101
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A review of trace “Touch DNA” deposits: Variability factors and an exploration of cellular composition. Forensic Sci Int Genet 2019; 39:8-18. [DOI: 10.1016/j.fsigen.2018.11.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/14/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023]
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102
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Wu J, Dai W, Wu L, Li W, Xia X, Wang J. Decoding genetic and epigenetic information embedded in cell free DNA with adapted SALP-seq. Int J Cancer 2019; 145:2395-2406. [PMID: 30746694 DOI: 10.1002/ijc.32206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/16/2019] [Accepted: 01/28/2019] [Indexed: 12/31/2022]
Abstract
Cell free DNA (cfDNA) in human plasma carries abundant information, which has therefore been the key sample for noninvasive prenatal testing (NIPT) and liquid biopsy. Especially by using the rapidly developed next-generation sequencing (NGS) techniques, the genetic and epigenetic information embedded in cfDNA has been effectively and extensively decoded. In this process, a key step is to construct the NGS library. Due to its high degradation, the single strand-based method was reported to be more qualified to construct the NGS library of cfDNA. In order to develop a new simple method for this application, this study adapted our recently developed single strand adaptor library preparation (SALP) method for constructing an NGS library of cfDNA. In the improved method, cfDNA was firstly denatured into single strands and then ligated with a single strand adaptor (SSA) that had a 3' overhang of 3 random bases by using T4 DNA ligase. The SSA-ligated DNA was converted into double-stranded DNA with an additional adenine at the other end by polymerizing with Taq polymerase. Next, a barcode T adaptor (BTA) was ligated to this end. Finally, the cfDNA ligated with two adaptors was amplified with the Illumina-compatible primers for NGS. Using the method, this study successfully sequenced 20 cfDNA samples from 16 esophageal cancer patients and 4 healthy people. By bioinformatics analysis, this study found the genetic and epigenetic difference between patients and healthy people and identified 23 epigenetic and 28 genetic altered esophageal cancer-specific genes.
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Affiliation(s)
- Jian Wu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Wei Dai
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Lin Wu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Weiwei Li
- Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xinyi Xia
- Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
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103
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Munakata Y, Shirasuna K, Kuwayama T, Iwata H. Cell-free DNA in medium is associated with the maturation ability of in vitro cultured oocytes. J Reprod Dev 2019; 65:171-175. [PMID: 30745495 PMCID: PMC6473116 DOI: 10.1262/jrd.2018-123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Follicular fluid contains cell-free DNA (cfDNA), which may serve as a useful biomarker of oocyte ability. The present study evaluates whether nuclear and mitochondrial cfDNAs in conditioned oocyte growth medium determine the quality of oocytes cultured in vitro. Oocyte and granulosa cell complexes (OGCs) derived from early antral follicles of gilt ovaries were cultured for 14 days and the amount of cfDNA and lactate concentration in the conditioned culture medium were measured and compared to evaluate oocyte maturation ability. The amount of nuclear cfDNA, but not mitochondrial cfDNA, strongly correlated with the number of dead cells in OGCs. Furthermore, low mitochondrial cfDNA content and high lactate concentration in the medium was associated with high maturation ability of oocytes cultured in vitro. In conclusion, the amounts of nuclear and mitochondrial cfDNAs differentially reflect the conditions of OGCs, and low mitochondrial cfDNA, low glucose content, and high lactate concentration in the medium are associated with the proper maturation of oocytes.
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Affiliation(s)
- Yasuhisa Munakata
- Department of Animal Reproduction, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Koumei Shirasuna
- Department of Animal Reproduction, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Takehito Kuwayama
- Department of Animal Reproduction, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Hisataka Iwata
- Department of Animal Reproduction, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
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104
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Panagopoulou M, Karaglani M, Balgkouranidou I, Pantazi C, Kolios G, Kakolyris S, Chatzaki E. Circulating cell-free DNA release in vitro: kinetics, size profiling, and cancer-related gene methylation. J Cell Physiol 2019; 234:14079-14089. [PMID: 30618174 DOI: 10.1002/jcp.28097] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/07/2018] [Indexed: 12/28/2022]
Abstract
Circulating cell-free DNA (ccfDNA) is a biological entity of great interest due to its potential as liquid biopsy biomaterial carrying clinically valuable information. To better understand its nature, we studied ccfDNA in vitro in two human cancer cell lines MCF-7 and HeLa. Normalized indexes of ccfDNA per cell population decreased over time of culture but were significantly elevated after exposure to IC50 doses of the demethylating/apoptotic agent 5-azacytidine (5-AZA-CR). Fragment-size profiling was indicative of active release, whereas exposure to 5-AZA-CR induced the release of additional shorter fragments, indicative of apoptosis. Finally, the methylation profile of a panel of cancer-specific genes as assessed by quantitative methylation analysis in ccfDNA was identical to the corresponding genomic DNA and followed accurately changes caused by 5-AZA-CR. Overall, our in vitro findings support that ccfDNA can be a reliable biosource of clinically relevant information that can be further studied in these cell culture models.
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Affiliation(s)
- Maria Panagopoulou
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Makrina Karaglani
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna Balgkouranidou
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece.,Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Chrisoula Pantazi
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Stylianos Kakolyris
- Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ekaterini Chatzaki
- Department of Medicine, Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
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105
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Ultrasensitive Detection of Circulating Tumor DNA in Lymphoma via Targeted Hybridization Capture and Deep Sequencing of Barcoded Libraries. Methods Mol Biol 2019; 1956:383-435. [PMID: 30779047 DOI: 10.1007/978-1-4939-9151-8_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Liquid biopsies are rapidly emerging as powerful tools for the early detection of cancer, noninvasive genomic profiling of localized or metastatic tumors, prompt detection of treatment resistance-associated mutations, and monitoring of therapeutic response and minimal residual disease in patients during clinical follow-up. Growing evidence strongly supports the utility of circulating tumor DNA (ctDNA) as a biomarker for the stratification and clinical management of lymphoma patients. However, ctDNA is diluted by variable amounts of cell-free DNA (cfDNA) shed by nonneoplastic cells causing a background signal of wild-type DNA that limits the sensitivity of methods that rely on DNA sequencing. Here, we describe an error suppression method for single-molecule counting that relies on targeted sequencing of cfDNA libraries constructed with semi-degenerate barcode adapters. Custom pools of biotinylated DNA baits for target enrichment can be designed to specifically track somatic mutations in one patient, survey mutation hotspots with diagnostic and prognostic value or be comprised of comprehensive gene panels with broad patient coverage in lymphoma. Such methods are amenable to track ctDNA levels during longitudinal liquid biopsy testing with high specificity and sensitivity and characterize, in real time, the genetic profiles of tumors without the need of standard invasive biopsies. The analysis of ultra-deep sequencing data according to the bioinformatics pipelines also described in this chapter affords to harness lower limits of detection for ctDNA below 0.1%.
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106
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Lee JS, Hur JY, Kim IA, Kim HJ, Choi CM, Lee JC, Kim WS, Lee KY. Liquid biopsy using the supernatant of a pleural effusion for EGFR genotyping in pulmonary adenocarcinoma patients: a comparison between cell-free DNA and extracellular vesicle-derived DNA. BMC Cancer 2018; 18:1236. [PMID: 30526536 PMCID: PMC6288853 DOI: 10.1186/s12885-018-5138-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND EGFR genotyping in pulmonary adenocarcinoma patients who develop pleural effusions is mostly performed using cytology or cell block slides with low sensitivity. Liquid biopsy using the supernatant of pleural effusions may be more effective because they contain many components released by cancer cells. Extracellular vesicles (EVs) are known to carry oncogenic double-stranded DNA that is considered a notable biomarker. Here, we investigate the efficiency of liquid biopsy using cell-free DNA (cfDNA) and extracellular vesicle-derived DNA (EV-derived DNA) from the supernatant of pleural effusions for EGFR genotyping in patients with pulmonary adenocarcinoma. METHODS Fifty pleural effusion samples from patients with pulmonary adenocarcinoma were evaluated. The supernatant, after removing the cell pellet by centrifugation, was used for liquid biopsy, and EVs were isolated from the pleural effusion by ultracentrifugation. EV-derived DNA and cfDNA were extracted separately, and EGFR genotyping was performed by the PNA clamping method. RESULTS Among 32 patients who were EGFR-tyrosine kinase inhibitor (TKI) naïve with a known tissue EGFR genotype, liquid biopsy using EV-derived DNA from the pleural effusion supernatant showed 100% matching results with tissue EGFR genotyping in 19 EGFR mutant cases and detected three additional EGFR mutations in patients with wild-type (WT) tissue. Liquid biopsy using cfDNA from pleural effusion supernatants missed two cases of tissue-based EGFR mutations and found two additional EGFR mutation cases. In 18 patients who acquired resistance to EGFR-TKI, EGFR genotyping using EV-derived DNA from the pleural effusion supernatant detected the T790 M mutation in 13 of 18 (72.2%) patients, and this mutation was detected in 11 (61.1%) patients using cfDNA. By contrast, only three patients were found to present the T790 M mutation when using cell block or cytology slides. CONCLUSIONS Liquid biopsy using the supernatant of pleural effusions showed significantly improved results for EGFR genotyping compared to those using conventional cell block or cytology samples. Liquid biopsy using EV-derived DNA is promising for EGFR genotyping, including T790 M detection in pulmonary adenocarcinoma patients who develop pleural effusions.
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Affiliation(s)
- Jong Sik Lee
- Department of Pulmonary, Lung Cancer Center, Konkuk University Medical Center and Medicine, Konkuk University School of Medicine, 120-1 Hwayang-dong, Gwangjin-Gu, Seoul, 05030, Republic of Korea
| | - Jae Young Hur
- Department of Pulmonary, Lung Cancer Center, Konkuk University Medical Center and Medicine, Konkuk University School of Medicine, 120-1 Hwayang-dong, Gwangjin-Gu, Seoul, 05030, Republic of Korea.,Department of Pathology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - In Ae Kim
- Department of Pulmonary, Lung Cancer Center, Konkuk University Medical Center and Medicine, Konkuk University School of Medicine, 120-1 Hwayang-dong, Gwangjin-Gu, Seoul, 05030, Republic of Korea
| | - Hee Joung Kim
- Department of Pulmonary, Lung Cancer Center, Konkuk University Medical Center and Medicine, Konkuk University School of Medicine, 120-1 Hwayang-dong, Gwangjin-Gu, Seoul, 05030, Republic of Korea.,Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Chang Min Choi
- Department of Pulmonary and Critical Care Medicine, University of Ulsan, College of Medicine, Asan Medical Center, Seoul, Republic of Korea.,Department of Oncology, University of Ulsan, College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Jae Chol Lee
- Department of Pulmonary and Critical Care Medicine, University of Ulsan, College of Medicine, Asan Medical Center, Seoul, Republic of Korea.,Department of Oncology, University of Ulsan, College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Wan Seop Kim
- Department of Pathology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Kye Young Lee
- Department of Pulmonary, Lung Cancer Center, Konkuk University Medical Center and Medicine, Konkuk University School of Medicine, 120-1 Hwayang-dong, Gwangjin-Gu, Seoul, 05030, Republic of Korea. .,Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul, Republic of Korea.
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107
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Characteristics, properties, and potential applications of circulating cell-free dna in clinical diagnostics: a focus on transplantation. J Immunol Methods 2018; 463:27-38. [DOI: 10.1016/j.jim.2018.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022]
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108
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Changes in the biochemical taste of cytoplasmic and cell-free DNA are major fuels for inflamm-aging. Semin Immunol 2018; 40:6-16. [DOI: 10.1016/j.smim.2018.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
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109
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Mouliere F, Chandrananda D, Piskorz AM, Moore EK, Morris J, Ahlborn LB, Mair R, Goranova T, Marass F, Heider K, Wan JCM, Supernat A, Hudecova I, Gounaris I, Ros S, Jimenez-Linan M, Garcia-Corbacho J, Patel K, Østrup O, Murphy S, Eldridge MD, Gale D, Stewart GD, Burge J, Cooper WN, van der Heijden MS, Massie CE, Watts C, Corrie P, Pacey S, Brindle KM, Baird RD, Mau-Sørensen M, Parkinson CA, Smith CG, Brenton JD, Rosenfeld N. Enhanced detection of circulating tumor DNA by fragment size analysis. Sci Transl Med 2018; 10:eaat4921. [PMID: 30404863 PMCID: PMC6483061 DOI: 10.1126/scitranslmed.aat4921] [Citation(s) in RCA: 596] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022]
Abstract
Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95% of cases and more than fourfold enrichment in >10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC <0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA.
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Affiliation(s)
- Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Anna M Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Elizabeth K Moore
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
| | - James Morris
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Lise Barlebo Ahlborn
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Teodora Goranova
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Francesco Marass
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Jonathan C M Wan
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Anna Supernat
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Irena Hudecova
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Ioannis Gounaris
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
| | - Susana Ros
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Mercedes Jimenez-Linan
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
| | - Javier Garcia-Corbacho
- Clinical Trials Unit, Clinic Institute of Haematological and Oncological Diseases, Hospital Clinic de Barcelona, 170 08036 Barcelona, Spain
| | - Keval Patel
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Olga Østrup
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Suzanne Murphy
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Grant D Stewart
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Academic Urology Group, Department of Surgery, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Johanna Burge
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Academic Urology Group, Department of Surgery, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Michiel S van der Heijden
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Charles E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Department of Oncology, University of Cambridge, CB2 0XZ Cambridge, UK
| | - Colin Watts
- Institute of Cancer Genomics Science, University of Birmingham, B15 2TT Birmingham, UK
| | - Pippa Corrie
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
| | - Simon Pacey
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Department of Oncology, University of Cambridge, CB2 0XZ Cambridge, UK
| | - Kevin M Brindle
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Department of Biochemistry, University of Cambridge, CB2 1QW Cambridge, UK
| | - Richard D Baird
- Early Phase Clinical Trials and Breast Cancer Research Teams, Cancer Research UK Cambridge Centre, CB2 0QQ Cambridge, UK
| | - Morten Mau-Sørensen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Christine A Parkinson
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, CB2 0XZ Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, CB2 0QQ Cambridge, UK
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, CB2 0XZ Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, CB2 0QQ Cambridge, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
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110
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Cell-free DNA release under psychosocial and physical stress conditions. Transl Psychiatry 2018; 8:236. [PMID: 30374018 PMCID: PMC6206142 DOI: 10.1038/s41398-018-0264-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/02/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022] Open
Abstract
The understanding of mechanisms linking psychological stress to disease risk depend on reliable stress biomarkers. Circulating cell-free DNA (cfDNA) has emerged as a potential biomarker of cellular stress, aging, inflammatory processes, and cell death. Recent studies indicated that psychosocial stress and physical exercise might also influence its release. We compared the effects of acute psychosocial and physical exercise stress on cfDNA release by exposing 20 young, healthy men to both an acute psychosocial laboratory stressor and an acute physical exercise stressor. Venous blood and saliva samples were collected before and after stress exposure. Cell-free DNA was extracted from plasma and quantified by qPCR. Furthermore, cfDNA fragment length was analyzed and cfDNA methylation patterns were assayed across time. In addition, release of stress hormones and subjective stress responses were measured. Results showed a twofold increase of cfDNA after TSST and fivefold increase after exhaustive treadmill exercise, with an overabundance of shorter cfDNA fragments after physical exhaustion. Interestingly, cell-free mitochondrial DNA showed similar increase after both stress paradigms. Furthermore, cfDNA methylation signatures-used here as a marker for diverse cellular origin-were significantly different post stress tests. While DNA methylation decreased immediately after psychosocial stress, it increased after physical stress, suggesting different cellular sources of active DNA release. In summary, our results suggest stimulus and cell-specific regulation of cfDNA release. Whereas the functional role of stress-associated cfDNA release remains elusive, it might serve as a valuable biomarker in molecular stress research as a part of the psychophysiological stress response.
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111
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Fettke H, Kwan EM, Azad AA. Cell-free DNA in cancer: current insights. Cell Oncol (Dordr) 2018; 42:13-28. [PMID: 30367445 DOI: 10.1007/s13402-018-0413-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The field of liquid biopsies in oncology is rapidly expanding, with the application of cell-free circulating tumour DNA (ctDNA) showing promise in this era of precision medicine. Compared with traditional clinical and radiographic tumour monitoring methods, the analysis of ctDNA provides a minimally-invasive and technically feasible approach to assess temporal and spatial molecular evolutions of the tumour landscape. The constantly advancing technological platforms available for ctDNA extraction and analysis allow greater analytical sensitivities than ever before. The potential translational impact of ctDNA as a blood-based biomarker for the identification, characterization and monitoring of cancer has been demonstrated in numerous proof-of-concept studies, with ctDNA analysis beginning to be applied clinically across multiple facets of oncology. CONCLUSIONS In this review we discuss the biology, recent advancements, technical considerations and clinical implications of ctDNA in the context of cancer, and highlight important challenges and future directions for the integration of ctDNA into standardised patient care.
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Affiliation(s)
- Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
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112
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Bronkhorst AJ, Wentzel JF, Ungerer V, Peters DL, Aucamp J, de Villiers EP, Holdenrieder S, Pretorius PJ. Sequence analysis of cell-free DNA derived from cultured human bone osteosarcoma (143B) cells. Tumour Biol 2018; 40:1010428318801190. [PMID: 30261820 DOI: 10.1177/1010428318801190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The true importance of cell-free DNA in human biology, together with the potential scale of its clinical utility, is tarnished by a lack of understanding of its composition and origin. In investigating the cell-free DNA present in the growth medium of cultured 143B cells, we previously demonstrated that the majority of cell-free DNA is neither a product of apoptosis nor necrosis. In the present study, we investigated the composition and origin of this cell-free DNA population using next-generation sequencing. We found that the cell-free DNA comprises mainly of repetitive DNA, including α-satellite DNA, mini satellites, and transposons that are currently active or exhibit the capacity to become reactivated. A significant portion of these cell-free DNA fragments originates from specific chromosomes, especially chromosomes 1 and 9. In healthy adult somatic cells, the centromeric and pericentromeric regions of these chromosomes are normally densely methylated. However, in many cancer types, these regions are preferentially hypomethylated. This can lead to double-stranded DNA breaks or it can directly impair the formation of proper kinetochore structures. This type of chromosomal instability is a precursor to the formation of nuclear anomalies, including lagging chromosomes and anaphase bridges. DNA fragments derived from these structures can recruit their own nuclear envelope and form secondary nuclear structures known as micronuclei, which can localize to the nuclear periphery and bud out from the membrane. We postulate that the majority of cell-free DNA present in the growth medium of cultured 143B cells originates from these micronuclei.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Johannes F Wentzel
- 2 Centre of Excellence for Nutrition (CEN), North-West University, Potchefstroom, South Africa
| | - Vida Ungerer
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Dimetrie L Peters
- 3 Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, South Africa
| | - Janine Aucamp
- 4 Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | | | - Stefan Holdenrieder
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Piet J Pretorius
- 3 Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, South Africa
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113
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Gasparello J, Allegretti M, Tremante E, Fabbri E, Amoreo CA, Romania P, Melucci E, Messana K, Borgatti M, Giacomini P, Gambari R, Finotti A. Liquid biopsy in mice bearing colorectal carcinoma xenografts: gateways regulating the levels of circulating tumor DNA (ctDNA) and miRNA (ctmiRNA). JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:124. [PMID: 29941002 PMCID: PMC6020232 DOI: 10.1186/s13046-018-0788-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/05/2018] [Indexed: 12/22/2022]
Abstract
Background Circulating tumor DNA (ctDNA) and miRNA (ctmiRNA) are promising biomarkers for early tumor diagnosis, prognosis and monitoring, and to predict therapeutic response. However, a clear understanding of the fine control on their circulating levels is still lacking. Methods Three human colorectal carcinoma cell lines were grown in culture and as tumor xenograft models in nude mice. Chip-based and droplet digital PCR platforms were used to systematically and quantitatively assess the levels of DNAs and miRNAs released into the culture supernatants and mouse blood plasma. Results Strikingly, mutated DNAs from the same (KRAS) and different (PIK3CA and FBWX7) genomic loci were differentially detected in culture supernatants and blood, with LS174T releasing 25 to 60 times less DNA in culture, but giving rise to 7 to 8 times more DNA in blood than LoVo cells. Greater LS174T ctDNA accumulation occurred in spite of similar CD31 immunostaining (micro-vascularization) and lesser proliferation and tissue necrosis as compared to LoVo. As to the three selected miRNAs (miR-221, miR-222 and miR-141), all of them were constitutively present in the plasma of tumor-free mice. Micro-RNA miR-141 was released into HT-29 cell supernatants 10 and 6.5 times less abundantly with respect to LoVo and LS174T, respectively; on the contrary, release of miR-141 in blood of HT-29 xenografted mice was found similar to that observed in LoVo and LS174T mice. Conclusions Taken together, our results support the existence of multiple, finely tuned (non-housekeeping) control gateways that selectively regulate the release/accumulation of distinct ctDNA and miRNA species in culture and tumor xenograft models. Different xenografts (proxies of different patients) considerably differ in gateway usage, adding several layers of complexity to the well-known idea of molecular heterogeneity. We predict that even high tissue representation of mutated DNA and miRNA may result in insufficient diagnostic analyte representation in blood. In this respect, our data show that careful modeling in mice may considerably help to alleviate complexity, for instance by pre-screening for the most abundant circulating analytes in enlarged sets of tumor xenografts. Electronic supplementary material The online version of this article (10.1186/s13046-018-0788-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Gasparello
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Matteo Allegretti
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Elisa Tremante
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | | | - Paolo Romania
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Elisa Melucci
- Pathology, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Katia Messana
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Patrizio Giacomini
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy.
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy
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114
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Automated DNA extraction using cellulose magnetic beads can improve EGFR point mutation detection with liquid biopsy by efficiently recovering short and long DNA fragments. Oncotarget 2018; 9:25181-25192. [PMID: 29861862 PMCID: PMC5982773 DOI: 10.18632/oncotarget.25388] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/28/2018] [Indexed: 12/19/2022] Open
Abstract
The clinical utility of plasma DNA for detecting cancer-specific mutations has rapidly achieved recognition, but reliability has not been established because of relatively low mutation-detection rates compared with those from tissue re-biopsy. To address this shortcoming we examined efficiency, in terms of mutation detection, of an automated DNA extraction system that uses cellulose magnetic beads. A fully automated, highly sensitive point-mutation-detection method, mutation-biased PCR and quenching probe (MBP-QP) system, was used for this study. Plasma DNA was extracted from 61 plasma samples collected from patients with advanced non-small cell lung cancer. Extraction was performed manually with 200 μl plasma (200-M) by using a silica membrane spin column system or an automated system using 200 μl (200-A) or 1000 μl (1000-A) plasma. Median DNA yield quantified by real-time PCR was 4.4, 4.5, and 17.3 ng with the three methods, respectively. Sensitivity for detecting epidermal growth factor receptor (EGFR) L858R point mutation was 36.6%, 58.5%, and 77.5%, and specificity was 93.3%, 100%, and 96.7%, respectively. Concordance rates were 60.6%, 76.1%, and 85.7%. The size distribution of plasma DNA with automated extraction was bimodal with modes at about 170 bp and 5 Kb, and plasma DNA of both sizes included tumor-derived DNA. In this report, we demonstrate that automated DNA extraction using cellulose magnetic beads can improve mutation-detection rates with plasma DNA in association with two overall sizes of DNA fragments recovered by this DNA isolation system. Examining the biological characteristics of these fragments will be the subject of further investigation.
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115
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Wang W, Kong P, Ma G, Li L, Zhu J, Xia T, Xie H, Zhou W, Wang S. Characterization of the release and biological significance of cell-free DNA from breast cancer cell lines. Oncotarget 2018; 8:43180-43191. [PMID: 28574818 PMCID: PMC5522137 DOI: 10.18632/oncotarget.17858] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/14/2017] [Indexed: 12/26/2022] Open
Abstract
In breast cancer, cell-free DNA (cfDNA) has been proven to be a diagnostic and prognostic biomarker. However, there have been few studies on the origin and biological significance of cfDNA. In this study, we assessed the release pattern of cfDNA from breast cancer cell lines under different culture conditions and investigated the biological significance of cfDNA. The cfDNA concentration increased rapidly (6 h) after passage, decreased gradually, and was then maintained at a relatively stable level after 24 h. In addition, the cfDNA concentration did not correlate with the amount of apoptotic and necrotic cells. Interestingly, if more cells were in the G1 phase, more cfDNA was detected (p < 0.01) and the cfDNA concentration correlated positively with the percent of cells in the G1 phase (p < 0.05). We observed that cells could release cfDNA actively, but not exclusively, via exosomes. Furthermore, we showed that cfDNA could stimulate hormone receptor-positive breast cancer cell proliferation by activating the TLR9-NF-κB-cyclin D1 pathway. In conclusion, cfDNA is released from breast cancer mainly by active secretion, and cfDNA could stimulate proliferation of breast cancer cells.
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Affiliation(s)
- Wei Wang
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Peng Kong
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Ge Ma
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Li Li
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Jin Zhu
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Tiansong Xia
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Hui Xie
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Wenbin Zhou
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Shui Wang
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
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116
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Nasrazadani A, Thomas RA, Oesterreich S, Lee AV. Precision Medicine in Hormone Receptor-Positive Breast Cancer. Front Oncol 2018; 8:144. [PMID: 29780747 PMCID: PMC5945817 DOI: 10.3389/fonc.2018.00144] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/19/2018] [Indexed: 01/07/2023] Open
Abstract
In recent decades, breast cancer has become largely manageable due to successes with hormone receptor targeting. Hormone receptor-positive tumors have favorable outcomes in comparison to estrogen receptor (ESR1, ER)/progesterone receptor-negative tumors given the targetable nature of these tumors, as well as their inherently less aggressive character. Nonetheless, treatment resistance is frequently encountered due to a variety of mechanisms, including ESR1 mutations and loss of ER expression. A new era of precision medicine utilizes a range of methodologies to allow real-time analysis of individual genomic signatures in metastases and liquid biopsies with the goal of finding clinically actionable targets. Preliminary studies have shown improved progression-free survival and overall survival with implementation of this information for clinical decision making. In this review, we will discuss the opportunities and challenges in integrating precision medicine through next-generation genomic sequencing into the management of breast cancer.
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Affiliation(s)
- Azadeh Nasrazadani
- Department of Medicine, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Roby A Thomas
- Department of Medicine, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Steffi Oesterreich
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, United States
| | - Adrian V Lee
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, United States
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117
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. The diverse origins of circulating cell-free DNA in the human body: a critical re-evaluation of the literature. Biol Rev Camb Philos Soc 2018; 93:1649-1683. [PMID: 29654714 DOI: 10.1111/brv.12413] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 12/13/2022]
Abstract
Since the detection of cell-free DNA (cfDNA) in human plasma in 1948, it has been investigated as a non-invasive screening tool for many diseases, especially solid tumours and foetal genetic abnormalities. However, to date our lack of knowledge regarding the origin and purpose of cfDNA in a physiological environment has limited its use to more obvious diagnostics, neglecting, for example, its potential utility in the identification of predisposition to disease, earlier detection of cancers, and lifestyle-induced epigenetic changes. Moreover, the concept or mechanism of cfDNA could also have potential therapeutic uses such as in immuno- or gene therapy. This review presents an extensive compilation of the putative origins of cfDNA and then contrasts the contributions of cellular breakdown processes with active mechanisms for the release of cfDNA into the extracellular environment. The involvement of cfDNA derived from both cellular breakdown and active release in lateral information transfer is also discussed. We hope to encourage researchers to adopt a more holistic view of cfDNA research, taking into account all the biological pathways in which cfDNA is involved, and to give serious consideration to the integration of in vitro and in vivo research. We also wish to encourage researchers not to limit their focus to the apoptotic or necrotic fraction of cfDNA, but to investigate the intercellular messaging capabilities of the actively released fraction of cfDNA and to study the role of cfDNA in pathogenesis.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
| | - Abel J Bronkhorst
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
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118
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Kansaku K, Munakata Y, Itami N, Shirasuna K, Kuwayama T, Iwata H. Mitochondrial dysfunction in cumulus-oocyte complexes increases cell-free mitochondrial DNA. J Reprod Dev 2018; 64:261-266. [PMID: 29618676 PMCID: PMC6021605 DOI: 10.1262/jrd.2018-012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
This study examined the concentration of cell-free mitochondrial DNA (cf-mtDNA) in porcine follicular fluid (FF) and explored whether the cfDNA level in the culture medium could reflect mitochondrial dysfunction in cumulus cell-oocyte complexes (COCs). cfDNA concentration was higher in the fluid of small-sized follicles, compared to that in larger follicles. The length of cfDNA ranged from short (152 bp) to long (1,914 bp) mtDNA in FF, detected by polymerase chain reaction (PCR). cfDNA concentration in FF significantly correlated with the mtDNA copy number in FF but not with the number of one-copy gene (nuclear DNA) in FF. When the COCs were treated with the mitochondrial uncoupler, namely carbonyl cyanide m-chlorophenyl hydrazone (CCCP), for 2 h and incubated for 42 h, subsequent real-time PCR detected significantly higher amount of cf-mtDNA, compared to nuclear cfDNA, in the spent culture medium. The mtDNA number and viability of cumulus cells and oocytes remained unchanged. When the oocytes were denuded from the cumulus cells following CCCP treatment, PCR detected very low levels of cfDNA in the spent culture medium of the denuded oocytes. In contrast, CCCP treatment of granulosa cells significantly increased the amount of cf-mtDNA in the spent culture medium, without any effect on other markers, including survival rate, apoptosis of cumulus cells, and lactate dehydrogenase levels. Thus, cf-mtDNA was present in FF in a wide range of length, and mitochondrial dysfunction in COCs increased the active secretion of cf-mtDNA in the cultural milieu.
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Affiliation(s)
- Kazuki Kansaku
- Department of Animal Science, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Yasuhisa Munakata
- Department of Animal Science, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Nobuhiko Itami
- Department of Animal Science, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Koumei Shirasuna
- Department of Animal Science, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Takehito Kuwayama
- Department of Animal Science, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Hisataka Iwata
- Department of Animal Science, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
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119
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Olmedillas‐López S, García‐Olmo DC, García‐Arranz M, Peiró‐Pastor R, Aguado B, García‐Olmo D. Liquid biopsy by NGS: differential presence of exons (DPE) in cell-free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer. Cancer Med 2018; 7:1706-1716. [PMID: 29573240 PMCID: PMC5943476 DOI: 10.1002/cam4.1399] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/15/2018] [Accepted: 01/26/2018] [Indexed: 12/22/2022] Open
Abstract
Next‐generation sequencing (NGS) has been proposed as a suitable tool for liquid biopsy in colorectal cancer (CRC), although most studies to date have focused almost exclusively on sequencing of panels of potential clinically actionable genes. We evaluated the clinical value of whole‐exome sequencing (WES) of cell‐free DNA (cfDNA) circulating in plasma, with the goal of identifying differential clinical profiles in patients with CRC. To this end, we applied an original concept, “differential presence of exons” (DPE). We determined differences in levels of 379 exons in plasma cfDNA and used DPE analysis to cluster and classify patients with disseminated and localized disease. The resultant bioinformatics analysis pipeline allowed us to design a predictive DPE algorithm in a small subset of patients that could not be initially classified based on the selection criteria. This DPE suggests that these nucleic acids could be actively released by both tumor and nontumor cells as a means of intercellular communication and might thus play a role in the process of malignant transformation. DPE is a new technique for the study of plasma cfDNA by WES that might have predictive and prognostic value in patients with CRC.
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Affiliation(s)
- Susana Olmedillas‐López
- New Therapies LaboratoryFoundation Health Research Institute‐Fundación Jiménez Díaz University Hospital (FIIS‐FJD)MadridSpain
| | - Dolores C. García‐Olmo
- Experimental Research UnitGeneral University Hospital of AlbaceteAlbaceteSpain
- Institut de Recerca Biomèdica de LleidaCentre de Recerca Experimental Biomèdica Aplicada (CREBA)LleidaSpain
| | - Mariano García‐Arranz
- New Therapies LaboratoryFoundation Health Research Institute‐Fundación Jiménez Díaz University Hospital (FIIS‐FJD)MadridSpain
- Department of SurgerySchool of MedicineUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Ramón Peiró‐Pastor
- Genomics and NGS ServiceCentro de Biología Molecular Severo Ochoa (CBMSO)CSIC‐UAMMadridSpain
| | - Begoña Aguado
- Genomics and NGS ServiceCentro de Biología Molecular Severo Ochoa (CBMSO)CSIC‐UAMMadridSpain
| | - Damián García‐Olmo
- New Therapies LaboratoryFoundation Health Research Institute‐Fundación Jiménez Díaz University Hospital (FIIS‐FJD)MadridSpain
- Department of SurgerySchool of MedicineUniversidad Autónoma de Madrid (UAM)MadridSpain
- Department of SurgeryFundación Jiménez Díaz University HospitalMadridSpain
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120
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Buedts L, Vandenberghe P. Circulating cell-free DNA in hematological malignancies. Haematologica 2018; 101:997-9. [PMID: 27582567 DOI: 10.3324/haematol.2015.131128] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Lieselot Buedts
- Center for Human Genetics, University Hospitals KU Leuven, Belgium
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121
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Bennett CW, Berchem G, Kim YJ, El-Khoury V. Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer. Oncotarget 2018; 7:71013-71035. [PMID: 27589834 PMCID: PMC5342606 DOI: 10.18632/oncotarget.11717] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/11/2016] [Indexed: 12/13/2022] Open
Abstract
Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer. We also present an analysis of the role of cfDNA as a liquid biopsy technique and NGS as an analytical tool in studying EGFR and MET, two frequently mutated genes in lung cancer. Ultimately, we hope that using cfDNA and NGS for cancer diagnosis and treatment will become standard for patients with lung cancer and across the field of oncology.
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Affiliation(s)
- Catherine W Bennett
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Guy Berchem
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg.,Centre Hospitalier de Luxembourg, L-1210 Luxembourg, Luxembourg
| | - Yeoun Jin Kim
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Victoria El-Khoury
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
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122
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Erichsen L, Beermann A, Arauzo-Bravo MJ, Hassan M, Dkhil MA, Al-Quraishy S, Hafiz TA, Fischer JC, Santourlidis S. Genome-wide hypomethylation of LINE-1 and Alu retroelements in cell-free DNA of blood is an epigenetic biomarker of human aging. Saudi J Biol Sci 2018; 25:1220-1226. [PMID: 30174526 PMCID: PMC6117241 DOI: 10.1016/j.sjbs.2018.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/31/2018] [Accepted: 02/11/2018] [Indexed: 11/26/2022] Open
Abstract
Aging associated DNA hypomethylation of LINE-1 and Alu retroelements may be a crucial determinant of loss of genomic integrity, deterioration and cancer. In peripheral blood LINE-1 hypomethylation has been reported to increase during aging, but other studies did not observe significant changes. We hypothesized that these apparently inconsistent reports might relate to differences between cellular and cell-free DNA. Using the technique of idiolocal normalization of real-time methylation-specific PCR (IDLN-MSP) for genetic imbalanced DNA specimens we obtained evidence that LINE-1 hypomethylation in cell-free DNA, but not cellular DNA from peripheral blood is an epigenetic biomarker for human aging. Furthermore, hypomethylation of cell-free DNA is more extensive in smokers, suggesting that it might be used as a surrogate marker for monitoring the improvement of smoking-induced adverse effects after cancelling smoking.
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Affiliation(s)
- Lars Erichsen
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany
| | - Agnes Beermann
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany
| | - Marcos J Arauzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Mohamed Hassan
- Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA.,Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France
| | - Mohamed A Dkhil
- Department of Zoology, College of Science, King Saud University, Saudi Arabia.,Department of Zoology and Entomology, Faculty of Science, Helwan University, Cairo, Egypt
| | - Saleh Al-Quraishy
- Department of Zoology, College of Science, King Saud University, Saudi Arabia
| | - Taghreed A Hafiz
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Saudi Arabia
| | - Johannes C Fischer
- Institute of Transplantation Diagnostics and Cell Therapeutics, University Hospital and Medical Faculty of the Heinrich-Heine-University Duesseldorf, Moorenstr. 5, Duesseldorf 40225, Germany
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany
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123
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Deswaerte V, Nguyen P, West A, Browning AF, Yu L, Ruwanpura SM, Balic J, Livis T, Girard C, Preaudet A, Oshima H, Fung KY, Tye H, Najdovska M, Ernst M, Oshima M, Gabay C, Putoczki T, Jenkins BJ. Inflammasome Adaptor ASC Suppresses Apoptosis of Gastric Cancer Cells by an IL18-Mediated Inflammation-Independent Mechanism. Cancer Res 2017; 78:1293-1307. [PMID: 29282220 DOI: 10.1158/0008-5472.can-17-1887] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/26/2017] [Accepted: 12/19/2017] [Indexed: 11/16/2022]
Abstract
Inflammasomes are key regulators of innate immunity in chronic inflammatory disorders and autoimmune diseases, but their role in inflammation-associated tumorigenesis remains ill-defined. Here we reveal a protumorigenic role in gastric cancer for the key inflammasome adaptor apoptosis-related speck-like protein containing a CARD (ASC) and its effector cytokine IL18. Genetic ablation of ASC in the gp130F/F spontaneous mouse model of intestinal-type gastric cancer suppressed tumorigenesis by augmenting caspase-8-like apoptosis in the gastric epithelium, independently from effects on myeloid cells and mucosal inflammation. This phenotype was characterized by reduced activation of caspase-1 and NF-κB activation and reduced expression of mature IL18, but not IL1β, in gastric tumors. Genetic ablation of IL18 in the same model also suppressed gastric tumorigenesis, whereas blockade of IL1β and IL1α activity upon genetic ablation of the IL1 receptor had no effect. The specific protumorigenic role for IL18 was associated with high IL18 gene expression in the gastric tumor epithelium compared with IL1β, which was preferentially expressed in immune cells. Supporting an epithelial-specific role for IL18, we found it to be highly secreted from human gastric cancer cell lines. Moreover, IL18 blockade either by a neutralizing anti-IL18 antibody or by CRISPR/Cas9-driven deletion of ASC augmented apoptosis in human gastric cancer cells. In clinical specimens of human gastric cancer tumors, we observed a significant positive correlation between elevated mature IL18 protein and ASC mRNA levels. Collectively, our findings reveal the ASC/IL18 signaling axis as a candidate therapeutic target in gastric cancer.Significance: Inflammasome activation that elevates IL18 helps drive gastric cancer by protecting cancer cells against apoptosis, with potential implications for new therapeutic strategies in this setting. Cancer Res; 78(5); 1293-307. ©2017 AACR.
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Affiliation(s)
- Virginie Deswaerte
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Paul Nguyen
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Alison West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Alison F Browning
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Liang Yu
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Saleela M Ruwanpura
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Jesse Balic
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Thaleia Livis
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Charlotte Girard
- Division of Rheumatology, University Hospital of Geneva, Geneva, Switzerland.,Department of Pathology and Immunology, University of Geneva School of Medicine, Geneva, Switzerland
| | - Adele Preaudet
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Hiroko Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Ka Yee Fung
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Hazel Tye
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Meri Najdovska
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Heidelberg, Victoria, Australia
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Cem Gabay
- Division of Rheumatology, University Hospital of Geneva, Geneva, Switzerland.,Department of Pathology and Immunology, University of Geneva School of Medicine, Geneva, Switzerland
| | - Tracy Putoczki
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia. .,Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
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Macías M, Alegre E, Díaz-Lagares A, Patiño A, Pérez-Gracia JL, Sanmamed M, López-López R, Varo N, González A. Liquid Biopsy: From Basic Research to Clinical Practice. Adv Clin Chem 2017; 83:73-119. [PMID: 29304904 DOI: 10.1016/bs.acc.2017.10.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the molecular analysis in biological fluids of nucleic acids, subcellular structures, especially exosomes, and, in the context of cancer, circulating tumor cells. In the last 10 years, there has been an intensive research in liquid biopsy to achieve a less invasive and more precise personalized medicine. Molecular assessment of these circulating biomarkers can complement or even surrogate tissue biopsy. Because of this research, liquid biopsy has been introduced in clinical practice, especially in oncology, prenatal screening, and transplantation. Here we review the biology, methodological approaches, and clinical applications of the main biomarkers involved in liquid biopsy.
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Affiliation(s)
| | - Estibaliz Alegre
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Angel Díaz-Lagares
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Ana Patiño
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Jose L Pérez-Gracia
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Miguel Sanmamed
- Yale University School of Medicine, New Haven, CT, United States
| | - Rafael López-López
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Nerea Varo
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Alvaro González
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain.
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125
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Postel M, Roosen A, Laurent-Puig P, Taly V, Wang-Renault SF. Droplet-based digital PCR and next generation sequencing for monitoring circulating tumor DNA: a cancer diagnostic perspective. Expert Rev Mol Diagn 2017; 18:7-17. [PMID: 29115895 DOI: 10.1080/14737159.2018.1400384] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Early detection of cancers through the analysis of ctDNA could have a significant impact on morbidity and mortality of cancer patients. However, using ctDNA for early cancer diagnosis is challenging partly due to the low amount of tumor DNA released in the circulation and its dilution within DNA originating from non-tumor cells. Development of new technologies such as droplet-based digital PCR (ddPCR) or optimized next generation sequencing (NGS) has greatly improved the sensitivity, specificity and precision for the detection of rare sequences. Areas covered: This paper will focus on the potential application of ddPCR and optimized NGS to detect ctDNA for detection of cancer recurrence and minimal residual disease as well as early diagnosis of cancer patients. Expert commentary: Compared to tumor tissue biopsies, blood-based ctDNA analyses are minimally invasive and accessible for regular follow-up of cancer patients. They are also described as a better picture of patients' pathology allowing to highlight both tumor heterogeneity and multiple tumor sites. After a brief introduction on the application of the follow-up of ctDNA using genetic or epigenetic biomarkers for prognosis and surveillance of cancer patients, potential perspectives of using ctDNA for early diagnosis of cancers will be presented.
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Affiliation(s)
- Mathilde Postel
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France
| | - Alice Roosen
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France
| | - Pierre Laurent-Puig
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France.,b Department of Biology , European Georges Pompidou Hospital, AP-HP , Paris , France
| | - Valerie Taly
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France
| | - Shu-Fang Wang-Renault
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France
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126
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Velcheti V, Pennell NA. Non-invasive diagnostic platforms in management of non-small cell lung cancer: opportunities and challenges. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:378. [PMID: 29057238 DOI: 10.21037/atm.2017.08.24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Several non-invasive diagnostic platforms are already being incorporated in routine clinical practice in the work up and monitoring of patients with lung cancer. These approaches have great potential to improve patient selection and monitor patients while on therapy, however several challenges exist in clinical validation and standardization of such platforms. In this review, we summarize the current technologies available for non-invasive diagnostic evaluation from the blood of patients with non-small cell lung cancer (NSCLC), and discuss the technical and logistical challenges associated incorporating such testing in clinical practice.
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Affiliation(s)
- Vamsidhar Velcheti
- Department of Hematology and Medical Oncology, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH, USA
| | - Nathan A Pennell
- Department of Hematology and Medical Oncology, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH, USA
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127
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Bartels S, Persing S, Hasemeier B, Schipper E, Kreipe H, Lehmann U. Molecular Analysis of Circulating Cell-Free DNA from Lung Cancer Patients in Routine Laboratory Practice. J Mol Diagn 2017; 19:722-732. [DOI: 10.1016/j.jmoldx.2017.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/18/2017] [Indexed: 01/30/2023] Open
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Aucamp J, Calitz C, Bronkhorst AJ, Wrzesinski K, Hamman S, Gouws C, Pretorius PJ. Cell-free DNA in a three-dimensional spheroid cell culture model: A preliminary study. Int J Biochem Cell Biol 2017; 89:182-192. [DOI: 10.1016/j.biocel.2017.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/07/2017] [Accepted: 06/22/2017] [Indexed: 02/07/2023]
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129
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Aucamp J, Bronkhorst AJ, Peters DL, Van Dyk HC, Van der Westhuizen FH, Pretorius PJ. Kinetic analysis, size profiling, and bioenergetic association of DNA released by selected cell lines in vitro. Cell Mol Life Sci 2017; 74:2689-2707. [PMID: 28315952 PMCID: PMC11107759 DOI: 10.1007/s00018-017-2495-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/19/2017] [Accepted: 02/22/2017] [Indexed: 01/09/2023]
Abstract
Although circulating DNA (cirDNA) analysis shows great promise as a screening tool for a wide range of pathologies, numerous stumbling blocks hinder the rapid translation of research to clinical practice. This is related directly to the inherent complexity of the in vivo setting, wherein the influence of complex systems of interconnected cellular responses and putative DNA sources creates a seemingly arbitrary representation of the quantitative and qualitative properties of the cirDNA in the blood of any individual. Therefore, to evaluate the potential of in vitro cell cultures to circumvent the difficulties encountered in in vivo investigations, the purpose of this work was to elucidate the characteristics of the DNA released [cell-free DNA (cfDNA)] by eight different cell lines. This revealed three different forms of cfDNA release patterns and the presence of nucleosomal fragments as well as actively released forms of DNA, which are not only consistently observed in every tested cell line, but also in plasma samples. Correlations between cfDNA release and cellular origin, growth rate, and cancer status were also investigated by screening and comparing bioenergetics flux parameters. These results show statistically significant correlations between cfDNA levels and glycolysis, while no correlations between cfDNA levels and oxidative phosphorylation were observed. Furthermore, several correlations between growth rate, cancer status, and dependency on aerobic glycolysis were observed. Cell cultures can, therefore, successfully serve as closed-circuit models to either replace or be used in conjunction with biofluid samples, which will enable sharper focus on specific cell types or DNA origins.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Dimetrie L Peters
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Hayley C Van Dyk
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | | | - Piet J Pretorius
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
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130
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Aucamp J, Van Dyk HC, Bronkhorst AJ, Pretorius PJ. Valproic acid alters the content and function of the cell-free DNA released by hepatocellular carcinoma (HepG2) cells in vitro. Biochimie 2017; 140:93-105. [PMID: 28668269 DOI: 10.1016/j.biochi.2017.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 06/27/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND It has long been believed that cell-free DNA (cfDNA) actively released into circulation can serve as intercellular messengers, and their involvement in processes such as the bystander effect strongly support this. However, this intercellular messaging function of cfDNA may have clinical implications that have not yet been considered. METHODS CfDNA was isolated from the growth medium of HepG2 cells treated with valproic acid (VPA). This cfDNA was then administered to untreated cells and cellular metabolic activity was measured. RESULTS VPA altered the characteristics of cfDNA released by treated HepG2 cells in vitro. When administered to untreated cells, the cfDNA from cells treated with VPA resulted in the dose-dependent induction of glycolytic activity within 36 min of administration, but little to no alterations in oxidative phosphorylation. The glycolytic activity lasted for 4-6 h, whereas changes in subsequent cfDNA release and characteristics were found to remain persistent after two 24 h treatments. Fragmented genomic DNA from VPA-treated cells did not induce the effects observed for cfDNA obtained VPA-treated cells. CONCLUSIONS It is possible for cfDNA to, under in vitro conditions, transfer pharmaceutically-induced effects to untreated recipient cells. Further investigation regarding this occurrence under in vivo conditions is, therefore, strongly encouraged. GENERAL SIGNIFICANCE The intercellular messaging functions of cfDNA present in donated biological fluids has potential clinical implications that require urgent attention. These implications may, however, also have potential as new forms of treatment that can circumvent pharmacological barriers.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa.
| | - Hayley C Van Dyk
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Abel J Bronkhorst
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Piet J Pretorius
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
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131
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Raymond CK, Hernandez J, Karr R, Hill K, Li M. Collection of cell-free DNA for genomic analysis of solid tumors in a clinical laboratory setting. PLoS One 2017; 12:e0176241. [PMID: 28448587 PMCID: PMC5407747 DOI: 10.1371/journal.pone.0176241] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/21/2017] [Indexed: 11/21/2022] Open
Abstract
The breadth of diagnostic procedures that utilize cell free DNA (cfDNA) from human plasma has increased dramatically in recent years. Here, we confirm that tumor-derived cfDNA fragments are similar in size distribution to cfDNA derived from normal tissues. Therefore, collection procedures optimized with healthy donor specimens are likely to be applicable to the diagnosis and monitoring of many different cancer types. We verify that the distribution and DNA sequences of fragmentation sites in cfDNA from both normal-germline and tumor-derived cfDNA are non-random. A broad survey of cfDNA from healthy donors suggests that average individuals possess ~6 ng of cfDNA per mL of plasma. Importantly, the cfDNA present in plasma samples that were initially collected as whole blood in K2-EDTA tubes and subsequently processed by centrifugation is stable for several days at ambient temperatures. This observation has the potential to significantly reduce the cost and logistical complexity of shipping clinical samples from the site of collection to centers proficient in diagnostic analysis. Finally, plasma samples collected with high-volume plasma collection devices possess abundant quantities of cfDNA. Since the quantity of analyzed cfDNA is directly proportional to sensitivity of diagnostic assays, this method of plasma collection, where available, could enable highly sensitive post-treatment disease monitoring and early detection of cancer in at-risk individuals.
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Affiliation(s)
| | | | - Reynold Karr
- PlasmaLab International, Everett, Washington, United States of America
- Dept. of Rheumatology, University of Washington, Seattle, Washington, United States of America
| | - Kay Hill
- PlasmaLab International, Everett, Washington, United States of America
| | - Mark Li
- Resolution Bioscience, Bellevue, Washington, United States of America
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Wentzel JF, Lewies A, Bronkhorst AJ, van Dyk E, du Plessis LH, Pretorius PJ. Exposure to high levels of fumarate and succinate leads to apoptotic cytotoxicity and altered global DNA methylation profiles in vitro. Biochimie 2017; 135:28-34. [PMID: 28104508 DOI: 10.1016/j.biochi.2017.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/12/2017] [Indexed: 11/13/2022]
Abstract
In the Krebs cycle, succinate is oxidized to fumarate by succinate dehydrogenase (SDH), followed by the conversion of fumarate to malate by fumarate hydratase (FH). In cells with defective SDH and FH, the Krebs cycle is congested, respiration impaired and fumarate and succinate accumulates. Several studies have indicated that the accumulation of these substrates are associated with cytotoxicity and oncogenesis. High levels of succinate and fumarate induce hypoxia inducible factor (HIF1A) hydroxylases, leading to the activation of oncogenic HIF pathways. However, the role of HIF as primary inducer of oncogenic change has been questioned, as other non-enzymatic mechanisms have been shown to interfere with cellular metabolism, cell signalling as well as disrupting protein function. Owing to the essential roles that SDH and FH play in cellular energy metabolism, and their associated tumor suppressor capacity, it is vital to understand the biochemical effects resulting from the accumulation of their associated metabolites. Therefore, in this study, we investigated the effect of high concentrations of succinate and fumarate exposure on cell viability, genome integrity and global DNA methylation using a human hepatocellular carcinoma (HepG2) cell culture model. It was found that relatively high concentrations of succinate and fumarate cause a loss of cell viability, which seems to be orchestrated through an apoptotic pathway. Cells exposed to high levels of succinate also presented with elevated caspase 3 and/or caspase 7 levels. In addition, elevated levels of fumarate lead to extensive DNA fragmentation, which may contribute pathophysiologically by inducing chromosomal instability, while succinate demonstrated lower genotoxicity. Furthermore, both succinate and fumarate altered the global DNA methylation patterns via significant DNA hypermethylation. Since numerous studies have reported correlations between aberrant DNA methylation and oncogenesis, hypermethylation may contribute to the oncogenesis observed in cells exposed to high concentrations of these metabolites.
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Affiliation(s)
- Johannes F Wentzel
- Centre of Excellence for Pharmaceutical Sciences (PHARMACEN), North-West University, Potchefstroom 2520, South Africa.
| | - Angélique Lewies
- Centre of Excellence for Pharmaceutical Sciences (PHARMACEN), North-West University, Potchefstroom 2520, South Africa
| | - Abel J Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | - Etresia van Dyk
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | - Lissinda H du Plessis
- Centre of Excellence for Pharmaceutical Sciences (PHARMACEN), North-West University, Potchefstroom 2520, South Africa
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
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Spindler KLG. Methodological, biological and clinical aspects of circulating free DNA in metastatic colorectal cancer. Acta Oncol 2017; 56:7-16. [PMID: 28010185 DOI: 10.1080/0284186x.2016.1253861] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Circulating DNA can be used to measure the total cell-free DNA (cfDNA) and for detection and quantification of tumor-specific genetic alterations in the peripheral blood, and the broad clinical potential of circulating DNA has attracted increasing focus over the past decade. Concentrations of circulating DNA are high in metastatic colorectal cancer (CRC), and the total levels of cfDNA have been reported to hold strong prognostic value. Colorectal tumors are characterized by a high frequency of well known, clinically relevant genetic alteration, which is readily detected in the cfDNA and holds potential for tailoring of palliative therapy and for monitoring during treatment. This review aims to present the current literature which has specifically reported data on the potential utility of cfDNA and on tumor-specific mutations in metastatic colorectal cancer (mCRC). METHOD Methodological, biological and clinical aspects are discussed based on the most recent development in this specific setting, and eligible studies were identified by systematic literature searched from Pubmed and EMBASE in addition to conference papers and communications. RESULTS The literature regarding cfDNA in CRC is broad and heterogeneous concerning aims, nomenclature, methods, cohorts and clinical endpoints and consequently difficult to include in a single systematic search. However, the available data underline a strong clinical value of measuring both total cfDNA levels and tumor-specific mutations in the plasma of patients with mCRC, pre- and during systemic therapy. CONCLUSION This paper had gathered the most recent literature on several aspects of cfDNA in mCRC, including methodological, biological and clinical aspects, and discussed the large clinical potential in this specific setting, which needs to be validated in carefully designed prospective studies in statistically relevant cohorts.
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Affiliation(s)
- Karen-Lise G Spindler
- a Department of Oncology , Aarhus University Hospital, Institute of Clinical Medicine, Aarhus University , Aarhus , Denmark
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134
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles. Cell Mol Life Sci 2016; 73:4355-4381. [PMID: 27652382 PMCID: PMC11108302 DOI: 10.1007/s00018-016-2370-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/20/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.
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Affiliation(s)
- Janine Aucamp
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
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Lowes LE, Bratman SV, Dittamore R, Done S, Kelley SO, Mai S, Morin RD, Wyatt AW, Allan AL. Circulating Tumor Cells (CTC) and Cell-Free DNA (cfDNA) Workshop 2016: Scientific Opportunities and Logistics for Cancer Clinical Trial Incorporation. Int J Mol Sci 2016; 17:ijms17091505. [PMID: 27618023 PMCID: PMC5037782 DOI: 10.3390/ijms17091505] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 12/31/2022] Open
Abstract
Despite the identification of circulating tumor cells (CTCs) and cell-free DNA (cfDNA) as potential blood-based biomarkers capable of providing prognostic and predictive information in cancer, they have not been incorporated into routine clinical practice. This resistance is due in part to technological limitations hampering CTC and cfDNA analysis, as well as a limited understanding of precisely how to interpret emergent biomarkers across various disease stages and tumor types. In recognition of these challenges, a group of researchers and clinicians focused on blood-based biomarker development met at the Canadian Cancer Trials Group (CCTG) Spring Meeting in Toronto, Canada on 29 April 2016 for a workshop discussing novel CTC/cfDNA technologies, interpretation of data obtained from CTCs versus cfDNA, challenges regarding disease evolution and heterogeneity, and logistical considerations for incorporation of CTCs/cfDNA into clinical trials, and ultimately into routine clinical use. The objectives of this workshop included discussion of the current barriers to clinical implementation and recent progress made in the field, as well as fueling meaningful collaborations and partnerships between researchers and clinicians. We anticipate that the considerations highlighted at this workshop will lead to advances in both basic and translational research and will ultimately impact patient management strategies and patient outcomes.
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Affiliation(s)
- Lori E Lowes
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6K 4L6, Canada.
- Special Hematology/Flow Cytometry, London Health Sciences Centre, London, ON N6K 4L6, Canada.
| | - Scott V Bratman
- Departments of Radiation Oncology and Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| | | | - Susan Done
- Campbell Family Institute for Breast Cancer Research and Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada.
- Departments of Laboratory Medicine and Pathobiology, and Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 2C4, Canada.
| | - Shana O Kelley
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON M5S 3M2, Canada.
- Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, ON M5S 3M2, Canada.
| | - Sabine Mai
- Manitoba Institute of Cell Biology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Alexander W Wyatt
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada.
| | - Alison L Allan
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6K 4L6, Canada.
- Departments of Anatomy & Cell Biology and Oncology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6K 4L6, Canada.
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