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Sue T, Ichikawa T, Hattori S, Otani H, Fujimura S, Higuchi T, Okumura N, Higuchi Y. Quantitative evaluation of citrullinated fibrinogen for detection of neutrophil extracellular traps. Immunol Res 2024; 72:409-417. [PMID: 38087184 DOI: 10.1007/s12026-023-09446-5] [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: 07/11/2023] [Accepted: 11/28/2023] [Indexed: 07/03/2024]
Abstract
Activated neutrophils release neutrophil extracellular traps (NETs) composed of chromatin filaments containing bactericidal proteins and enzymes. This process, known as NETosis, is an innate host defense mechanism. However, NET accumulation can lead to uncontrolled inflammation and organ damage. Therefore, NET detection provides clinically important information for the assessment of inflammatory conditions. We investigated whether quantification of citrullinated fibrinogen (C-Fbg), which is catalyzed by peptidylarginine deiminase (PAD) released during NETosis, can be used to detect NETs. Human neutrophils were stimulated with fibrinogen using phorbol 12-myristate 13-acetate (PMA). The myeloperoxidase (MPO)-DNA complex and C-Fbg concentrations in the culture supernatants were quantified using an enzyme-linked immunosorbent assay. The protein levels of peptidylarginine deiminase 2 and 4 in culture supernatants and mRNA levels in PMA-stimulated neutrophils were also assessed. The levels of the MPO-DNA complex in the supernatants of PMA-stimulated neutrophils increased, indicating NETosis. C-Fbg level also increased, which was suppressed by both NETosis and PAD inhibitors. PAD2 was detected in the culture supernatant; however, PAD4, but not PAD2, mRNA levels increased in PMA-stimulated neutrophils. This study quantitatively demonstrates that fibrinogen is citrullinated by PAD derived from PMA-stimulated neutrophils upon NETosis. Although further studies are needed for clinical application, quantification of C-Fbg in blood may help detect the presence of NETs.
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Affiliation(s)
- Tsubasa Sue
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Tomoki Ichikawa
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Shu Hattori
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Hikaru Otani
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Satoshi Fujimura
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Tsukasa Higuchi
- Department of General Pediatrics, Nagano Children's Hospital, Azumino, Japan
- Life Science Research Center, Nagano Children's Hospital, Azumino, Japan
| | - Nobuo Okumura
- Department of Biomedical Laboratory Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yumiko Higuchi
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
- Department of Biomedical Laboratory Sciences, Shinshu University School of Medicine, Matsumoto, Japan.
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2
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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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3
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Song HH, Park H, Cho D, Bang HI, Oh HJ, Kim J. Optimization of a Protocol for Isolating Cell-free DNA From Cerebrospinal Fluid. Ann Lab Med 2024; 44:294-298. [PMID: 38151854 PMCID: PMC10813833 DOI: 10.3343/alm.2023.0267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/01/2023] [Accepted: 12/08/2023] [Indexed: 12/29/2023] Open
Abstract
A standardized protocol for the isolation of cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) is lacking. Therefore, we established a cfDNA isolation protocol optimized for clinical CSF specimens, integrating acceptable modifications and using artificial CSF generated from remnant CSF spiked with reference cell-free tumor DNA (ctDNA). We compared the isolation yields of in vitro diagnostic (IVD)-certified column-based (CB) and magnetic bead-based (MB) isolation. Furthermore, we modified both methods, including pre- and post-elution steps. To confirm ctDNA integrity and quantify the variant allele frequency after isolation, we performed droplet digital PCR (ddPCR) targeting IDH1 R132C in the reference ctDNA. MB isolation had a higher yield than CB isolation (P<0.0001), and post-isolation vacuum increased the final concentration in both methods, with little effect on cfDNA integrity. Our study provides a protocol to maximize CSF-ctDNA concentrations in IVD testing and future studies.
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Affiliation(s)
- Ho Hyun Song
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Asan, Korea
| | - Hyeran Park
- Department of Neurosurgery, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Doohwan Cho
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Hae In Bang
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Hyuk-Jin Oh
- Department of Neurosurgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
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4
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Terp SK, Pedersen IS, Stoico MP. Extraction of Cell-Free DNA: Evaluation of Efficiency, Quantity, and Quality. J Mol Diagn 2024; 26:310-319. [PMID: 38336350 DOI: 10.1016/j.jmoldx.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/12/2024] Open
Abstract
Cell-free DNA (cfDNA) serves as a valuable biomarker for early disease detection and monitoring. However, the use of cfDNA for analysis faces challenges owing to general low but variable abundance and fragmentation. Preanalytical factors, including cfDNA extraction, impact cfDNA quality and quantity. Efficient and robust cfDNA extraction is essential for reliable results in downstream applications, and various commercial extraction methods exist, each with trade-offs. To aid researchers and clinicians in choosing the proper cfDNA extraction method, manual, semiautomated, and automated methods were evaluated, including the QIAamp Circulating Nucleic Acid Kit (manual and QIAcube), QIAamp MinElute ccfDNA Kit (QIAcube), and QIAsymphony DSP Circulating DNA Kit (QIAsymphony). For each extraction method, cfDNA was extracted on two separate days, using samples obtained from 18 healthy donors. This study assessed extraction efficiency, quantity, and quality using droplet digital PCR and TapeStation. The QIAamp Circulating Nucleic Acid Kit, both manual and semiautomated, outperformed the QIAamp MinElute ccfDNA Kit (QIAcube) and QIAsymphony DSP Circulating DNA Kit (QIAsymphony), showing higher recovery rates and cfDNA quantity. All methods were reproducible, with no day-to-day variability and no contamination by high-molecular-weight DNA. The QIAamp Circulating Nucleic Acid Kit offers high yield without compromising quality. Implementation of the method should consider specific study and clinical needs, taking into account each method's advantages and limitations for optimal outcomes.
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Affiliation(s)
- Simone K Terp
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| | - Inge S Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Malene P Stoico
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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van der Leest P, Schuuring E. Critical Factors in the Analytical Work Flow of Circulating Tumor DNA-Based Molecular Profiling. Clin Chem 2024; 70:220-233. [PMID: 38175597 DOI: 10.1093/clinchem/hvad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Liquid biopsy testing, especially molecular tumor profiling of circulating tumor DNA (ctDNA) in cell-free plasma, has received increasing interest in recent years as it serves as a reliable alternative for the detection of tumor-specific aberrations to guide treatment decision-making in oncology. Many (commercially available) applications have been developed, however, broad divergences in (pre)analytical work flows and lack of universally applied guidelines impede routine clinical implementation. In this review, critical factors in the blood-based ctDNA liquid biopsy work flow are evaluated. CONTENT In the preanalytical phase, several aspects (e.g., blood collection tubes [BCTs], plasma processing, and extraction method) affect the quantity and quality of the circulating cell-free DNA (ccfDNA) applicable for subsequent molecular analyses and should meet certain standards to be applied in diagnostic work flows. Analytical considerations, such as analytical input and choice of assay, might vary based on the clinical application (i.e., screening, primary diagnosis, minimal residual disease [MRD], response monitoring, and resistance identification). In addition to practical procedures, variant interpretation and reporting ctDNA results should be harmonized. Collaborative efforts in (inter)national consortia and societies are essential for the establishment of standard operating procedures (SOPs) in attempts to standardize the plasma-based ctDNA analysis work flow. SUMMARY Development of universally applicable guidelines regarding the critical factors in liquid biopsy testing are necessary to pave the way to clinical implementation for routine diagnostics.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Bronkhorst AJ, Holdenrieder S. A pocket companion to cell-free DNA (cfDNA) preanalytics. Tumour Biol 2024; 46:S297-S308. [PMID: 37840517 DOI: 10.3233/tub-230011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
The cumulative pool of cell-free DNA (cfDNA) molecules within bodily fluids represents a highly dense and multidimensional information repository. This "biological mirror" provides real-time insights into the composition, function, and dynamics of the diverse genomes within the body, enabling significant advancements in personalized molecular medicine. However, effective use of this information necessitates meticulous classification of distinct cfDNA subtypes with exceptional precision. While cfDNA molecules originating from different sources exhibit numerous genetic, epigenetic, and physico-chemical variations, they also share common features that complicate analyses. Considerable progress has been achieved in mapping the landscape of cfDNA features, their clinical correlations, and optimizing extraction procedures, analytical approaches, bioinformatics pipelines, and machine learning algorithms. Nevertheless, preanalytical workflows, despite their profound impact on cfDNA measurements, have not progressed at a corresponding pace. In this perspective article, we emphasize the pivotal role of robust preanalytical procedures in the development and clinical integration of cfDNA assays, highlighting persistent obstacles and emerging challenges.
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Affiliation(s)
- Abel J Bronkhorst
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, Munich, Germany
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7
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Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
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Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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Lelliott PM, Hobro AJ, Pavillon N, Nishide M, Okita Y, Mizuno Y, Obata S, Nameki S, Yoshimura H, Kumanogoh A, Smith NI. Single-cell Raman microscopy with machine learning highlights distinct biochemical features of neutrophil extracellular traps and necrosis. Sci Rep 2023; 13:10093. [PMID: 37344494 DOI: 10.1038/s41598-023-36667-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
The defining biology that distinguishes neutrophil extracellular traps (NETs) from other forms of cell death is unresolved, and techniques which unambiguously identify NETs remain elusive. Raman scattering measurement provides a holistic overview of cell molecular composition based on characteristic bond vibrations in components such as lipids and proteins. We collected Raman spectra from NETs and freeze/thaw necrotic cells using a custom built high-throughput platform which is able to rapidly measure spectra from single cells. Principal component analysis of Raman spectra from NETs clearly distinguished them from necrotic cells despite their similar morphology, demonstrating their fundamental molecular differences. In contrast, classical techniques used for NET analysis, immunofluorescence microscopy, extracellular DNA, and ELISA, could not differentiate these cells. Additionally, machine learning analysis of Raman spectra indicated subtle differences in lipopolysaccharide (LPS)-induced as opposed to phorbol myristate acetate (PMA)-induced NETs, demonstrating the molecular composition of NETs varies depending on the stimulant used. This study demonstrates the benefits of Raman microscopy in discriminating NETs from other types of cell death and by their pathway of induction.
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Affiliation(s)
- Patrick Michael Lelliott
- Laboratory of Biophotonics, Immunology Frontier Research Center, Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan.
| | - Alison Jane Hobro
- Laboratory of Biophotonics, Immunology Frontier Research Center, Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan
| | - Nicolas Pavillon
- Laboratory of Biophotonics, Immunology Frontier Research Center, Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan
| | - Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yasutaka Okita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yumiko Mizuno
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Sho Obata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinichiro Nameki
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hanako Yoshimura
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory of Immunopathology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Open and Transdisciplinary Research Institute (OTRI), Osaka University, Osaka, Japan
| | - Nicholas Isaac Smith
- Laboratory of Biophotonics, Immunology Frontier Research Center, Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan.
- Open and Transdisciplinary Research Institute (OTRI), Osaka University, Osaka, Japan.
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Assi T, Khoury R, Ibrahim R, Baz M, Ibrahim T, LE Cesne A. Overview of the role of liquid biopsy in cancer management. Transl Oncol 2023; 34:101702. [PMID: 37267803 DOI: 10.1016/j.tranon.2023.101702] [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: 01/30/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023] Open
Abstract
With the emergence of novel targeted therapeutic options in early-stage and advanced-stage malignancies, researchers have shifted their focus on developing personalized treatment plans through molecular profiling. Circulating tumor DNA (ctDNA) is a cell-free DNA (ctDNA) fragment, originating from tumor cells, and circulating in the bloodstream as well as biological fluids. Over the past decade, many techniques were developed for liquid biopsies through next-generation sequencing. This alternative non-invasive biopsy offers several advantages in various types of tumors over traditional tissue biopsy. The process of liquid biopsy is considered minimally invasive and therefore easily repeatable when needed, providing a more dynamic analysis of the tumor cells. Moreover, it has an advantage in patients with tumors that are not candidates for tissue sampling. Besides, it offers a deeper understanding of tumor burden as well as treatment response, thereby enhancing the detection of minimal residual disease and therapeutic guidance for personalized medicine. Despite its many advantages, ctDNA and liquid biopsy do have some limitations. This paper discusses the basis of ctDNA and the current data available on the subject, as well as its clinical utility. We also reflect on the limitations of using ctDNA in addition to its future perspectives in clinical oncology and precision medicine.
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Affiliation(s)
- Tarek Assi
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France.
| | - Rita Khoury
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Rebecca Ibrahim
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Maria Baz
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Tony Ibrahim
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Axel LE Cesne
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
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11
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Diaz IM, Nocon A, Held SAE, Kobilay M, Skowasch D, Bronkhorst AJ, Ungerer V, Fredebohm J, Diehl F, Holdenrieder S, Holtrup F. Pre-Analytical Evaluation of Streck Cell-Free DNA Blood Collection Tubes for Liquid Profiling in Oncology. Diagnostics (Basel) 2023; 13:diagnostics13071288. [PMID: 37046506 PMCID: PMC10093569 DOI: 10.3390/diagnostics13071288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Excellent pre-analytical stability is an essential precondition for reliable molecular profiling of circulating tumor DNA (ctDNA) in oncological diagnostics. Therefore, in vitro degradation of ctDNA and the additional release of contaminating genomic DNA from lysed blood cells must be prevented. Streck Cell-Free DNA blood collection tubes (cfDNA BCTs) have proposed advantages over standard K2EDTA tubes, but mainly have been tested in healthy individuals. Blood was collected from cancer patients (n = 53) suffering from colorectal (n = 21), pancreatic (n = 11), and non-small-cell lung cancer (n = 21) using cfDNA BCT tubes and K2EDTA tubes that were processed immediately or after 3 days (BCTs) or 6 hours (K2EDTA) at room temperature. The cfDNA isolated from these samples was characterized in terms of yield using LINE-1 qPCR; the level of gDNA contamination; and the mutation status of KRAS, NRAS, and EGFR genes using BEAMing ddPCR. CfDNA yield and gDNA levels were comparable in both tube types and were not affected by prolonged storage of blood samples for at least 3 days in cfDNA BCTs or 6 hours in K2EDTA tubes. In addition, biospecimens collected in K2EDTA tubes and cfDNA BCTs stored for up to 3 days demonstrated highly comparable levels of mutational load across all respective cancer patient cohorts and a wide range of concentrations. Our data support the applicability of clinical oncology specimens collected and stored in cfDNA BCTs for up to 3 days for reliable cfDNA and mutation analyses.
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12
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Dameri M, Cirmena G, Ravera F, Ferrando L, Cuccarolo P, Stabile M, Fanelli GN, Nuzzo PV, Calabrese M, Tagliafico A, Ballestrero A, Zoppoli G. Standard Operating Procedures (SOPs) for non-invasive multiple biomarkers detection in an academic setting: a critical review of the literature for the RENOVATE study protocol. Crit Rev Oncol Hematol 2023; 185:103963. [PMID: 36931614 DOI: 10.1016/j.critrevonc.2023.103963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 03/17/2023] Open
Abstract
Liquid biopsy has the potential to drastically change clinical practice, paving the way to a novel non-invasive approach for cancer diagnosis and treatment. One of the limitations for the implementation of liquid biopsy in clinical practice is the lack of shared and reproducible standard operating procedures (SOPs) for sample collection, processing and storage. Here, we present a critical review of the literature focusing on the available SOPs to guide liquid biopsy management in research settings and describe SOPs that our laboratory developed and employed in the context of a prospective clinical-translational trial (RENOVATE, NCT04781062). The main aim of this manuscript is to address common issues, towards the implementation of interlaboratory shared protocols for optimized preanalytical handling of blood and urine samples. To our knowledge, this work is one of the few up-to-date, freely available comprehensive reports on trial-level procedures for the handling of liquid biopsy.
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Affiliation(s)
- Martina Dameri
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | | | - Francesco Ravera
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, 10044, New York, NY, USA
| | | | - Paola Cuccarolo
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | - Mario Stabile
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | - Giuseppe Nicolò Fanelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 10021, New York, NY, USA; First Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Pier Vitale Nuzzo
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, 10044, New York, NY, USA
| | | | - Alberto Tagliafico
- IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy; Department of Health Sciences DISSAL, University of Genoa, 16132, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
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13
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Aucamp J, van der Zwan H, Geldenhuys Z, Abera A, Louw R, van der Sluis R. Diagnostic applications and limitations for the use of cell-free fetal DNA (cffDNA) in animal husbandry and wildlife management. Res Vet Sci 2023; 158:106-116. [PMID: 36989830 DOI: 10.1016/j.rvsc.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/02/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
In animal breeding, a species sex can influence the value of the animal. For example, in the horse breeding industry, mares are preferred as polo horses, while in wildlife breeding males with larger horns are more valuable. Therefore, the economic advantages of knowing the unborn fetus' sex are important to successful animal management. Ultrasonography is used to determine the sex of unborn fetuses, but this method places additional stress on the animal and require specialized equipment and expertise. Conversely, molecular-based sexing techniques require less invasive sampling and can determine sex more reliably. Although in humans, various studies have evaluated the use of cell-free fetal DNA (cffDNA) for prenatal sexing, very few animal studies have been published in this field. Several factors can affect the sensitivity of cffDNA-based sex determination, for example the gestational age. These factors are often not optimized and validated when establishing a protocol for prenatal sexing. In this review, we summarize the current literature on cffDNA in animals. We discuss the diagnostic applications and limitations in the use thereof in animal husbandry and wildlife management. Lastly, the feasibility of implementing diagnostic tests is evaluated and solutions are given to the current drawbacks of the technology.
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14
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Soscia R, Della Starza I, De Novi LA, Ilari C, Ansuinelli M, Cavalli M, Bellomarino V, Cafforio L, Di Trani M, Cazzaniga G, Fazio G, Santoro A, Salemi D, Spinelli O, Tosi M, Terragna C, Robustelli V, Bellissimo T, Colafigli G, Breccia M, Chiaretti S, Di Rocco A, Martelli M, Guarini A, Del Giudice I, Foà R. Circulating cell-free DNA for target quantification in hematologic malignancies: Validation of a protocol to overcome pre-analytical biases. Hematol Oncol 2023; 41:50-60. [PMID: 36251440 DOI: 10.1002/hon.3087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 02/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has become the most investigated analyte in blood. It is shed from the tumor into the circulation and represents a subset of the total cell-free DNA (cfDNA) pool released into the peripheral blood. In order to define if ctDNA could represent a useful tool to monitor hematologic malignancies, we analyzed 81 plasma samples from patients affected by different diseases. The results showed that: (i) the comparison between two different extraction methods Qiagen (Hilden, Germany) and Promega (Madison, WI) showed no significant differences in cfDNA yield, though the first recovered higher amounts of larger DNA fragments; (ii) cfDNA concentrations showed a notable inter-patient variability and differed among diseases: acute lymphoblastic leukemia and chronic myeloid leukemia released higher amounts of cfDNA than chronic lymphocytic leukemia, and diffuse large B-cell lymphoma released higher cfDNA quantities than localized and advanced follicular lymphoma; (iii) focusing on the tumor fraction of cfDNA, the quantity of ctDNA released was insufficient for an adequate target quantification for minimal residual disease monitoring; (iv) an amplification system proved to be free of analytical biases and efficient in increasing ctDNA amounts at diagnosis and in follow-up samples as shown by droplet digital PCR target quantification. The protocol has been validated by quality control rounds involving external laboratories. To conclusively document the feasibility of a ctDNA-based monitoring of patients with hematologic malignancies, more post-treatment samples need to be evaluated. This will open new possibilities for ctDNA use in the clinical practice.
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Affiliation(s)
- Roberta Soscia
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy.,GIMEMA Foundation, Rome, Italy
| | - Lucia Anna De Novi
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Caterina Ilari
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Michela Ansuinelli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Marzia Cavalli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Vittorio Bellomarino
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Luciana Cafforio
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Mariangela Di Trani
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Giovanni Cazzaniga
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Grazia Fazio
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Alessandra Santoro
- Division of Hematology and Bone Marrow Transplantation, Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Domenico Salemi
- Division of Hematology and Bone Marrow Transplantation, Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Orietta Spinelli
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Manuela Tosi
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Carolina Terragna
- Seràgnoli Institute of Hematology, Azienda Ospedaliero-Universitaria Sant'Orsola-Malpighi, Bologna, Italy
| | - Valentina Robustelli
- Dipartimento di Medicina Specialistica Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Teresa Bellissimo
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Gioia Colafigli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Massimo Breccia
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Sabina Chiaretti
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Alice Di Rocco
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Maurizio Martelli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Anna Guarini
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy.,Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Ilaria Del Giudice
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
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15
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Optimizing Molecular Minimal Residual Disease Analysis in Adult Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:cancers15020374. [PMID: 36672325 PMCID: PMC9856386 DOI: 10.3390/cancers15020374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Minimal/measurable residual disease (MRD) evaluation has resulted in a fundamental instrument to guide patient management in acute lymphoblastic leukemia (ALL). From a methodological standpoint, MRD is defined as any approach aimed at detecting and possibly quantifying residual neoplastic cells beyond the sensitivity level of cytomorphology. The molecular methods to study MRD in ALL are polymerase chain reaction (PCR) amplification-based approaches and are the most standardized techniques. However, there are some limitations, and emerging technologies, such as digital droplet PCR (ddPCR) and next-generation sequencing (NGS), seem to have advantages that could improve MRD analysis in ALL patients. Furthermore, other blood components, namely cell-free DNA (cfDNA), appear promising and are also being investigated for their potential role in monitoring tumor burden and response to treatment in hematologic malignancies. Based on the review of the literature and on our own data, we hereby discuss how emerging molecular technologies are helping to refine the molecular monitoring of MRD in ALL and may help to overcome some of the limitations of standard approaches, providing a benefit for the care of patients.
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16
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Maurer K, Schandl CA. Liquid Biopsy for Advanced Cancer: An Amplicon-Based Massively Parallel Sequencing Panel Approach to Precision Oncology. Methods Mol Biol 2023; 2621:111-126. [PMID: 37041443 DOI: 10.1007/978-1-0716-2950-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Although discovered in the 1940s (Mandel and Metais, C R Seances Soc Biol Fil 142:241-243, 1948), cell-free DNA has only recently become a tool practical for use in clinical settings. The challenges associated with detection of circulating tumor DNA (ctDNA) in patient plasma are many and exist in the pre-analytical, analytical, and post-analytical periods. Initiation of a ctDNA program in a small academic clinical laboratory setting can be challenging. Thus, cost-effective, fast methods should be leveraged to promote a self-supporting system. Any assay should be based on clinical utility and have the potential to adapt in order to maintain relevance in a rapidly developing genomic landscape. Herein is described one of many approaches to ctDNA mutation testing - a massively parallel sequencing (MPS) method that is widely applicable and relatively easy to perform. Sensitivity and specificity are enhanced by unique molecular identification tagging and deep sequencing.
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Affiliation(s)
- Kristen Maurer
- Medical University of South Carolina, Charleston, SC, USA
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17
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Zhao Z, Pan Z, Zhang S, Ma G, Zhang W, Song J, Wang Y, Kong L, Du G. Neutrophil extracellular traps: A novel target for the treatment of stroke. Pharmacol Ther 2023; 241:108328. [PMID: 36481433 DOI: 10.1016/j.pharmthera.2022.108328] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Stroke is a threatening cerebrovascular disease caused by thrombus with high morbidity and mortality rates. Neutrophils are the first to be recruited in the brain after stroke, which aggravate brain injury through multiple mechanisms. Neutrophil extracellular traps (NETs), as a novel regulatory mechanism of neutrophils, can trap bacteria and secret antimicrobial molecules, thereby degrading pathogenic factors and killing bacteria. However, NETs also exacerbate certain non-infectious diseases by activating autoimmune or inflammatory responses. NETs have been found to play important roles in the pathological process of stroke in recent years. In this review, the mechanisms of NETs formation, the physiological roles of NETs, and the dynamic changes of NETs after stroke are summarized. NETs participate in stroke through various mechanisms. NETs promote the coagulation cascade and interact with platelets to induce thrombosis. tPA induces the degranulation of neutrophils to form NETs, leading to hemorrhagic transformation and thrombolytic resistance. NETs aggravate stroke by mediating inflammation, atherosclerosis and vascular injury. In addition, the regulation of NETs in stroke, the potential of NETs as biomarker and the treatment of stroke targeting NETs are discussed. The increasing evidences suggest that NETs may be a potential target for stroke treatment. Inhibition of NETs formation or promotion of NETs degradation plays protective effects in stroke. However, how to avoid the adverse effects of NETs-targeted therapy deserves further study. In summary, this review provides a reference for the pathogenesis, drug targets, biomarkers and drug development of NETs in stroke.
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Affiliation(s)
- Ziyuan Zhao
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Zirong Pan
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Sen Zhang
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Guodong Ma
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Wen Zhang
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Junke Song
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yuehua Wang
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Linglei Kong
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Guanhua Du
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
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18
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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19
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Fathima N, Manorenj S, Vishwakarma SK, Khan AA. Role of cell-free DNA for predicting incidence and outcome of patients with ischemic stroke. World J Neurol 2022; 8:1-9. [DOI: 10.5316/wjn.v8.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/11/2022] [Accepted: 07/31/2022] [Indexed: 02/08/2023] Open
Abstract
Early diagnosis and prognosis of ischemic stroke remains a critical challenge in clinical settings. A blood biomarker can be a promising quantitative tool to represent the clinical manifestations in ischemic stroke. Cell-free DNA (cfDNA) has recently turned out to be a popular circulating biomarker due to its potential relevance for diagnostic applications in a variety of disorders. Despite bright outlook of cfDNA in clinical applications, very less is known about its origin, composition, or function. Several recent studies have identified cell-derived mitochondrial components including mitochondrial DNA (mtDNA) in the extracellular spaces including blood and cerebrospinal fluid. However, the time course of alterations in plasma mtDNA concentrations in patients after an ischemic stroke is poorly understood. DNA is thought to be freed into the plasma shortly after the commencement of an ischemic stroke and then gradually decreased. However, the importance of cell-free mtDNA (cf-mtDNA) in ischemic stroke is still unknown. This review summarizes about the utility of biomarkers which has been standardized in clinical settings and role of cfDNA including cf-mtDNA as a non-invasive potential biomarker of ischemic stroke.
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Affiliation(s)
- Nusrath Fathima
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad 500058, Telangana, India
| | - Sandhya Manorenj
- Department of Neurology, Princess Esra Hospital, Deccan College of Medical Sciences, Hyderabad 500002, Telangana, India
| | - Sandeep Kumar Vishwakarma
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad 500058, Telangana, India
| | - Aleem Ahmed Khan
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad 500058, Telangana, India
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20
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Preanalytical Variables in the Analysis of Mitochondrial DNA in Whole Blood and Plasma from Pancreatic Cancer Patients. Diagnostics (Basel) 2022; 12:diagnostics12081905. [PMID: 36010255 PMCID: PMC9406772 DOI: 10.3390/diagnostics12081905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 02/07/2023] Open
Abstract
Given the crucial role of mitochondria as the main cellular energy provider and its contribution towards tumor growth, chemoresistance, and cancer cell plasticity, mitochondrial DNA (mtDNA) could serve as a relevant biomarker. Thus, the profiling of mtDNA mutations and copy number variations is receiving increasing attention for its possible role in the early diagnosis and monitoring therapies of human cancers. This applies particularly to highly aggressive pancreatic cancer, which is often diagnosed late and is associated with poor prognosis. As current diagnostic procedures are based on imaging, tissue histology, and protein biomarkers with rather low specificity, tumor-derived mtDNA mutations detected from whole blood represents a potential significant leap forward towards early cancer diagnosis. However, for future routine use in clinical settings it is essential that preanalytics related to the characterization of mtDNA in whole blood are thoroughly standardized, controlled, and subject to proper quality assurance, yet this is largely lacking. Therefore, in this study we carried out a comprehensive preanalytical workup comparing different mtDNA extraction methods and testing important preanalytical steps, such as the use of different blood collection tubes, different storage temperatures, length of storage time, and yields in plasma vs. whole blood. To identify analytical and preanalytical differences, all variables were tested in both healthy subjects and pancreatic carcinoma patients. Our results demonstrated a significant difference between cancer patients and healthy subjects for some preanalytical workflows, while other workflows failed to yield statistically significant differences. This underscores the importance of controlling and standardizing preanalytical procedures in the development of clinical assays based on the measurement of mtDNA.
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21
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Cell-Free DNA Fragmentation Patterns in a Cancer Cell Line. Diagnostics (Basel) 2022; 12:diagnostics12081896. [PMID: 36010246 PMCID: PMC9406536 DOI: 10.3390/diagnostics12081896] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 12/20/2022] Open
Abstract
Unique bits of genetic, biological and pathological information occur in differently sized cell-free DNA (cfDNA) populations. This is a significant discovery, but much of the phenomenon remains to be explored. We investigated cfDNA fragmentation patterns in cultured human bone cancer (143B) cells using increasingly sensitive electrophoresis assays, including four automated microfluidic capillary electrophoresis assays from Agilent, i.e., DNA 1000, High Sensitivity DNA, dsDNA 915 and dsDNA 930, and an optimized manual agarose gel electrophoresis protocol. This comparison showed that (i) as the sensitivity and resolution of the sizing methods increase incrementally, additional nucleosomal multiples are revealed (hepta-nucleosomes were detectable with manual agarose gel electrophoresis), while the estimated size range of high molecular weight (HMW) cfDNA fragments narrow correspondingly; (ii) the cfDNA laddering pattern extends well beyond the 1–3 nucleosomal multiples detected by commonly used methods; and (iii) the modal size of HMW cfDNA populations is exaggerated due to the limited resolving power of electrophoresis, and instead consists of several poly-nucleosomal subpopulations that continue the series of DNA laddering. Furthermore, the most sensitive automated assay used in this study (Agilent dsDNA 930) revealed an exponential decay in the relative contribution of increasingly longer cfDNA populations. This power-law distribution suggests the involvement of a stochastic inter-nucleosomal DNA cleavage process, wherein shorter populations accumulate rapidly as they are fed by the degradation of all larger populations. This may explain why similar size profiles have historically been reported for cfDNA populations originating from different processes, such as apoptosis, necrosis, accidental cell lysis and purported active release. These results not only demonstrate the diversity of size profiles generated by different methods, but also highlight the importance of caution when drawing conclusions on the mechanisms that generate different cfDNA size populations, especially when only a single method is used for sizing.
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22
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Sánchez-Herrero E, Serna-Blasco R, Robado de Lope L, González-Rumayor V, Romero A, Provencio M. Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis. Front Oncol 2022; 12:943253. [PMID: 35936733 PMCID: PMC9350013 DOI: 10.3389/fonc.2022.943253] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer cells release nucleic acids, freely or associated with other structures such as vesicles into body fluids, including blood. Among these nucleic acids, circulating tumor DNA (ctDNA) has emerged as a minimally invasive biomarker for tumor molecular profiling. However, certain biological characteristics of ctDNA are still unknown. Here, we provide an overview of the current knowledge about ctDNA biological features, including size and structure as well as the mechanisms of ctDNA shedding and clearance, and the physio-pathological factors that determine ctDNA levels. A better understanding of ctDNA biology is essential for the development of new methods that enable the analysis of ctDNA.
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Affiliation(s)
- Estela Sánchez-Herrero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- +D Department, Atrys Health, Barcelona, Spain
| | - Roberto Serna-Blasco
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | - Lucia Robado de Lope
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | | | - Atocha Romero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
- *Correspondence: Atocha Romero, ; orcid.org/0000-0002-1634-7397
| | - Mariano Provencio
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
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23
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Doculara L, Trahair TN, Bayat N, Lock RB. Circulating Tumor DNA in Pediatric Cancer. Front Mol Biosci 2022; 9:885597. [PMID: 35647029 PMCID: PMC9133724 DOI: 10.3389/fmolb.2022.885597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.
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Affiliation(s)
- Louise Doculara
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Narges Bayat
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B. Lock
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Richard B. Lock,
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24
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Haselmann V, Hedtke M, Neumaier M. Liquid Profiling for Cancer Patient Stratification in Precision Medicine—Current Status and Challenges for Successful Implementation in Standard Care. Diagnostics (Basel) 2022; 12:diagnostics12030748. [PMID: 35328301 PMCID: PMC8947441 DOI: 10.3390/diagnostics12030748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating tumor DNA (ctDNA), accurately described by the term liquid profiling (LP), enables real-time assessment of the tumor mutational profile as a minimally invasive test and has therefore rapidly gained traction, particular for the management of cancer patients. By LP, tumor-specific genetic alterations can be determined as part of companion diagnostics to guide selection of appropriate targeted therapeutics. Because LP facilitates longitudinal monitoring of cancer patients, it can be used to detect acquired resistant mechanisms or as a personalized biomarker for earlier detection of disease recurrence, among other applications. However, LP is not yet integrated into routine care to the extent that might be expected. This is due to the lack of harmonization and standardization of preanalytical and analytical workflows, the lack of proper quality controls, limited evidence of its clinical utility, heterogeneous study results, the uncertainty of clinicians regarding the value and appropriate indications for LP and its interpretation, and finally, the lack of reimbursement for most LP tests. In this review, the value proposition of LP for cancer patient management and treatment optimization, the current status of implementation in standard care, and the main challenges that need to be overcome are discussed in detail.
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Morita S, Nakamaru Y, Fukuda A, Fujiwara K, Suzuki M, Hoshino K, Honma A, Homma A. The Quantification of Extracellular Trap Cell Death-Derived Products as Diagnostic Biomarkers for Otitis Media With Antineutrophil Cytoplasmic Antibody-Associated Vasculitis and Eosinophilic Otitis Media. Otol Neurotol 2022; 43:e337-e343. [PMID: 34802016 DOI: 10.1097/mao.0000000000003431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE This study aimed to quantify the cell-free deoxyribonucleic acid (DNA), citrullinated-histone H3 (cit-H3)-DNA complex, and myeloperoxidase (MPO)-DNA complex as extracellular trap cell death (ETosis)-derived products in the middle ear fluid, and to identify diagnostic biomarkers for the discrimination of antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (OMAAV) from eosinophilic otitis media (EOM). STUDY DESIGN Prospective study. SETTING Tertiary referral center. PATIENTS OMAAV patients were eligible for inclusion in this analysis. Patients with EOM were examined as controls. INTERVENTION All samples were obtained from the middle ear fluid in patients with OMAAV or EOM. The fluid samples were aspirated from the middle ear through the anterior-inferior portion of the tympanic membrane using a 1-ml tuberculin syringe with a 24- or 26-gauge needle under a microscope. MAIN OUTCOME MEASURES The levels of cell-free DNA, cit-H3-DNA complex and MPO-DNA complex in the fluid samples were quantified using an enzyme-linked immunosorbent assay. RESULTS Patients with OMAAV showed significantly higher levels of MPO-DNA complex compared to patients with EOM, regardless of the serum ANCA status at the time of sampling (p < 0.001 and p < 0.001, respectively). Meanwhile, there were no significant differences in the values of cell-free DNA or cit-H3-DNA complex between the OMAAV and EOM patients. CONCLUSION The findings of this study suggest that the detection and quantification of MPO-DNA complex in the otitis media fluid can be utilized to discriminate OMAAV, especially in cases of eosinophilic granulomatosis with polyangiitis, from EOM regardless of the serum ANCA status. It should be noted that it is possible for cell-free DNA and cit-H3-DNA complex in fluid samples to be derived from dead cells other than neutrophils that undergo ETosis.
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Affiliation(s)
- Shinya Morita
- Department of Otolaryngology - Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
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Kondratskaya VA, Pokrovskaya MS, Doludin YV, Borisova AL, Limonova AS, Meshkov АN, Drapkina OM. Influence of preanalytical variables on the quality of cell-free DNA. Biobanking of cell-free DNA material. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2021-3114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The search for early disease markers and the development of diagnostic systems has recently been expanding within genomics. Genomic deoxyribonucleic acid (DNA), cell-free DNA (cfDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. It has been shown that cfDNA that enters the bloodstream, in particular, as a result of apoptosis, necrosis, active tumor secretion and metastasis, is of great importance for studying molecular mechanisms of the pathological process and application in clinical practice. Circulating nucleic acid analysis can be used to monitor response to treatment, assess drug resistance, and quantify minimal residual disease. The review article reflects the following information about the biomaterial: source of cfDNA, methods of cfDNA isolation, storage and use for the diagnosis of certain diseases. Cell-free DNA can be present in biological fluids such as blood, urine, saliva, synovial and cerebrospinal fluid. In most cases, cfDNA is isolated from blood derivatives (serum and plasma), while it is most correct to use blood plasma for cfDNA isolation. Optimal and economically justifiable is the use of ethylenediaminetetra-acetic acid tubes for taking blood and obtaining plasma with subsequent cfDNA isolation. There is evidence that the optimal shelf life in an ethylenediaminetetra-acetic acid tube from the moment of blood sampling to subsequent isolation is a 2-hour interval. After centrifugation, cfDNA in plasma (or serum) can be stored for a long time at a temperature of -80O C. Storage at -20O C is undesirable, since DNA fragmentation increases.
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Affiliation(s)
| | - M. S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | - Yu. V. Doludin
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. L. Borisova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. S. Limonova
- National Medical Research Center for Therapy and Preventive Medicine
| | - А. N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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Van Paemel R, Vandeputte C, Raman L, Van Thorre J, Willems L, Van Dorpe J, Van Der Linden M, De Wilde J, De Koker A, Menten B, Devalck C, Vicha A, Grega M, Schleiermacher G, Iddir Y, Chicard M, van Zogchel L, Stutterheim J, Lak NSM, Tytgat GAM, Laureys G, Speleman F, De Wilde B, Lammens T, De Preter K, Van Roy N. The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples. Eur J Cancer 2021; 160:12-23. [PMID: 34794856 DOI: 10.1016/j.ejca.2021.09.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/27/2021] [Accepted: 09/11/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity. PROCEDURE The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma. RESULTS Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification. CONCLUSION In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.
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Affiliation(s)
- Ruben Van Paemel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Research Foundation Flanders, Belgium
| | - Charlotte Vandeputte
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Raman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jolien Van Thorre
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Leen Willems
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Malaïka Van Der Linden
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jilke De Wilde
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, Flemish Institute Biotechnology (VIB), Ghent, Belgium; Research Foundation Flanders, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Ales Vicha
- Department of Pediatric Hematology and Oncology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marek Grega
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Gudrun Schleiermacher
- Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
| | - Yasmine Iddir
- Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
| | - Mathieu Chicard
- Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
| | - Lieke van Zogchel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | | | - Nathalie S M Lak
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - G A M Tytgat
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Geneviève Laureys
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bram De Wilde
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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Vogt SL, Patel M, Lakha A, Philip V, Omar T, Ashmore P, Pather S, Haley LM, Zheng G, Stone J, Mayne E, Stevens W, Wagner-Johnston N, Gocke CD, Martinson NA, Ambinder RF, Xian RR. Feasibility of Cell-Free DNA Collection and Clonal Immunoglobulin Sequencing in South African Patients With HIV-Associated Lymphoma. JCO Glob Oncol 2021; 7:611-621. [PMID: 33909482 PMCID: PMC8162966 DOI: 10.1200/go.20.00651] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Diagnosis of AIDS lymphoma in low-resource settings, like South Africa, is often delayed, leaving patients with limited treatment options. In tuberculosis (TB) endemic regions, overlapping signs and symptoms often lead to diagnostic delays. Assessment of plasma cell-free DNA (cfDNA) by next-generation sequencing (NGS) may expedite the diagnosis of lymphoma but requires high-quality cfDNA. METHODS People living with HIV with newly diagnosed aggressive B-cell lymphoma and those with newly diagnosed TB seeking care at Chris Hani Baragwanath Academic Hospital and its surrounding clinics, in Soweto, South Africa, were enrolled in this study. Each participant provided a whole blood specimen collected in cell-stabilizing tubes. Quantity and quality of plasma cfDNA were assessed. NGS of the immunoglobulin heavy chain was performed. RESULTS Nine HIV+ patients with untreated lymphoma and eight HIV+ patients with TB, but without lymphoma, were enrolled. All cfDNA quantity and quality metrics were similar between the two groups, except that cfDNA accounted for a larger fraction of recovered plasma DNA in patients with lymphoma. The concentration of cfDNA in plasma also trended higher in patients with lymphoma. NGS of immunoglobulin heavy chain showed robust amplification of DNA, with large amplicons (> 250 bp) being more readily detected in patients with lymphoma. Clonal sequences were detected in five of nine patients with lymphoma, and none of the patients with TB. CONCLUSION This proof-of-principle study demonstrates that whole blood collected for cfDNA in a low-resource setting is suitable for sophisticated sequencing analyses, including clonal immunoglobulin NGS. The detection of clonal sequences in more than half of patients with lymphoma shows promise as a diagnostic marker that may be explored in future studies.
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Affiliation(s)
- Samantha L Vogt
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Moosa Patel
- Clinical Haematology Unit, Department of Medicine, Chris Hani Baragwanath Academic Hospital and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Atul Lakha
- Clinical Haematology Unit, Department of Medicine, Chris Hani Baragwanath Academic Hospital and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vinitha Philip
- Clinical Haematology Unit, Department of Medicine, Chris Hani Baragwanath Academic Hospital and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tanvier Omar
- Division of Anatomical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Philippa Ashmore
- Clinical Haematology, Netcare Olivedale Hospital, Johannesburg, South Africa
| | - Sugeshnee Pather
- Division of Anatomical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lisa M Haley
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Gang Zheng
- Department of Pathology, Mayo Clinic, Rochester, MN
| | - Jennifer Stone
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Elizabeth Mayne
- Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Wendy Stevens
- Department of Immunology, Faculty of Health Sciences, University of Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Nina Wagner-Johnston
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Neil A Martinson
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD.,Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Richard F Ambinder
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD.,Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Rena R Xian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
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The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes. Surgeon 2021; 20:e163-e173. [PMID: 34362650 DOI: 10.1016/j.surge.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Liquid biopsy is gaining increasing clinical utility in the management of cancer patients. The main components of a liquid biopsy are circulating nucleic acids, circulating tumour cells and extracellular vesicles such as exosomes. Circulating nucleic acids including cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) in particular have been the focus of recent attention as they have demonstrated excellent potential in cancer screening, provision of prognostic information and in genomic profiling of a tumour without the need for repeated tissue biopsies. The aim of this review was to explore the current evidence in relation to the use of liquid biopsy in the perioperative setting and identify ways in which liquid biopsy may be applied in the future. METHODS This narrative review is based on a comprehensive literature search up to the 1st of June 2020 for papers relevant to the application of liquid biopsy in surgical oncology, focusing particularly on the perioperative period. RESULTS Recent evidence has demonstrated that perioperative liquid biopsy can accurately stratify patients' risk of recurrence compared to conventional biomarkers. Attention to the perioperative dynamics of liquid biopsy components can potentially provide new understanding of the complex relationship between surgery and cancer outcome. In addition, careful evaluation of liquid biopsy components in the perioperative window may provide important diagnostic and therapeutic information for cancer patients. CONCLUSION The rapidly evolving concept of the liquid biopsy has the potential to become the cornerstone for decision making around surveillance and adjuvant therapies the era of personalised medicine.
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Samoila A, Sosa J, Padilla J, Wutkowski M, Vanness K, Viale A, Berger M, Houck-Loomis B, Pessin M, Peerschke EI. Developing Quality Programs for Cell-Free DNA (cfDNA) Extraction from Peripheral Blood. J Appl Lab Med 2021; 5:788-797. [PMID: 32603443 DOI: 10.1093/jalm/jfaa050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 01/09/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Cell-free DNA (cfDNA) analysis using peripheral blood represents an exciting, minimally invasive technology for cancer diagnosis and monitoring. The reliability of testing is dependent on the accuracy and sensitivity of specific molecular analyses to detect tumor-associated genomic variants and on the quantity and quality of cfDNA available for testing. Specific guidelines for standardization and design of appropriate quality programs focused specifically on cfDNA isolation are lacking, as are standardized quality control reagents. CONTENT This report describes and illustrates quality control and quality assurance processes, supported by generation of in-house quality control material, to ensure the reliability of the preanalytical phase of cfDNA analysis. SUMMARY We have developed a robust quality program to support high-volume automated cfDNA extraction from peripheral blood by implementing processes and procedures designed to monitor the adequacy of specimen collection, specimen stability, efficiency of cfDNA extraction, and cfDNA quality.
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Affiliation(s)
- Aliaksandra Samoila
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jose Sosa
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jessica Padilla
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Wutkowski
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Katelynd Vanness
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brian Houck-Loomis
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melissa Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ellinor I Peerschke
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Assessment of Circulating Nucleic Acids in Cancer: From Current Status to Future Perspectives and Potential Clinical Applications. Cancers (Basel) 2021; 13:cancers13143460. [PMID: 34298675 PMCID: PMC8307284 DOI: 10.3390/cancers13143460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Current approaches for cancer detection and characterization are based on radiological procedures coupled with tissue biopsies, despite relevant limitations in terms of overall accuracy and feasibility, including relevant patients' discomfort. Liquid biopsies enable the minimally invasive collection and analysis of circulating biomarkers released from cancer cells and stroma, representing therefore a promising candidate for the substitution or integration in the current standard of care. Despite the potential, the current clinical applications of liquid biopsies are limited to a few specific purposes. The lack of standardized procedures for the pre-analytical management of body fluids samples and the detection of circulating biomarkers is one of the main factors impacting the effective advancement in the applicability of liquid biopsies to clinical practice. The aim of this work, besides depicting current methods for samples collection, storage, quality check and biomarker extraction, is to review the current techniques aimed at analyzing one of the main circulating biomarkers assessed through liquid biopsy, namely cell-free nucleic acids, with particular regard to circulating tumor DNA (ctDNA). ctDNA current and potential applications are reviewed as well.
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Voss T, Ullius A, Schönborn M, Oelmüller U. Sensitivity assessment of workflows detecting rare circulating cell-free DNA targets: A study design proposal. PLoS One 2021; 16:e0253401. [PMID: 34228726 PMCID: PMC8260181 DOI: 10.1371/journal.pone.0253401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022] Open
Abstract
The field of liquid biopsy has seen extensive growth in recent decades, making it one of the most promising areas in molecular diagnostics. Circulating cell-free DNA (ccfDNA) especially is used as an analyte in a growing number of diagnostic assays. These assays require specified preanalytical workflows delivering ccfDNA in qualities and quantities that facilitate correct and reliable results. As each step and component used in the preanalytical process has the potential to influence the assay sensitivity and other performance characteristics, it is key to find an unbiased experimental setup to test these factors in diagnostic or research laboratories. We defined one such setup by using blood from healthy subjects and commercially available products for blood collection, spike-in material, ccfDNA isolation, and qPCR assays. As the primary read-out, we calculated the probit model-based LOD95 (limit of detection of the 95th percentile) from the qPCR assay results. In a proof of principle study we tested two different but widely used blood ccfDNA profile stabilization technologies in blood collection tubes, the Cell-Free DNA BCT and the PAXgene Blood ccfDNA Tube. We tested assays for three different EGFR gene mutations and one BRAF gene mutation. The study design revealed differences in performance between the two tested technologies for all four mutations. In conclusion, we successfully established a blueprint for a test procedure capable of verifying and validating a liquid biopsy workflow from blood collection to the analytical result.
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Affiliation(s)
- Thorsten Voss
- R&D Department, QIAGEN GmbH, Hilden, Germany
- * E-mail:
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Ungerer V, Bronkhorst AJ, Van den Ackerveken P, Herzog M, Holdenrieder S. Serial profiling of cell-free DNA and nucleosome histone modifications in cell cultures. Sci Rep 2021; 11:9460. [PMID: 33947882 PMCID: PMC8096822 DOI: 10.1038/s41598-021-88866-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Recent advances in basic research have unveiled several strategies for improving the sensitivity and specificity of cell-free DNA (cfDNA) based assays, which is a prerequisite for broadening its clinical use. Included among these strategies is leveraging knowledge of both the biogenesis and physico-chemical properties of cfDNA towards the identification of better disease-defining features and optimization of methods. While good progress has been made on this front, much of cfDNA biology remains uncharted. Here, we correlated serial measurements of cfDNA size, concentration and nucleosome histone modifications with various cellular parameters, including cell growth rate, viability, apoptosis, necrosis, and cell cycle phase in three different cell lines. Collectively, the picture emerged that temporal changes in cfDNA levels are rather irregular and not the result of constitutive release from live cells. Instead, changes in cfDNA levels correlated with intermittent cell death events, wherein apoptosis contributed more to cfDNA release in non-cancer cells and necrosis more in cancer cells. Interestingly, the presence of a ~ 3 kbp cfDNA population, which is often deemed to originate from accidental cell lysis or active release, was found to originate from necrosis. High-resolution analysis of this cfDNA population revealed an underlying DNA laddering pattern consisting of several oligo-nucleosomes, identical to those generated by apoptosis. This suggests that necrosis may contribute significantly to the pool of mono-nucleosomal cfDNA fragments that are generally interrogated for cancer mutational profiling. Furthermore, since active steps are often taken to exclude longer oligo-nucleosomes from clinical biospecimens and subsequent assays this raises the question of whether important pathological information is lost.
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Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Abel J Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | | | - Marielle Herzog
- Belgian Volition SRL, 22 Rue Phocas Lejeune, Parc Scientifique Crealys, 5032, Isnes, Belgium
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany.
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González de Aledo-Castillo JM, Casanueva-Eliceiry S, Soler-Perromat A, Fuster D, Pastor V, Reguart N, Viñolas N, Reyes R, Vollmer I, Paredes P, Puig-Butillé JA. Cell-free DNA concentration and fragment size fraction correlate with FDG PET/CT-derived parameters in NSCLC patients. Eur J Nucl Med Mol Imaging 2021; 48:3631-3642. [PMID: 33797597 DOI: 10.1007/s00259-021-05306-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/07/2021] [Indexed: 01/26/2023]
Abstract
PURPOSE The aim of our study was to investigate the correlation between cfDNA concentration and fragment size fraction with FDG PET/CT- and CT-derived parameters in untreated NSCLC patient. METHODS Fifty-three patients diagnosed of locally advanced or metastatic NSCLC who had undergone FDG PET/CT, CT and cfDNA analysis prior to any treatment were included in this retrospective study. CfDNA concentration was measured by fluorometry and fragment size fractions were determined by microchip electrophoresis. [18F]F-FDG PET/CT was performed and standardised uptake values (SUV), metabolic tumour volume (MTV) and total lesion glycolysis (TLG) were calculated for primary, extrapulmonary and total disease. CT scans were evaluated according to RECIST 1.1 criteria. RESULTS CfDNA concentration showed a positive correlation with extrapulmonary MTV (r2 = 0.36, P = 0.009), and extrapulmonary TLG (r2 = 0.35, P = 0.009) and their whole-body (wb) ratios. Higher concentrations of total cfDNA were found in patients with liver lesions. Short fragments of cfDNA (100-250 bp) showed a positive correlation with extrapulmonary MTV (r2 = 0.49, P = 0.0005) and extrapulmonary TLG (r2 = 0.39, P = 0.006) and their respective wb ratios, and a negative correlation with SUVmean (r2 = -0.31, P = 0.03) and SUVmean/SUVmax ratio (r2 = -0.34, P = 0.02). A higher fraction of short cfDNA fragments was found in patients with liver and pleural lesions. CONCLUSIONS This study supports the hypothesis that cfDNA concentration and short cfDNA fragment size fraction reflect the tumour burden as well as metabolic activity in advanced NSCLC patients. This suggests their suitability as complementary tests for a more accurate diagnosis of tumour metabolic behaviour and to allow personalised therapies.
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Affiliation(s)
| | | | | | - D Fuster
- Nuclear Medicine Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - V Pastor
- Molecular Biology CORE, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - N Reguart
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,Medical Oncology Department, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - N Viñolas
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - R Reyes
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - I Vollmer
- Radiology Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
| | - P Paredes
- Nuclear Medicine Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - J A Puig-Butillé
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain. .,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain. .,Molecular Biology CORE, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain.
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36
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González de Aledo-Castillo JM, Arcocha A, Victoria I, Martinez-Puchol AI, Sánchez C, Jares P, Rodríguez GF, Viñolas N, Reyes R, Reguart N, Puig-Butillé JA. Molecular characterization of advanced non-small cell lung cancer patients by cfDNA analysis: experience from routine laboratory practice. J Thorac Dis 2021; 13:1658-1670. [PMID: 33841957 PMCID: PMC8024825 DOI: 10.21037/jtd-20-3142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Analysis of circulating free DNA (cfDNA) by the real-time PCR cobas® EGFR Mutation Test v2 (cobas® EGFR Test) is a diagnostic approach used in clinical practice for the characterization of advanced non-small cell lung cancer (NSCLC) patients. The test additionally outputs a semiquantitative index (SQI) which reflects the proportion of mutated versus wild-type copies of the EGFR gene in cfDNA with potential use as a biomarker. CfDNA concentration and cfDNA fragmentation pattern have also shown potential utility as biomarkers for cancer patients. We evaluated the implementation of EGFR testing and cfDNA related parameters in NSCLC patients in routine clinical setting as biomarkers for disease stage and diagnosis. METHODS A prospective cohort of 173 locally advanced or metastatic NSCLC TKI-naïve patients analyzed by the cobas® EGFR Test were included in the study. Reproducibility of the test was assessed in 56 patients. The concentration of cfDNA and fragment size pattern was measured using fluorometry and microchip electrophoresis respectively. RESULTS The test showed high diagnostic accuracy when compared to the gold standard of biopsy tumor tissue testing. The SQI value showed a moderate reproducibility (r2=0.70) and did not correlate with cfDNA concentration (r2=0.17, P=0.28) or disease stage (stage III patients SQI =9.1±3.1 and stage IV patients SQI =11.5±4.8, P=0.41). We found differences in SQI values according to the type of EGFR mutation (Ex19Del mutations, SQI =13.6; p.L858R, SQI =8.88; P=0.001). Stage IV patients had higher concentrations of cfDNA (P<0.0001) and higher fractions of cfDNA 100-250 base pairs (bp) fragments (P=0.01) compared to stage III patients. From the ROC curve analysis, cfDNA concentration showed higher AUC compared to cfDNA 100-250 bp fragments (0.86 vs. 0.71). We obtained a cut-off value for cfDNA concentration of 20.3 ng/mL with 72.3% sensitivity and 95% specificity for predicting disease stage in TKI-naïve advanced NSCLC patients. CONCLUSIONS The study indicates that cfDNA analysis in plasma for EGFR testing by RT-PCR is an accurate and fast method to initially stratify NSCLC patients in a real-world clinical setting. However, the SQI has limited clinical value. The cfDNA concentration and fragmentation pattern have clear potential clinical utility for tumor staging in NSCLC patients.
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Affiliation(s)
| | - Ainara Arcocha
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Iván Victoria
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | | | | | - Pedro Jares
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Molecular Biology CORE, Hospital Clínic, Barcelona, Spain
- Pathology Department, Hospital Clínic, Barcelona, Spain
| | | | - Núria Viñolas
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Roxana Reyes
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Noemí Reguart
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Joan Antón Puig-Butillé
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Molecular Biology CORE, Hospital Clínic, Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
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Martins VF, Dobson CR, Begur M, Parekh J, Ball ST, Gonzalez F, Hughes-Austin JM, Schenk S. Surgical site peptidylarginine deaminase 4 (PAD4), a biomarker of NETosis, correlates with insulin resistance in total joint arthroplasty patients: A preliminary report. PLoS One 2021; 16:e0245594. [PMID: 33481860 PMCID: PMC7822240 DOI: 10.1371/journal.pone.0245594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/04/2021] [Indexed: 01/12/2023] Open
Abstract
While obesity and insulin resistance are known risk factors for wound complications after total joint arthroplasty (TJA), the biologic causes remain to be elucidated. Recently, neutrophil extracellular trap formation (NETosis) was identified as a mediator of delayed wound healing in insulin resistant states. Herein, we explored the relationship between obesity, insulin resistance and biomarkers of NET formation in TJA subjects. We enrolled 14 obese (body mass index [BMI]≥30 kg/m2), and 15 lean (BMI<30 kg/m2) subjects undergoing primary knee or hip TJA. On the day of surgery, skeletal muscle proximal to the operated joint and plasma were collected. Protein abundance of NETosis biomarkers, peptidylarginine deaminase 4 (PAD4) and neutrophil elastase (NE) were assessed in skeletal muscle by immunoblotting and metabolic parameters (glucose, insulin, triglycerides, free fatty acids) and cell-free double-stranded DNA (cf-dsDNA) were assessed in plasma and were correlated with obesity and insulin resistance (as measured by the homeostatic model assessment for insulin resistance). When comparing lean and obese subjects, there were no significant differences in plasma cf-dsDNA or skeletal muscle NE or PAD4 abundance. In contrast, skeletal muscle PAD4 abundance, but not NE or plasma cf-dsDNA, was positively correlated with insulin resistance. Compared to insulin sensitive subjects, insulin resistant TJA subjects have higher expression of PAD4 at the surgical site and therefore may have higher rates of NET formation, which may lead to delayed surgical site wound healing.
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Affiliation(s)
- Vitor F. Martins
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States of America
| | - Christopher R. Dobson
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Maedha Begur
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Jesal Parekh
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Scott T. Ball
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Francis Gonzalez
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Jan M. Hughes-Austin
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States of America
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Doludin YV, Limonova AS, Kozlova VA, Efimova AI, Borisova AL, Meshkov AN, Pokrovskaya MS, Drapkina OM. Collection and storage of DNA-containing biomaterial and isolated DNA. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2020. [DOI: 10.15829/1728-8800-2020-2730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The advances of biomedicine include the new technologies, diagnosis and treatment techniques, as well as the practical use of new types of biological targets, in particular, nucleic acids. Genomic deoxyribonucleic acid (DNA), extracellular DNA (exDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. The use of new technologies for DNA analysis required the development of standardized methods for processing biological samples in order to obtain high-quality DNA samples. The research uses various methods for collecting, preparing samples and storing various DNA-containing biomaterials and isolated DNA, as well as methods for assessing the quality of samples and biobank standards. It is obvious that the use of uniform standards will allow large-scale genetic research on the basis of biobanks and research laboratories. Specialists from professional organizations such as International Society for Biological and Environmental Repositories (ISBER), Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), European, Middle Eastern & African Society for Biopreservationa and Biobanking (ESBB) and the Russian National Association of Biobanks and Biobanking Professionals.
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Affiliation(s)
- Yu. V. Doludin
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. S. Limonova
- National Medical Research Center for Therapy and Preventive Medicine
| | - V. A. Kozlova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. I. Efimova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. L. Borisova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine
| | - M. S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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Yang WY, Feng LF, Meng X, Chen R, Xu WH, Hou J, Xu T, Zhang L. Liquid biopsy in head and neck squamous cell carcinoma: circulating tumor cells, circulating tumor DNA, and exosomes. Expert Rev Mol Diagn 2020; 20:1213-1227. [PMID: 33232189 DOI: 10.1080/14737159.2020.1855977] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Introduction: Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide. Due to a lack of reliable markers, HNSCC patients are usually diagnosed at a late stage, which will lead to a worse outcome. Therefore, it is critical to improve the clinical management of cancer patients. Nowadays, the development of liquid biopsy enables a minimally invasive manner to extract molecular information from HNSCCs. Thus, this review aims to outline the clinical value of liquid biopsy in early detection, real-time monitoring, and prognostic evaluation of HNSCC. Areas covered: This comprehensive review focused on the characteristics as well as clinical applications of three liquid biopsy markers (CTCs, ctDNA, and exosomes) in HNSCC. What is more, it is promising to incorporate machine learning and 3D organoid models in the liquid biopsy of HNSCC. Expert opinion: Liquid biopsy provides a noninvasive technique to reflect the inter and intra-lesional heterogeneity through the detection of tumor cells or materials released from the primary and secondary tumors. Recently, some evolving technologies have the potential to combine with liquid biopsy to improve clinical management of HNSCC patients.
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Affiliation(s)
- Wen-Ying Yang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. Of Oral Diseases Research of Anhui Province , Hefei, 230032, China
| | - Lin-Fei Feng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Anhui Medical University , Hefei, 230032, China
| | - Xiang Meng
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. Of Oral Diseases Research of Anhui Province , Hefei, 230032, China
| | - Ran Chen
- School of Stomatology, Anhui Medical University , Hefei, 230032, China
| | - Wen-Hua Xu
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. Of Oral Diseases Research of Anhui Province , Hefei, 230032, China
| | - Jun Hou
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Anhui Medical University , Hefei, 230032, China
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University , Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University , Hefei, 230032, China
| | - Lei Zhang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. Of Oral Diseases Research of Anhui Province , Hefei, 230032, China.,Periodontal Department, Anhui Stomatology Hospital affiliated to Anhui Medical University , Hefei, 230032, China
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40
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Pös Z, Pös O, Styk J, Mocova A, Strieskova L, Budis J, Kadasi L, Radvanszky J, Szemes T. Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes. Int J Mol Sci 2020; 21:ijms21228634. [PMID: 33207777 PMCID: PMC7697251 DOI: 10.3390/ijms21228634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Affiliation(s)
- Zuzana Pös
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jakub Styk
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Faculty of Medicine, Institute of Medical Biology, Genetics and Clinical Genetics, 811 08 Bratislava, Slovakia
| | - Angelika Mocova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | | | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jan Radvanszky
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
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Van Paemel R, De Koker A, Caggiano C, Morlion A, Mestdagh P, De Wilde B, Vandesompele J, De Preter K. Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome. Epigenetics 2020; 16:797-807. [PMID: 33074045 PMCID: PMC8216177 DOI: 10.1080/15592294.2020.1827714] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulphite-based cfDNA methylation profiling. Fifteen tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulphite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives.
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Affiliation(s)
- Ruben Van Paemel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Andries De Koker
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Center for Medical Biotechnology, Flemish Institute Biotechnology (VIB), Ghent, Belgium
| | - Christa Caggiano
- Departments of Neurology and Computational Medicine, University of California, Los Angeles, CA, USA
| | - Annelien Morlion
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Biogazelle NV, Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Biogazelle NV, Ghent, Belgium
| | - Katleen De Preter
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Pellini B, Szymanski J, Chin RI, Jones PA, Chaudhuri AA. Liquid Biopsies Using Circulating Tumor DNA in Non-Small Cell Lung Cancer. Thorac Surg Clin 2020; 30:165-177. [PMID: 32327175 DOI: 10.1016/j.thorsurg.2020.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Liquid biopsies for the diagnosis and treatment of lung cancer have developed rapidly, driven primarily by technical advances in sensitivity to detect circulating tumor DNA (ctDNA). Still, technical limitations such as the challenge of detecting low-level ctDNA variants and distinguishing tumor-related variants from clonal hematopoiesis remain. With further technical advancements, new applications for ctDNA analysis are emerging including detection of post-treatment molecular residual disease (MRD), clinical trial selection, and early cancer detection. This chapter reviews the current state of ctDNA testing in NSCLC, the underlying technological advances enabling ctDNA detection, and the potential to expand ctDNA analysis to new applications.
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Affiliation(s)
- Bruna Pellini
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Division of Oncology Campus Box 8056, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Jeffrey Szymanski
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, Radiation Oncology Campus Box 8224, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Re-I Chin
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, Radiation Oncology Campus Box 8224, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Paul A Jones
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, Radiation Oncology Campus Box 8224, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, Radiation Oncology Campus Box 8224, 660 South Euclid Avenue, St Louis, MO 63110, USA.
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Lampignano R, Neumann MHD, Weber S, Kloten V, Herdean A, Voss T, Groelz D, Babayan A, Tibbesma M, Schlumpberger M, Chemi F, Rothwell DG, Wikman H, Galizzi JP, Riise Bergheim I, Russnes H, Mussolin B, Bonin S, Voigt C, Musa H, Pinzani P, Lianidou E, Brady G, Speicher MR, Pantel K, Betsou F, Schuuring E, Kubista M, Ammerlaan W, Sprenger-Haussels M, Schlange T, Heitzer E. Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows. Clin Chem 2020; 66:149-160. [PMID: 31628139 DOI: 10.1373/clinchem.2019.306837] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/05/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND In cancer patients, circulating cell-free DNA (ccfDNA) can contain tumor-derived DNA (ctDNA), which enables noninvasive diagnosis, real-time monitoring, and treatment susceptibility testing. However, ctDNA fractions are highly variable, which challenges downstream applications. Therefore, established preanalytical work flows in combination with cost-efficient and reproducible reference materials for ccfDNA analyses are crucial for analytical validity and subsequently for clinical decision-making. METHODS We describe the efforts of the Innovative Medicines Initiative consortium CANCER-ID (http://www.cancer-id.eu) for comparing different technologies for ccfDNA purification, quantification, and characterization in a multicenter setting. To this end, in-house generated mononucleosomal DNA (mnDNA) from lung cancer cell lines carrying known TP53 mutations was spiked in pools of plasma from healthy donors generated from 2 different blood collection tubes (BCTs). ccfDNA extraction was performed at 15 partner sites according to their respective routine practice. Downstream analysis of ccfDNA with respect to recovery, integrity, and mutation analysis was performed centralized at 4 different sites. RESULTS We demonstrate suitability of mnDNA as a surrogate for ccfDNA as a process quality control from nucleic acid extraction to mutation detection. Although automated extraction protocols and quantitative PCR-based quantification methods yielded the most consistent and precise results, some kits preferentially recovered spiked mnDNA over endogenous ccfDNA. Mutated TP53 fragments derived from mnDNA were consistently detected using both next-generation sequencing-based deep sequencing and droplet digital PCR independently of BCT. CONCLUSIONS This comprehensive multicenter comparison of ccfDNA preanalytical and analytical work flows is an important contribution to establishing evidence-based guidelines for clinically feasible (pre)analytical work flows.
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Affiliation(s)
| | | | - Sabrina Weber
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Vera Kloten
- Bayer AG, Biomarker Research, Wuppertal, Germany
| | | | | | | | - Anna Babayan
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marco Tibbesma
- University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | | | - Francesca Chemi
- CR-UK Manchester Institute, University of Manchester, Manchester, UK
| | | | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Inger Riise Bergheim
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Hege Russnes
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Serena Bonin
- University of Trieste, DSM-Cattinara Hospital, Trieste, Italy
| | | | - Hanny Musa
- Boehringer-Ingelheim, Ingelheim am Rhein, Germany
| | | | | | - Ged Brady
- CR-UK Manchester Institute, University of Manchester, Manchester, UK
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fay Betsou
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Ed Schuuring
- University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | | | - Wim Ammerlaan
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
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Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
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Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
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Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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Emaus MN, Anderson JL. Allelic discrimination between circulating tumor DNA fragments enabled by a multiplex-qPCR assay containing DNA-enriched magnetic ionic liquids. Anal Chim Acta 2020; 1124:184-193. [PMID: 32534671 DOI: 10.1016/j.aca.2020.04.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 12/19/2022]
Abstract
Multiplex amplification of DNA can be highly valuable in circulating tumor DNA (ctDNA) analysis due to the sheer number of potential mutations. However, commercial ctDNA extraction methods struggle to preconcentrate low concentrations of DNA and require multiple sample handling steps. Recently, magnetic ionic liquids (MILs) have been used to extract DNA and were integrated with a quantitative polymerase chain reaction (qPCR). However, in previous studies, DNA could not be preconcentrated from plasma and only one fragment could be amplified per reaction. In this study, MILs were utilized as DNA extraction solvents and directly integrated into a multiplex-qPCR buffer to simultaneously amplify wild-type KRAS, G12S KRAS, and wild-type BRAF, three clinically-relevant genes whose mutation status can affect the success of anti-EGFR therapy. DNA was desorbed from the MIL solvent during a multiplex-PCR without having a significant effect on the amplification efficiency, and allelic discrimination of single-nucleotide polymorphisms could still be achieved. Enrichment factors over 35 for all three sequences were achieved from Tris buffer using the [N8,8,8,Bz+][Ni(hfacac)3-]) and [P6,6,6,14+][Ni(Phtfacac)3-] MILs. DNA could still be preconcentrated from 2-fold diluted human plasma using the [N8,8,8,Bz+][Ni(hfacac)3-] MIL. Extractions from undiluted plasma were reproducible with the [P6,6,6,14+][Ni(Phtfacac)3-] MIL although DNA was not preconcentrated with enrichment factors around 0.6 for all three fragments. Compared to commercial DNA extraction methods (i.e., silica-based spin columns and magnetic beads), the MIL-based extraction achieved higher enrichment factors in Tris buffer and plasma. The ability of the MIL-based dispersive liquid-liquid microextraction (DLLME) direct-multiplex-qPCR method to simultaneously achieve high enrichment factors of multiple DNA fragments from human plasma is highly promising in the field of ctDNA detection.
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Affiliation(s)
- Miranda N Emaus
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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Lee EY, Lee EJ, Yoon H, Lee DH, Kim KH. Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions. Diagnostics (Basel) 2020; 10:diagnostics10040234. [PMID: 32325682 PMCID: PMC7236016 DOI: 10.3390/diagnostics10040234] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/25/2022] Open
Abstract
Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection.
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Affiliation(s)
- Eun Young Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Ewha Medical Research Institute, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Eun-Ju Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Ewha Medical Research Institute, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Hana Yoon
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
| | - Dong Hyeon Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
| | - Kwang Hyun Kim
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Correspondence: ; Tel.: +82-2-6986-1685; Fax: +82-2-6986-3258
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Taus Á, Camacho L, Rocha P, Hernández A, Longarón R, Clavé S, Fernández-Ibarrondo L, Salido M, Hardy-Werbin M, Fernández-Rodríguez C, Albanell J, Bellosillo B, Arriola E. Plasmatic KRAS Kinetics for the Prediction of Treatment Response and Progression in Patients With KRAS-mutant Lung Adenocarcinoma. Arch Bronconeumol 2020; 57:323-329. [PMID: 32253118 DOI: 10.1016/j.arbres.2020.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 12/25/2022]
Abstract
INTRODUCTION KRAS is the most common driver mutation in lung cancer. ctDNA-based assessment offers advantages over tumor as a minimally invasive method able to capture tumor heterogeneity. Monitoring KRAS mutational load in ctDNA may be useful in the management of the patients. METHODS Consecutive patients diagnosed with KRAS mutant lung adenocarcinoma in the tumor biopsy were included in this study. Plasma samples were obtained at different time points during the course of the disease. KRAS mutations in plasma were quantified using digital PCR and correlated with mutations in tumor and with radiological response and progression. RESULTS Two hundred and forty-five plasma samples from 56 patients were analyzed. The rate of detection of KRAS mutations in plasma in our previously characterized KRAS-mutant cases was 82% overall, reaching 96% in cases with more than 1 metastatic location. The dynamics of KRAS mutational load predicted response in 93% and progression in 63% of cases, 33 and 50 days respectively in advance of radiological evaluation. Progression-free survival for patients in whom ctDNA was not detectable in plasma after treatment initiation was significantly longer than for those in whom ctDNA remained detectable (7.7 versus 3.2 months; HR: 0.44, p=0.004). CONCLUSIONS The detection of KRAS mutations in ctDNA showed a good correlation with that in tumor biopsy and, in most cases, predicted tumor response and progression to chemotherapy in advance of radiographic evaluation. The liquid biopsies for ctDNA-based molecular analyses are a reliable tool for KRAS testing in clinical practice.
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Affiliation(s)
- Álvaro Taus
- Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain; Departamento de Medicina, Universidad Autónoma de Barcelona (UAB), Barcelona, Spain; Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Laura Camacho
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Pedro Rocha
- Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain
| | - Ainhoa Hernández
- Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain
| | - Raquel Longarón
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Sergi Clavé
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, Hospital del Mar, Barcelona, Spain
| | | | - Marta Salido
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Max Hardy-Werbin
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Joan Albanell
- Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain; Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Beatriz Bellosillo
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Edurne Arriola
- Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain; Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.
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Greytak SR, Engel KB, Parpart-Li S, Murtaza M, Bronkhorst AJ, Pertile MD, Moore HM. Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance. Clin Cancer Res 2020; 26:3104-3109. [PMID: 32122922 DOI: 10.1158/1078-0432.ccr-19-3015] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/25/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022]
Abstract
Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization of preanalytic practices across institutions may compromise the reproducibility of cfDNA-derived data and hamper advancements in cfDNA testing in the clinic. Differences in cellular genomic contamination, cfDNA yield, integrity, and fragment length have been attributed to different collection tube types and anticoagulants, processing delays and temperatures, tube agitation, centrifugation protocols and speeds, plasma storage duration and temperature, the number of freeze-thaw events, and cfDNA extraction and quantification methods, all of which can also ultimately impact subsequent downstream analysis. Thus, there is a pressing need for widely applicable standards tailored for cfDNA analysis that include all preanalytic steps from blood draw to analysis. The NCI's Biorepositories and Biospecimen Research Branch has developed cfDNA-specific guidelines that are based upon published evidence and have been vetted by a panel of internationally recognized experts in the field. The guidelines include optimal procedures as well as acceptable alternatives to facilitate the generation of evidence-based protocols by individual laboratories and institutions. The aim of the document, which is entitled "Biospecimen Evidence-based Best Practices for Cell-free DNA: Biospecimen Collection and Processing," is to improve the accuracy of cfDNA analysis in both basic research and the clinic by improving and harmonizing practices across institutions.
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Affiliation(s)
| | | | | | - Muhammed Murtaza
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, Arizona
| | | | - Mark D Pertile
- Victorian Clinical Genetics Services (VCGS), Parkville, Australia
| | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, NCI, Bethesda, Maryland.
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Boldrin E, Curtarello M, Dallan M, Alfieri R, Realdon S, Fassan M, Saggioro D. Detection of LINE-1 hypomethylation in cfDNA of Esophageal Adenocarcinoma Patients. Int J Mol Sci 2020; 21:ijms21041547. [PMID: 32102481 PMCID: PMC7073170 DOI: 10.3390/ijms21041547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/13/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
DNA methylation plays an important role in cancer development. Cancer cells exhibit two types of DNA methylation alteration: site-specific hypermethylation at promoter of oncosuppressor genes and global DNA hypomethylation. This study evaluated the methylation patterns of long interspersed nuclear element (LINE-1) sequences which, due to their relative abundance in the genome, are considered a good surrogate indicator of global DNA methylation. LINE-1 methylation status was investigated in the cell-free DNA (cfDNA) of 21 patients, 19 with esophageal adenocarcinoma (EADC) and 2 with Barrett’s esophagus (BE). The two BE patients and one EADC patient were also analyzed longitudinally. Methylation status was analyzed using restriction enzymes and DNA amplification. This methodology was chosen to avoid bisulfite conversion, which we considered inadequate for cfDNA analysis. Indeed, cfDNA is characterized by poor quality and low concentration, and bisulfite conversion might worsen these conditions. Results showed that hypomethylated LINE-1 sequences are present in EADC cfDNA. Furthermore, longitudinal studies in BE suggested a correlation between methylation status of LINE-1 sequences in cfDNA and progression to EADC. In conclusion, our study indicated the feasibility of our methodological approach to detect hypomethylation events in cfDNA from EADC patients, and suggests LINE-1 methylation analysis as a new possible molecular assay to integrate into patient monitoring.
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Affiliation(s)
- Elisa Boldrin
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV-IRCCS, Via Gattamelata 64, 35128 Padova, Italy; (M.C.); (M.D.); (D.S.)
- Correspondence: ; Tel.: +39-04-9821-6161
| | - Matteo Curtarello
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV-IRCCS, Via Gattamelata 64, 35128 Padova, Italy; (M.C.); (M.D.); (D.S.)
| | - Marco Dallan
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV-IRCCS, Via Gattamelata 64, 35128 Padova, Italy; (M.C.); (M.D.); (D.S.)
| | - Rita Alfieri
- Oncological Surgery, Veneto Institute of Oncology IOV-IRCCS, via dei Carpani 16, 31033 Castelfranco Veneto, Italy;
| | - Stefano Realdon
- Endoscopy Unit, Veneto Institute of Oncology IOV-IRCCS, via Gattamelata 64, 35128 Padova, Italy;
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology and Cytopathology, University of Padova, via Giustiniani 2, 35128 Padova, Italy;
| | - Daniela Saggioro
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV-IRCCS, Via Gattamelata 64, 35128 Padova, Italy; (M.C.); (M.D.); (D.S.)
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