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Wang D, Trimbos KB, Gomes SIF, Jacquemyn H, Merckx VSFT. Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR. THE NEW PHYTOLOGIST 2024; 242:1825-1834. [PMID: 37929750 DOI: 10.1111/nph.19385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances. Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding. Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low-abundance families. This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.
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Affiliation(s)
- Deyi Wang
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, 2333 CC, Leiden University, Leiden, the Netherlands
| | - Sofia I F Gomes
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Heverlee, 3001, Leuven, Belgium
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
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Gai W, Yu SCY, Chan WTC, Peng W, Lau SL, Leung TY, Jiang P, Chan KCA, Lo YMD. Droplet digital PCR is a cost-effective method for analyzing long cell-free DNA in maternal plasma: Application in preeclampsia. Prenat Diagn 2023; 43:1385-1393. [PMID: 37655424 DOI: 10.1002/pd.6432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/06/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
OBJECTIVE Long cell-free DNA (cfDNA) can be found in the plasma of pregnant women and cancer patients. We investigated if droplet digital PCR (ddPCR) can analyze such molecules for diagnostic purposes using preeclampsia as a model. METHOD Plasma samples from ten preeclamptic and sixteen normal pregnancies were analyzed. Two ddPCR assays targeting a single-copy gene, VCP, and one ddPCR assay targeting LINE-1 repetitive regions were used to measure the percentages of long cfDNA >533, 1001, and 170 bp, respectively. The LINE-1 assay was developed as guided by in silico PCR analyses to better differentiate preeclamptic and normal pregnancies. RESULTS Preeclamptic patients had a significantly lower median percentage of long cfDNA than healthy pregnant controls, as determined by the LINE-1 170 bp assay (28.9% vs. 35.1%, p < 0.0001) and the VCP 533 bp assay (6.6% vs. 8.7%, p = 0.014). The LINE-1 assay provided a better differentiation than the VCP 533 bp assay (area under ROC curves, 0.94 vs. 0.79). CONCLUSION ddPCR is a cost-effective approach for unlocking diagnostic information carried by long cfDNA in plasma and may have applications for the detection of preeclampsia. Further longitudinal studies with larger cohorts are required to assess the clinical utility of this test.
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Affiliation(s)
- Wanxia Gai
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Stephanie C Y Yu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - W T Charlotte Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Wenlei Peng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - So Ling Lau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - K C Allen Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
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Koval AP, Khromova AS, Blagodatskikh KA, Zhitnyuk YV, Shtykova YA, Alferov AA, Kushlinskii NE, Shcherbo DS. Application of PCR-based approaches for evaluation of cell-free DNA fragmentation in colorectal cancer. Front Mol Biosci 2023; 10:1101179. [PMID: 37051326 PMCID: PMC10083340 DOI: 10.3389/fmolb.2023.1101179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Cell-free DNA (cfDNA) testing is the core of most liquid biopsy assays. In particular, cfDNA fragmentation features could facilitate non-invasive cancer detection due to their interconnection with tumor-specific epigenetic alterations. However, the final cfDNA fragmentation profile in a purified sample is the result of a complex interplay between informative biological and artificial technical factors. In this work, we use ddPCR to study cfDNA lengths in colorectal cancer patients and observe shorter and more variable cfDNA fragments in accessible chromatin loci compared to the densely packed pericentromeric region. We also report a convenient qPCR system suitable for screening cfDNA samples for artificial high molecular weight DNA contamination.
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Affiliation(s)
- Anastasia P. Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexandra S. Khromova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A. Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Center of Genetics and Reproductive Medicine “Genetico”, Moscow, Russia
| | - Yulia V. Zhitnyuk
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Aleksandr A. Alferov
- Laboratory of Clinical Biochemistry, N. N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Nikolay E. Kushlinskii
- Laboratory of Clinical Biochemistry, N. N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S. Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- *Correspondence: Dmitry S. Shcherbo,
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Abstract
The high fragmentation of nuclear circulating DNA (cirDNA) relies on chromatin organization and protection or packaging within mononucleosomes, the smallest and the most stabilized structure in the bloodstream. The detection of differing size patterns, termed fragmentomics, exploits information about the nucleosomal packing of DNA. Fragmentomics not only implies size pattern characterization but also considers the positioning and occupancy of nucleosomes, which result in cirDNA fragments being protected and persisting in the circulation. Fragmentomics can determine tissue of origin and distinguish cancer-derived cirDNA. The screening power of fragmentomics has been considerably strengthened in the omics era, as shown in the ongoing development of sophisticated technologies assisted by machine learning. Fragmentomics can thus be regarded as a strategy for characterizing cancer within individuals and offers an alternative or a synergistic supplement to mutation searches, methylation, or nucleosome positioning. As such, it offers potential for improving diagnostics and cancer screening.
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Affiliation(s)
- A.R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, and ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France,Corresponding author
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Tsering T, Li M, Chen Y, Nadeau A, Laskaris A, Abdouh M, Bustamante P, Burnier JV. EV-ADD, a database for EV-associated DNA in human liquid biopsy samples. J Extracell Vesicles 2022; 11:e12270. [PMID: 36271888 PMCID: PMC9587709 DOI: 10.1002/jev2.12270] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/20/2022] [Accepted: 09/06/2022] [Indexed: 11/06/2022] Open
Abstract
Extracellular vesicles (EVs) play a key role in cellular communication both in physiological conditions and in pathologies such as cancer. Emerging evidence has shown that EVs are active carriers of molecular cargo (e.g. protein and nucleic acids) and a powerful source of biomarkers and targets. While recent studies on EV‐associated DNA (EV‐DNA) in human biofluids have generated a large amount of data, there is currently no database that catalogues information on EV‐DNA. To fill this gap, we have manually curated a database of EV‐DNA data derived from human biofluids (liquid biopsy) and in‐vitro studies, called the Extracellular Vesicle‐Associated DNA Database (EV‐ADD). This database contains validated experimental details and data extracted from peer‐reviewed published literature. It can be easily queried to search for EV isolation methods and characterization, EV‐DNA isolation techniques, quality validation, DNA fragment size, volume of starting material, gene names and disease context. Currently, our database contains samples representing 23 diseases, with 13 different types of EV isolation techniques applied on eight different human biofluids (e.g. blood, saliva). In addition, EV‐ADD encompasses EV‐DNA data both representing the whole genome and specifically including oncogenes, such as KRAS, EGFR, BRAF, MYC, and mitochondrial DNA (mtDNA). An EV‐ADD data metric system was also integrated to assign a compliancy score to the MISEV guidelines based on experimental parameters reported in each study. While currently available databases document the presence of proteins, lipids, RNA and metabolites in EVs (e.g. Vesiclepedia, ExoCarta, ExoBCD, EVpedia, and EV‐TRACK), to the best of our knowledge, EV‐ADD is the first of its kind to compile all available EV‐DNA datasets derived from human biofluid samples. We believe that this database provides an important reference resource on EV‐DNA‐based liquid biopsy research, serving as a learning tool and to showcase the latest developments in the EV‐DNA field. EV‐ADD will be updated yearly as newly published EV‐DNA data becomes available and it is freely available at www.evdnadatabase.com.
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Affiliation(s)
- Thupten Tsering
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Mingyang Li
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Yunxi Chen
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Amélie Nadeau
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Alexander Laskaris
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Mohamed Abdouh
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Prisca Bustamante
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Julia V. Burnier
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
- Experimental Pathology UnitDepartment of PathologyMcGill UniversityMontrealQuebecCanada
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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: 27] [Impact Index Per Article: 13.5] [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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Ferchiou S, Caza F, de Boissel PGJ, Villemur R, St-Pierre Y. Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems. ISME COMMUNICATIONS 2022; 2:61. [PMID: 37938655 PMCID: PMC9723566 DOI: 10.1038/s43705-022-00145-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 10/04/2023]
Abstract
Liquid biopsy (LB) is a concept that is rapidly gaining ground in the biomedical field. Its concept is largely based on the detection of circulating cell-free DNA (ccfDNA) fragments that are mostly released as small fragments following cell death in various tissues. A small percentage of these fragments are from foreign (nonself) tissues or organisms. In the present work, we applied this concept to mussels, a sentinel species known for its high filtration capacity of seawater. We exploited the capacity of mussels to be used as natural filters to capture environmental DNA fragments of different origins to provide information on the biodiversity of marine coastal ecosystems. Our results showed that hemolymph of mussels contains DNA fragments that varied considerably in size, ranging from 1 to 5 kb. Shotgun sequencing revealed that a significant amount of DNA fragments had a nonself microbial origin. Among these, we found DNA fragments derived from bacteria, archaea, and viruses, including viruses known to infect a variety of hosts that commonly populate coastal marine ecosystems. Taken together, our study shows that the concept of LB applied to mussels provides a rich and yet unexplored source of knowledge regarding the microbial biodiversity of a marine coastal ecosystem.
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Affiliation(s)
- Sophia Ferchiou
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - France Caza
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | | | - Richard Villemur
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - Yves St-Pierre
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada.
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Milin-Lazovic J, Madzarevic P, Rajovic N, Djordjevic V, Milic N, Pavlovic S, Veljkovic N, Milic NM, Radenkovic D. Meta-Analysis of Circulating Cell-Free DNA's Role in the Prognosis of Pancreatic Cancer. Cancers (Basel) 2021; 13:3378. [PMID: 34298594 PMCID: PMC8303288 DOI: 10.3390/cancers13143378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 01/14/2023] Open
Abstract
INTRODUCTION The analysis of cell-free DNA (cfDNA) for genetic abnormalities is a promising new approach for the diagnosis and prognosis of pancreatic cancer patients. Insights into the molecular characteristics of pancreatic cancer may provide valuable information, leading to its earlier detection and the development of targeted therapies. MATERIAL AND METHODS We conducted a systematic review and a meta-analysis of studies that reported cfDNA in pancreatic ductal adenocarcinoma (PDAC). The studies were considered eligible if they included patients with PDAC, if they had blood tests for cfDNA/ctDNA, and if they analyzed the prognostic value of cfDNA/ctDNA for patients' survival. The studies published before 22 October 2020 were identified through the PubMED, EMBASE, Web of Science and Cochrane Library databases. The assessed outcomes were the overall (OS) and progression-free survival (PFS), expressed as the log hazard ratio (HR) and standard error (SE). The summary of the HR effect size was estimated by pooling the individual trial results using the Review Manager, version 5.3, Cochrane Collaboration. The heterogeneity was assessed using the Cochran Q test and I2 statistic. RESULTS In total, 48 studies were included in the qualitative review, while 44 were assessed in the quantitative synthesis, with the total number of patients included being 3524. Overall negative impacts of cfDNA and KRAS mutations on OS and PFS in PDAC (HR = 2.42, 95% CI: 1.95-2.99 and HR = 2.46, 95% CI: 2.01-3.00, respectively) were found. The subgroup analysis of the locally advanced and metastatic disease presented similar results (HR = 2.51, 95% CI: 1.90-3.31). In the studies assessing the pre-treatment presence of KRAS, there was a moderate to high degree of heterogeneity (I2 = 87% and I2 = 48%, for OS and PFS, respectively), which was remarkably decreased in the analysis of the studies measuring post-treatment KRAS (I2 = 24% and I2 = 0%, for OS and PFS, respectively). The patients who were KRAS positive before but KRAS negative after treatment had a better prognosis than the persistently KRAS-positive patients (HR = 5.30, 95% CI: 1.02-27.63). CONCLUSION The assessment of KRAS mutation by liquid biopsy can be considered as an additional tool for the estimation of the disease course and outcome in PDAC patients.
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Affiliation(s)
- Jelena Milin-Lazovic
- Institute for Medical Statistics and Informatics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (J.M.-L.); (P.M.); (N.R.); (N.M.M.)
| | - Petar Madzarevic
- Institute for Medical Statistics and Informatics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (J.M.-L.); (P.M.); (N.R.); (N.M.M.)
| | - Nina Rajovic
- Institute for Medical Statistics and Informatics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (J.M.-L.); (P.M.); (N.R.); (N.M.M.)
| | - Vladimir Djordjevic
- Department of Surgery, University Clinical Center of Serbia, 11000 Belgrade, Serbia;
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
| | - Nikola Milic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia;
| | - Nevena Veljkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia;
- Heliant Ltd., 11000 Belgrade, Serbia
| | - Natasa M. Milic
- Institute for Medical Statistics and Informatics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (J.M.-L.); (P.M.); (N.R.); (N.M.M.)
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Dejan Radenkovic
- Department of Surgery, University Clinical Center of Serbia, 11000 Belgrade, Serbia;
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
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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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Sanchez C, Roch B, Mazard T, Blache P, Dache ZAA, Pastor B, Pisareva E, Tanos R, Thierry AR. Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics. JCI Insight 2021; 6:144561. [PMID: 33571170 PMCID: PMC8119211 DOI: 10.1172/jci.insight.144561] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
To unequivocally address their unresolved intimate structures in blood, we scrutinized the size distribution of circulating cell-free DNA (cfDNA) using whole-genome sequencing (WGS) from both double- and single-strand DNA library preparations (DSP and SSP, n = 7) and using quantitative PCR (Q-PCR, n = 116). The size profile in healthy individuals was remarkably homogenous when using DSP sequencing or SSP sequencing. CfDNA size profile had a characteristic nucleosome fragmentation pattern. Overall, our data indicate that the proportion of cfDNA inserted in mono-nucleosomes, di-nucleosomes, and chromatin of higher molecular size (>1000 bp) can be estimated as 67.5% to 80%, 9.4% to 11.5%, and 8.5% to 21.0%, respectively. Although DNA on single chromatosomes or mono-nucleosomes is detectable, our data revealed that cfDNA is highly nicked (97%–98%) on those structures, which appear to be subjected to continuous nuclease activity in the bloodstream. Fragments analysis allows the distinction of cfDNA of different origins: first, cfDNA size profile analysis may be useful in cfDNA extract quality control; second, subtle but reliable differences between metastatic colorectal cancer patients and healthy individuals vary with the proportion of malignant cell-derived cfDNA in plasma extracts, pointing to a higher degree of cfDNA fragmentation and nuclease activity in samples with high malignant cell cfDNA content.
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Affiliation(s)
- Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Benoit Roch
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,Thoracic Oncology Unit, Arnaud de Villeneuve Hospital, University Hospital of Montpellier, Montpellier, France
| | - Thibault Mazard
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Philippe Blache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Zahra Al Amir Dache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Rita Tanos
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
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11
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Evaluating the quantity, quality and size distribution of cell-free DNA by multiplex droplet digital PCR. Sci Rep 2020; 10:12564. [PMID: 32724107 PMCID: PMC7387491 DOI: 10.1038/s41598-020-69432-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/07/2020] [Indexed: 01/06/2023] Open
Abstract
Cell-free DNA (cfDNA) has become a comprehensive biomarker in the fields of non-invasive cancer detection and monitoring, organ transplantation, prenatal genetic testing and pathogen detection. While cfDNA samples can be obtained using a broad variety of approaches, there is an urgent need to standardize analytical tools aimed at assessing its basic properties. Typical methods to determine the yield and fragment size distribution of cfDNA samples are usually either blind to genomic DNA contamination or the presence of enzymatic inhibitors, which can confound and undermine downstream analyses. Here, we present a novel droplet digital PCR assay to identify suboptimal samples and aberrant cfDNA size distributions, the latter typically associated with high levels of circulating tumour DNA (ctDNA). Our assay was designed to promiscuously cross-amplify members of the human olfactory receptor (OR) gene family and includes a customizable diploid locus for the determination of absolute cfDNA concentrations. We demonstrate here the utility of our assay to estimate the yield and quality of cfDNA extracts and deduce fragment size distributions that correlate well with those inferred by capillary electrophoresis and high throughput sequencing. The assay described herein is a powerful tool to establish quality controls and stratify cfDNA samples based on presumed ctDNA levels, then facilitating the implementation of robust, cost-effective and standardized analytical workflows into clinical practice.
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12
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Ermakov KV, Bukhvostov AA, Vedenkin AS, Stovbun SV, Dvornikov AS, Kuznetsov DA. Ultrashort ssDNA in Retinoblastoma Patients Blood Plasma Detected by a Novel High Resolution HPLC Technique: a Preliminary Report. ACTA MEDICA (HRADEC KRÁLOVÉ) 2020; 62:170-173. [PMID: 32036851 DOI: 10.14712/18059694.2020.8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A significant population of ultrashort (50-150n) single-stranded DNA fragments were found in exosome-free blood plasma of retinoblastoma patients (6.84 ng mL-1), but not in plasma of healthy donors. An original high resolution HPLC technique has been proposed to reveal and characterize this peculiarity. To solve this task, a novel molecular size exclusion - anion exchange analytical technique was developed. Its applicability to diagnostics and oncogenesis research is quizzed here.
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Affiliation(s)
- Kirill V Ermakov
- N.I. Pirogov Russian National Research Medical University, Russian Federal Ministry of Health, Ostrovityanov St., 1, Moscow 117997, Russia.
| | - Alexander A Bukhvostov
- N.I. Pirogov Russian National Research Medical University, Russian Federal Ministry of Health, Ostrovityanov St., 1, Moscow 117997, Russia
| | - Alexander S Vedenkin
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin St., 4, Moscow 119991, Russia
| | - Sergey V Stovbun
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin St., 4, Moscow 119991, Russia
| | - Anton S Dvornikov
- N.I. Pirogov Russian National Research Medical University, Russian Federal Ministry of Health, Ostrovityanov St., 1, Moscow 117997, Russia
| | - Dmitry A Kuznetsov
- N.I. Pirogov Russian National Research Medical University, Russian Federal Ministry of Health, Ostrovityanov St., 1, Moscow 117997, Russia.,N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin St., 4, Moscow 119991, Russia
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13
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Tu M, Cheng J, Chen YL, Jea WC, Chen WL, Chen CJ, Ho CL, Huang WL, Lin CC, Su WC, Ye Q, Deignan J, Grody W, Li F, Chia D, Wei F, Liao W, Wong DTW, Strom CM. Electric Field-Induced Release and Measurement (EFIRM): Characterization and Technical Validation of a Novel Liquid Biopsy Platform in Plasma and Saliva. J Mol Diagn 2020; 22:1050-1062. [PMID: 32497715 DOI: 10.1016/j.jmoldx.2020.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/23/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022] Open
Abstract
Electric field-induced release and measurement (EFIRM) is a novel, plate-based, liquid biopsy platform capable of detecting circulating tumor DNA containing EGFR mutations directly from saliva and plasma in both early- and late-stage patients with non-small-cell lung cancer. We investigated the properties of the target molecule for EFIRM and determined that the platform preferentially detects single-stranded DNA molecules. We then investigated the properties of the EFIRM assay and determined the linearity, linear range, precision, and limit of detection for six different EGFR variants (the four most common g.Exon19del variants), p.T790M, and p.L858R). The limit of detection was in single-digit copy number for the latter two mutations, and the limit of detection for Exon19del was 5000 copies. Following these investigations, technical validations were performed for four separate EFIRM liquid biopsy assays, qualitative and quantitative assays for both saliva and plasma. We conclude that EFIRM liquid biopsy is an assay platform that interrogates a biomarker not targeted by any other extant platform (namely, circulating single-stranded DNA molecules). The assay has acceptable performance characteristics in both quantitative and qualitative assays on both saliva and plasma.
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Affiliation(s)
- Michael Tu
- UCLA School of Dentistry, University of California, Los Angeles, Los Angeles, California; Liquid Diagnostics LLC, San Clemente, California
| | - Jordan Cheng
- UCLA School of Dentistry, University of California, Los Angeles, Los Angeles, California
| | - Yi-Lin Chen
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chien Jea
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Li Chen
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Jung Chen
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Liang Ho
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Lun Huang
- Center of Applied Nanotechnology, National Cheng Kung University Center of Applied Nanomedicine, Tainan, Taiwan
| | - Chien-Chung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Wu-Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Qianlin Ye
- UCLA School of Dentistry, University of California, Los Angeles, Los Angeles, California
| | - Josh Deignan
- School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Wayne Grody
- School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Feng Li
- UCLA School of Dentistry, University of California, Los Angeles, Los Angeles, California
| | - David Chia
- School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Fang Wei
- UCLA School of Dentistry, University of California, Los Angeles, Los Angeles, California
| | - Wei Liao
- EZLife Bio Inc., Los Angeles, California
| | - David T W Wong
- UCLA School of Dentistry, University of California, Los Angeles, Los Angeles, California; Department of Head and Neck Surgery, Otolaryngology, School of Engineering, University of California, Los Angeles, Los Angeles, California; Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California.
| | - Charles M Strom
- UCLA School of Dentistry, University of California, Los Angeles, Los Angeles, California; Liquid Diagnostics LLC, San Clemente, California.
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14
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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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15
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Lasham A, Tsai P, Fitzgerald SJ, Mehta SY, Knowlton NS, Braithwaite AW, Print CG. Accessing a New Dimension in TP53 Biology: Multiplex Long Amplicon Digital PCR to Specifically Detect and Quantitate Individual TP53 Transcripts. Cancers (Basel) 2020; 12:cancers12030769. [PMID: 32213968 PMCID: PMC7140069 DOI: 10.3390/cancers12030769] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/21/2022] Open
Abstract
TP53, the most commonly-mutated gene in cancer, undergoes complex alternative splicing. Different TP53 transcripts play different biological roles, both in normal function and in the progression of diseases such as cancer. The study of TP53’s alternative RNA splice forms and their use as clinical biomarkers has been hampered by limited specificity and quantitative accuracy of current methods. TP53 RNA splice variants differ at both 5’ and 3’ ends, but because they have a common central region of 618 bp, the individual TP53 transcripts are impossible to specifically detect and precisely quantitate using standard PCR-based methods or short-read RNA sequencing. Therefore, we devised multiplex probe-based long amplicon droplet digital PCR (ddPCR) assays, which for the first time allow precise end-to-end quantitation of the seven major TP53 transcripts, with amplicons ranging from 0.85 to 1.85 kb. Multiple modifications to standard ddPCR assay procedures were required to enable specific co-amplification of these long transcripts and to overcome issues with secondary structure. Using these assays, we show that several TP53 transcripts are co-expressed in breast cancers, and illustrate the potential for this method to identify novel TP53 transcripts in tumour cells. This capability will facilitate a new level of biological and clinical understanding of the alternatively-spliced TP53 isoforms.
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Affiliation(s)
- Annette Lasham
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1142, New Zealand; (P.T.); (S.J.F.); (N.S.K.); (C.G.P.)
- Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand; (S.Y.M.); (A.W.B.)
- Correspondence:
| | - Peter Tsai
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1142, New Zealand; (P.T.); (S.J.F.); (N.S.K.); (C.G.P.)
- Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand; (S.Y.M.); (A.W.B.)
| | - Sandra J. Fitzgerald
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1142, New Zealand; (P.T.); (S.J.F.); (N.S.K.); (C.G.P.)
- Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand; (S.Y.M.); (A.W.B.)
| | - Sunali Y. Mehta
- Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand; (S.Y.M.); (A.W.B.)
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Nicholas S. Knowlton
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1142, New Zealand; (P.T.); (S.J.F.); (N.S.K.); (C.G.P.)
- Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand; (S.Y.M.); (A.W.B.)
| | - Antony W. Braithwaite
- Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand; (S.Y.M.); (A.W.B.)
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Cristin G. Print
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1142, New Zealand; (P.T.); (S.J.F.); (N.S.K.); (C.G.P.)
- Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand; (S.Y.M.); (A.W.B.)
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16
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Jiang X, Li H, Liu J, Sun H, Zhang L, Li W, Yao J, Cheng Y. Feasibility Analysis of Cell-Free DNA Derived from Plasma of Lung Cancer Patients for Next-Generation Sequencing. Biopreserv Biobank 2020; 18:117-121. [PMID: 32083487 DOI: 10.1089/bio.2019.0115] [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] [Indexed: 12/20/2022] Open
Abstract
Purpose: The quality of specimens directly affects the experimental results. The stability and structural integrity of nucleic acids in samples have a decisive influence on high-throughput sequencing results. Next-generation sequencing (NGS) provides the most comprehensive criteria for evaluating the specimen quality. To test the quality of cell-free DNA (cfDNA) from lung cancer plasma samples stored in our biobank, we conducted a study to evaluate the quality in terms of the genetic level. Methods: A total of 189 peripheral blood samples were collected from patients from patients with EGFR-positive nonsmall cell lung cancer who were seen and treated in Jilin Provincial Cancer Hospital from August 2012 to March 2018. Twelve milliliters of peripheral blood samples were collected and centrifuged at 4°C, 2000 rpm for 15 minutes. Plasma samples were dispensed into cryotubes and stored at -80°C. Plasma cfDNA was extracted by a DNA extraction kit (Qiagen) and the DNA concentration was detected by a Qubit 3.0 fluorometer. Results: The total volume of cfDNA extraction at baseline was 50 μL, the median concentration according to Qubit was 0.633 ng/μL, the range was 0.331-6.09 ng/μL, and the median total DNA was 34.25 ng, ranging from 20.35 to 304.5 ng. The median value of the Qubit concentration in advanced plasma samples was 0.838 ng/μL, ranging from 0.24 to 21.9 ng/μL, and median total DNA was 41.9 ng, ranging from 12.0 to 1095.0 ng. Based on the aforementioned quality assessment factors, 4 of 189 frozen lung cancer baseline plasma samples were not included in further analyses, and for the remaining 185 cases of cfDNA >20 ng, the pass rate was 97.9%. In 143 frozen lung cancer advanced stage plasma samples, 133 cases of cfDNA >20 ng, the pass rate was 93%. Conclusion: Frozen lung cancer plasma samples stored in the biobank for 1-6 years at -80°C under certain conditions still retain a high level of cfDNA, which is suitable for NGS detection.
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Affiliation(s)
- Xueli Jiang
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Hui Li
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China.,Medical Oncology Translational Research Lab, Jilin Provincial Cancer Hospital, Changchun, China
| | - Jingjing Liu
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Heping Sun
- Clinical Trial Institution, Jilin Provincial Cancer Hospital, Changchun, China
| | - Linna Zhang
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Wenxiu Li
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Jie Yao
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Ying Cheng
- Medical Oncology Translational Research Lab, Jilin Provincial Cancer Hospital, Changchun, China.,Department of Medical Thoracic Oncology, Jilin Provincial Cancer Hospital, Changchun, China
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17
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Vincze B, Gáspárdy A, Biácsi A, Papp EÁ, Garamvölgyi L, Sós E, Cseh S, Kovács G, Pádár Z, Zenke P. Sex determination using circulating cell-free fetal DNA in small volume of maternal plasma in elephants. Sci Rep 2019; 9:15254. [PMID: 31649290 PMCID: PMC6813297 DOI: 10.1038/s41598-019-51641-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/04/2019] [Indexed: 11/09/2022] Open
Abstract
The genetic sexing of animals having long gestation periods offers significant benefits in regard to breeding management among their populations living in captivity. In our study, a new increased-sensitivity PCR method for fetal sexing was developed and tested successfully on elephants, from only a small volume of maternal plasma. Suitable sensitivity was obtained by using short, reduced amplicon lengths with fluorescent labelling for capillary electrophoresis detection. The fundamental principle for this technique was based on the detection of two Y-specific markers (AmelY and SRY), the presence of which indicates the mother is carrying a male fetus and the absence of these markers designates a female fetus. As a reaction control, the X-chromosomal marker (PlpX) was used. To the best of our knowledge, this is the first report on this topic, confirming the presence of fetal cell-free DNA from the plasma of a pregnant captive elephant, and demonstrating a new opportunity for non-invasive assessment in fetal sex determination.
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Affiliation(s)
- Boglárka Vincze
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, 1078, István utca 2., Budapest, Hungary.
| | - András Gáspárdy
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, 1078, István utca 2., Budapest, Hungary
| | | | - Endre Ákos Papp
- Sóstó Zoo, Sóstófürdő, 4431, Sóstói út, Nyíregyháza, Hungary
| | | | - Endre Sós
- Budapest Zoo and Botanic Garden, 1146 Állatkerti krt. 6-12., Budapest, Hungary
| | - Sándor Cseh
- Department of Reproduction and Obstetrics, University of Veterinary Medicine Budapest, 1078, István utca 2., Budapest, Hungary
| | - Gábor Kovács
- Research Centre for Forensic Sciences and Criminology, University Széchenyi István, Győr, 9026, Egyetem tér 1., Győr, Hungary
| | - Zsolt Pádár
- Research Centre for Forensic Sciences and Criminology, University Széchenyi István, Győr, 9026, Egyetem tér 1., Győr, Hungary.,Department of Forensic Medicine, Medical School, University of Pécs, 7624, Szigeti út 12., Pécs, Hungary
| | - Petra Zenke
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, 1078, István utca 2., Budapest, Hungary.
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18
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Application of digital PCR for assessing DNA fragmentation in cytotoxicity response. Biochim Biophys Acta Gen Subj 2019; 1863:1235-1242. [DOI: 10.1016/j.bbagen.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/04/2019] [Accepted: 05/02/2019] [Indexed: 12/18/2022]
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19
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Konečná B, Tóthová Ľ, Repiská G. Exosomes-Associated DNA-New Marker in Pregnancy Complications? Int J Mol Sci 2019; 20:ijms20122890. [PMID: 31200554 PMCID: PMC6627934 DOI: 10.3390/ijms20122890] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/14/2022] Open
Abstract
Despite a large number of studies, the etiology of pregnancy complications remains unknown. The involvement of cell-free DNA or fetal cell-free DNA in the pathogenesis of pregnancy complications is currently being hypothesized. Cell-free DNA occurs in different forms-free; part of neutrophil extracellular traps; or as recently discovered, carried by extracellular vesicles. Cell-free DNA is believed to activate an inflammatory pathway, which could possibly cause pregnancy complications. It could be hypothesized that DNA in its free form could be easily degraded by nucleases to prevent the inflammatory activation. However, recently, there has been a growing interest in the role of exosomes, potential protectors of cell-free DNA, in pregnancy complications. Most of the interest from recent years is directed towards the micro RNA carried by exosomes. However, exosome-associated DNA in relation to pregnancy complications has not been truly studied yet. DNA, as an important cargo of exosomes, has been so far studied mostly in cancer research. This review collects all the known information on the topic of not only exosome-associated DNA but also some information on vesicles-associated DNA and the studies regarding the role of exosomes in pregnancy complications from recent years. It also suggests possible analysis of exosome-associated DNA in pregnancy from plasma and emphasizes the importance of such analysis for future investigations of pregnancy complications. A major obstacle to the advancement in this field is the proper uniformed technique for exosomes isolation. Similarly, the sensitivity of methods analyzing a small fraction of DNA, potentially fetal DNA, carried by exosomes is variable.
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Affiliation(s)
- Barbora Konečná
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava 81108, Slovakia.
| | - Ľubomíra Tóthová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava 81108, Slovakia.
| | - Gabriela Repiská
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, Bratislava 81372, Slovakia.
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