNA. When using the plasmids pEGFP and pEGFP-rDNA, an increase in the amount of the DNA EGFP, RNA EGFP, and EGFP proteins was detected in the cells. These facts suggest that GC-DNA penetrates the cells and the EGFP gene is expressed. Insertions of the rDNA significantly increase the GC-DNA oxidation degree as well as the rate of plasmid transfection into the cells and the EGFP expression level. In the nucleus, the oxidized GC-rDNA fragments, but not the vectors, are localized within the nucleolus. Conclusions GC-rich cfDNA fragments that are prone to oxidation can easily penetrate the cancer cells and be expressed. The cfDNA should become a target for the antitumor therapy.
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Rushton JG, Ertl R, Klein D, Tichy A, Nell B. Circulating cell-free DNA does not harbour a diagnostic benefit in cats with feline diffuse iris melanomas. J Feline Med Surg 2019; 21:124-132. [PMID: 29529957 PMCID: PMC10814613 DOI: 10.1177/1098612x18762017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Feline diffuse iris melanoma (FDIM) is the most common malignant primary intraocular tumour in cats, with reported metastases rates between 19% and 63%. Currently, the only available diagnostic tool for a tentative diagnosis is histopathological examination of the enucleated eye. Therefore, the veterinary ophthalmologist is often faced with the dilemma of whether to enucleate an oftentimes visual eye or to continue monitoring, with the risk of metastases developing. In the past, cell-free DNA (cfDNA) gained more attention in human medicine, especially in the field of oncology. Prior studies have shown the use of cfDNA as diagnostic or prognostic markers in canine and human cancer patients. Therefore, the aim of this study was to investigate cfDNA concentration and integrity in cats with FDIMs compared with cats with benign iris naevi and without ocular abnormalities. METHODS cfDNA from plasma of cats with iris melanoma (n = 34), iris naevus (n = 30) and without ocular abnormalities (n = 32) were extracted. Primer and probes for feline amyloid beta precursor protein ( APP) and beta actin ( ACTB) were designed for amplicons of various lengths and quantitative PCRs of extracted cfDNA were performed to measure cfDNA concentration and integrity of the plasma samples. Differences of cfDNA concentrations and integrity levels between the three groups (iris melanoma, iris naevi and controls) were analysed using the Mann-Whitney U-test. RESULTS cfDNA concentration and integrity analysis revealed no significant differences between the cats with iris melanoma, iris naevus or the control group ( P >0.01). Cats with metastases showed similar cfDNA concentration and integrity to cats without metastases. CONCLUSIONS AND RELEVANCE cfDNA concentration and integrity seem to be insufficient as a diagnostic or prognostic marker in cats with FDIMs.
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Affiliation(s)
- Jessica G Rushton
- Department for Companion Animals and Horses, Vetmeduni Vienna, Vienna, Austria
| | - Reinhard Ertl
- VetCore Facility for Research, Vetmeduni Vienna, Vienna, Austria
| | - Dieter Klein
- VetCore Facility for Research, Vetmeduni Vienna, Vienna, Austria
| | - Alexander Tichy
- Department of Biomedical Sciences, Vetmeduni Vienna, Vienna, Austria
| | - Barbara Nell
- Department for Companion Animals and Horses, Vetmeduni Vienna, Vienna, Austria
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