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Green EA, Li R, Albiges L, Choueiri TK, Freedman M, Pal S, Dyrskjøt L, Kamat AM. Clinical Utility of Cell-free and Circulating Tumor DNA in Kidney and Bladder Cancer: A Critical Review of Current Literature. Eur Urol Oncol 2021; 4:893-903. [DOI: 10.1016/j.euo.2021.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/28/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022]
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52
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Wahl SGF, Dai HY, Emdal EF, Ottestad AL, Dale VG, Richardsen E, Halvorsen TO, Grønberg BH. Prognostic value of absolute quantification of mutated KRAS in circulating tumour DNA in lung adenocarcinoma patients prior to therapy. J Pathol Clin Res 2021; 7:209-219. [PMID: 33502820 PMCID: PMC8073004 DOI: 10.1002/cjp2.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a highly sensitive and accurate method for quantification of nucleic acid sequences. We used absolute quantification of mutated v-Ki-ras2 Kirsten rat sarcoma viral oncogene homology gene (KRAS) by ddPCR to investigate the prognostic role of mutated KRAS in patients with KRAS-mutated lung adenocarcinomas. Pre-treatment plasma samples from 60 patients with stages I-IV KRAS-mutated lung adenocarcinomas were analysed for KRAS mutations. The associations between survival, detectable KRAS mutations in plasma, and the plasma concentration of mutated KRAS were assessed. Overall, 23 of 60 (38%) patients had detectable KRAS mutation in plasma. The percentage of patients with detectable mutation was 8% in stage I, 30% in stage II, 71% in stage III, and 73% in stage IV. Estimated overall median progression-free survival (PFS) and overall survival (OS) were 26.2 months [95% confidence interval (CI) 12.5-39.9] and 50.8 months (95% CI 0-107.3), respectively. Patients with detectable mutations in plasma had significantly worse median PFS compared to patients with undetectable mutation (13.1 versus 70.1 months) and shorter median OS (20.7 versus not reached). High circulating tumour DNA (ctDNA) concentrations of mutated KRAS were significantly associated with shorter PFS [hazard ratio (HR) 1.008, 95% CI 1.004-1.012] and OS (HR 1.007, 95% CI 1.003-1.011). All associations remained statistically significant in multivariable analyses. In conclusion, ddPCR is an accurate and easily feasible technique for quantification of KRAS mutations in ctDNA. The presence of detectable KRAS mutation in plasma at baseline was associated with worse PFS and OS. High concentration of mutated KRAS in ctDNA was an independent negative prognostic factor for both PFS and OS.
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Affiliation(s)
- Sissel Gyrid Freim Wahl
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Hong Yan Dai
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Elisabeth F Emdal
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Anine L Ottestad
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Vibeke G Dale
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Elin Richardsen
- Department of Medical BiologyUiT, The Arctic University of NorwayTromsøNorway
- Department of Clinical PathologyUniversity Hospital of North NorwayTromsøNorway
| | - Tarje O Halvorsen
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
- Department of OncologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
- Department of OncologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
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53
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Moradi-Marjaneh R, Asgharzadeh F, Khordad E, Marjaneh MM. The Clinical Impact of Quantitative Cell-free DNA, KRAS, and BRAF Mutations on Response to Anti-EGFR Treatment in Patients with Metastatic Colorectal Cancer. Curr Pharm Des 2021; 27:942-952. [PMID: 33030125 DOI: 10.2174/1381612826666201007163116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
Colorectal cancer (CRC) is one of the most common leading causes of cancer death in the world. Although EGFR inhibitors have established efficacy in metastatic colorectal cancer (mCRC), some patients do not respond to this treatment. The EGFR inhibitors' failure and acquired resistance are partly due to KRAS and BRAF mutations. Thus, prognostic biomarkers that help to select eligible patients are highly in demand. To improve patient selection, assessment of mutational status in circulating cell free DNA (cfDNA), which possibly represents the dynamicity of tumor genetic status better than tumor tissue, could be advantageous. This review summarizes the current knowledge of the prognostic value of cfDNA in patients with mCRC treated with EGFR inhibitors with emphasis on the clinical importance of identification of KRAS and BRAF mutations.
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Affiliation(s)
- Reyhaneh Moradi-Marjaneh
- Department of Basic Sciences, Faculty of Medicine, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Fereshteh Asgharzadeh
- Department of Physiology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Khordad
- Department of Physiology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
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54
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Fernández-Domínguez IJ, Manzo-Merino J, Taja-Chayeb L, Dueñas-González A, Pérez-Cárdenas E, Trejo-Becerril C. The role of extracellular DNA (exDNA) in cellular processes. Cancer Biol Ther 2021; 22:267-278. [PMID: 33858306 DOI: 10.1080/15384047.2021.1890319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nowadays, extracellular DNA or circulating cell-free DNA is considered to be a molecule with clinical applications (diagnosis, prognosis, monitoring of treatment responses, or patient follow-up) in diverse pathologies, especially in cancer. Nevertheless, because of its molecular characteristics, it can have many other functions. This review focuses on the participation of extracellular DNA (exDNA) in fundamental processes such as cell signaling, coagulation, immunity, evolution through horizontal transfer of genetic information, and adaptive response to inflammatory processes. A deeper understanding of its role in each of these processes will allow development of better tools to monitor and control pathologies, as well as helping to generate new therapeutic options, beyond the applicability of DNA in liquid biopsy.
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Affiliation(s)
| | | | - Lucia Taja-Chayeb
- Division of Basic Research, Instituto Nacional de Cancerología, México City
| | - Alfonso Dueñas-González
- Division of Basic Research, Instituto Nacional de Cancerología, México City.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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55
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Sanchez C, Roch B, Mazard T, Blache P, Dache ZAA, Pastor B, Pisareva E, Tanos R, Thierry AR. Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics. JCI Insight 2021; 6:144561. [PMID: 33571170 PMCID: PMC8119211 DOI: 10.1172/jci.insight.144561] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
To unequivocally address their unresolved intimate structures in blood, we scrutinized the size distribution of circulating cell-free DNA (cfDNA) using whole-genome sequencing (WGS) from both double- and single-strand DNA library preparations (DSP and SSP, n = 7) and using quantitative PCR (Q-PCR, n = 116). The size profile in healthy individuals was remarkably homogenous when using DSP sequencing or SSP sequencing. CfDNA size profile had a characteristic nucleosome fragmentation pattern. Overall, our data indicate that the proportion of cfDNA inserted in mono-nucleosomes, di-nucleosomes, and chromatin of higher molecular size (>1000 bp) can be estimated as 67.5% to 80%, 9.4% to 11.5%, and 8.5% to 21.0%, respectively. Although DNA on single chromatosomes or mono-nucleosomes is detectable, our data revealed that cfDNA is highly nicked (97%–98%) on those structures, which appear to be subjected to continuous nuclease activity in the bloodstream. Fragments analysis allows the distinction of cfDNA of different origins: first, cfDNA size profile analysis may be useful in cfDNA extract quality control; second, subtle but reliable differences between metastatic colorectal cancer patients and healthy individuals vary with the proportion of malignant cell-derived cfDNA in plasma extracts, pointing to a higher degree of cfDNA fragmentation and nuclease activity in samples with high malignant cell cfDNA content.
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Affiliation(s)
- Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Benoit Roch
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.,Thoracic Oncology Unit, Arnaud de Villeneuve Hospital, University Hospital of Montpellier, Montpellier, France
| | - Thibault Mazard
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Philippe Blache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Zahra Al Amir Dache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Rita Tanos
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
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Quantification of Circulating Cell Free Mitochondrial DNA in Extracellular Vesicles with PicoGreen™ in Liquid Biopsies: Fast Assessment of Disease/Trauma Severity. Cells 2021; 10:cells10040819. [PMID: 33917426 PMCID: PMC8067453 DOI: 10.3390/cells10040819] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/25/2022] Open
Abstract
The analysis of circulating cell free DNA (ccf-DNA) is an emerging diagnostic tool for the detection and monitoring of tissue injury, disease progression, and potential treatment effects. Currently, most of ccf-DNA in tissue and liquid biopsies is analysed with real-time quantitative PCR (qPCR) that is primer- and template-specific, labour intensive and cost-inefficient. In this report we directly compare the amounts of ccf-DNA in serum of healthy volunteers, and subjects presenting with various stages of lung adenocarcinoma, and survivors of traumatic brain injury using qPCR and quantitative PicoGreen™ fluorescence assay. A significant increase of ccf-DNA in lung adenocarcinoma and traumatic brain injury patients, in comparison to the group of healthy human subjects, was found using both analytical methods. However, the direct correlation between PicoGreen™ fluorescence and qPCR was found only when mitochondrial DNA (mtDNA)-specific primers were used. Further analysis of the location of ccf-DNA indicated that the majority of DNA is located within lumen of extracellular vesicles (EVs) and is easily detected with mtDNA-specific primers. We have concluded that due to the presence of active DNases in the blood, the analysis of DNA within EVs has the potential of providing rapid diagnostic outcomes. Moreover, we speculate that accurate and rapid quantification of ccf-DNA with PicoGreen™ fluorescent probe used as a point of care approach could facilitate immediate assessment and treatment of critically ill patients.
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57
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Neuberger EWI, Hillen B, Mayr K, Simon P, Krämer-Albers EM, Brahmer A. Kinetics and Topology of DNA Associated with Circulating Extracellular Vesicles Released during Exercise. Genes (Basel) 2021; 12:522. [PMID: 33918465 PMCID: PMC8065814 DOI: 10.3390/genes12040522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 12/22/2022] Open
Abstract
Although it is widely accepted that cancer-derived extracellular vesicles (EVs) carry DNA cargo, the association of cell-free circulating DNA (cfDNA) and EVs in plasma of healthy humans remains elusive. Using a physiological exercise model, where EVs and cfDNA are synchronously released, we aimed to characterize the kinetics and localization of DNA associated with EVs. EVs were separated from human plasma using size exclusion chromatography or immuno-affinity capture for CD9+, CD63+, and CD81+ EVs. DNA was quantified with an ultra-sensitive qPCR assay targeting repetitive LINE elements, with or without DNase digestion. This model shows that a minute part of circulating cell-free DNA is associated with EVs. During rest and following exercise, only 0.12% of the total cfDNA occurs in association with CD9+/CD63+/CD81+EVs. DNase digestion experiments indicate that the largest part of EV associated DNA is sensitive to DNase digestion and only ~20% are protected within the lumen of the separated EVs. A single bout of running or cycling exercise increases the levels of EVs, cfDNA, and EV-associated DNA. While EV surface DNA is increasing, DNAse-resistant DNA remains at resting levels, indicating that EVs released during exercise (ExerVs) do not contain DNA. Consequently, DNA is largely associated with the outer surface of circulating EVs. ExerVs recruit cfDNA to their corona, but do not carry DNA in their lumen.
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Affiliation(s)
- Elmo W. I. Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Barlo Hillen
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Katharina Mayr
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Eva-Maria Krämer-Albers
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
| | - Alexandra Brahmer
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
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58
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Mokánszki A, Bádon ES, Mónus A, Tóth L, Bittner N, Méhes G. Cell-free DNA From Pleural Effusion Samples: Is It Right for Molecular Testing in Lung Adenocarcinoma? Pathol Oncol Res 2021; 27:613071. [PMID: 34257581 PMCID: PMC8262152 DOI: 10.3389/pore.2021.613071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 12/03/2022]
Abstract
Pathogenic molecular features gained specific significance in therapeutic decisions in lung carcinoma in the past decade. Initial and follow up genetic testing requres appropriate amounts and quality of tumor derived DNA, but tumor sampling, especially for disease monitoring is generally limited. Further to the peripheral blood (PB), samples from pleural fluid, accumulating in diverse lung processes might serve as an alternative source for cell-free DNA (cfDNA) for genetic profiling. In our study, cfDNA isolated from the pleural effusion and from the PB, and genomic DNA (gDNA) obtained from tissue/cellular samples were analyzed and compared from altogether 65 patients with pulmonary disease, including 36 lung adenocarcinomas. The quantity of effusion cfDNA yield appeared to be significantly higher compared to that from simultaneously collected PB plasma (23.2 vs. 4.8 ng/μl, p < 0.05). Gene mutations could be safely demonstrated from the effusion cfDNA fraction obtained from adenocarcinoma patients, 3/36 EGFR, 9/36 KRAS and 1/36 BRAF gene variants were detected. In this series, 9/13 samples showed an effusion+/plasma-mutational status, while only 1/13 samples presented with the opposite findings (effusion-/plasma+). gDNA analysis from sediment cell blocks from the identical effusion sample was surprisingly ineffective for lung adenocarcinoma profiling due to the low DNA yield. In conclusion, the cell free supernatant of pleural effusions appears to concentrate cancer derived cfDNA and seems to be particularly suitable for serial genotyping of pulmonary adenocarcinoma.
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Affiliation(s)
- Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Tóth
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Nóra Bittner
- Department of Pulmonology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Andersson D, Kristiansson H, Kubista M, Ståhlberg A. Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations. Expert Rev Mol Diagn 2021; 21:299-310. [PMID: 33683971 DOI: 10.1080/14737159.2021.1889371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation.Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications.Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Helena Kristiansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Kubista
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.,TATAA Biocenter, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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60
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Wang YF, Wang XJ, Lu Z, Liu SR, Jiang Y, Wan XQ, Cheng CC, Shi LH, Wang LH, Ding Y. Overexpression of Stat3 increases circulating cfDNA in breast cancer. Breast Cancer Res Treat 2021; 187:69-80. [PMID: 33630196 DOI: 10.1007/s10549-021-06142-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE Current studies on circulating cell-free DNA (cfDNA) have been focusing on its potential as biomarkers in liquid biopsy by detecting its content or genetic and epigenetic changes for the evaluation of tumor burden and therapeutic efficacy. However, the regulatory mechanism of cfDNA release remains unclear. Stat3 has been documented as an oncogene for the development and metastasis of breast cancer cells. In this study, we investigated whether Stat3 affects the release of cfDNA into blood and its association with the number of circulating tumor cells (CTCs). METHODS The cfDNA level in plasma of patients with breast cancer and healthy volunteers were determined by quantitative real-time PCR. Three mouse breast cancer models with different Stat3 expression were generated and used to established three breast cancer orthotopic animal models to examine the effect of Stat3 on cfDNA release in vivo. Stat3 mediated Epithelial-mesenchymal phenotype transition of CTCs was determined by immunofluorescence assay and Western blot assay. RESULTS The data showed that Stat3 increased circulating cfDNA, which is correlated with the increased volume of primary tumors and number of CTCs, accompanied with the dynamic EMT changes regulated by Snail induction. Furthermore, the high level of total circulating cfDNA and Stat3-cfDNA in patients with breast cancer were detected by quantitative real-time PCR using GAPDH and Stat3 primers. CONCLUSION Our results suggested that Stat3 increases the circulating cfDNA and CTCs in breast cancer.
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Affiliation(s)
- Yi-Fei Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xue-Jian Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Zhong Lu
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Shu-Rong Liu
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Yu Jiang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xiao-Qing Wan
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China
| | - Cong-Cong Cheng
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Li-Hong Shi
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Li-Hua Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Yi Ding
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China. .,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China.
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Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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Hu Z, Chen H, Long Y, Li P, Gu Y. The main sources of circulating cell-free DNA: Apoptosis, necrosis and active secretion. Crit Rev Oncol Hematol 2021; 157:103166. [DOI: 10.1016/j.critrevonc.2020.103166] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 01/05/2023] Open
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Keller L, Belloum Y, Wikman H, Pantel K. Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond. Br J Cancer 2021; 124:345-358. [PMID: 32968207 PMCID: PMC7852556 DOI: 10.1038/s41416-020-01047-5] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/22/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) derived from tumours is present in the plasma of cancer patients. The majority of currently available studies on the use of this circulating tumour DNA (ctDNA) deal with the detection of mutations. The analysis of cfDNA is often discussed in the context of the noninvasive detection of mutations that lead to resistance mechanisms and therapeutic and disease monitoring in cancer patients. Indeed, substantial advances have been made in this area, with the development of methods that reach high sensitivity and can interrogate a large number of genes. Interestingly, however, cfDNA can also be used to analyse different features of DNA, such as methylation status, size fragment patterns, transcriptomics and viral load, which open new avenues for the analysis of liquid biopsy samples from cancer patients. This review will focus on the new perspectives and challenges of cfDNA analysis from mutation detection in patients with solid malignancies.
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Affiliation(s)
- Laura Keller
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Yassine Belloum
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany.
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64
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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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65
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Ray SK, Mukherjee S. Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology. Curr Pharm Biotechnol 2020; 23:112-122. [PMID: 33308128 DOI: 10.2174/1389201021666201211102710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/26/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022]
Abstract
Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry. All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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66
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Souza AGD, Bastos VAF, Fujimura PT, Ferreira ICC, Leal LF, da Silva LS, Laus AC, Reis RM, Martins MM, Santos PS, Corrêa NCR, Marangoni K, Thomé CH, Colli LM, Goulart LR, Goulart VA. Cell-free DNA promotes malignant transformation in non-tumor cells. Sci Rep 2020; 10:21674. [PMID: 33303880 PMCID: PMC7728762 DOI: 10.1038/s41598-020-78766-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free DNA is present in different biological fluids and when released by tumor cells may contribute to pro-tumor events such as malignant transformation of cells adjacent to the tumor and metastasis. Thus, this study analyzed the effect of tumor cell-free DNA, isolated from the blood of prostate cancer patients, on non-tumor prostate cell lines (RWPE-1 and PNT-2). To achieve this, we performed cell-free DNA quantification and characterization assays, evaluation of gene and miRNA expression profiling focused on cancer progression and EMT, and metabolomics by mass spectrometry and cellular migration. The results showed that tumor-free cell DNA was able to alter the gene expression of MMP9 and CD44, alter the expression profile of nine miRNAs, and increased the tryptophan consumption and cell migration rates in non-tumor cells. Therefore, tumor cell-free DNA was capable of altering the receptor cell phenotype, triggering events related to malignant transformation in these cells, and can thus be considered a potential target for cancer diagnosis and therapy.
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Affiliation(s)
- Aline Gomes de Souza
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil.
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil.
| | - Victor Alexandre F Bastos
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Patricia Tieme Fujimura
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Izabella Cristina C Ferreira
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
- 3ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Mario Machado Martins
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Paula Souza Santos
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Natássia C Resende Corrêa
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Karina Marangoni
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Carolina Hassibe Thomé
- Center for Cell Based Therapy, Hemotherapy Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Leandro Machado Colli
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz Ricardo Goulart
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, USA
| | - Vivian Alonso Goulart
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
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67
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Yuan Z, Wang X, Geng X, Li Y, Mu J, Tan F, Xue Q, Gao S, He J. Liquid biopsy for esophageal cancer: Is detection of circulating cell-free DNA as a biomarker feasible? Cancer Commun (Lond) 2020; 41:3-15. [PMID: 33264481 PMCID: PMC7819547 DOI: 10.1002/cac2.12118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/19/2020] [Accepted: 11/19/2020] [Indexed: 12/25/2022] Open
Abstract
Esophageal cancer (EC) is a common cancer and is histopathologically classified into esophageal squamous cell carcinoma and esophageal adenocarcinoma. EC is a worldwide public health issue because of late diagnosis and lack of effective therapy. In contrast to standard tumor biopsies, liquid biopsies are emerging as a tool which is minimally invasive that can complement or even substitute more classical approaches. Specifically, cell-free DNA (cfDNA) has shown promise in cancer-related clinical applications. Indeed, cfDNA has been shown to be an effective circulating biomarker for non-invasive cancer diagnosis and monitoring of cancer patients. Although the clinical application of cfDNA has been reported on other cancers, few studies have evaluated its use in EC. Here, we review this relevant literature and discuss limitations and advantages of its application in the diagnosis and monitoring of EC.
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Affiliation(s)
- Zuyang Yuan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xinfeng Wang
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xiao Geng
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Yin Li
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Juwei Mu
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Fengwei Tan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Qi Xue
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Shugeng Gao
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Jie He
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
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68
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Cirillo M, Craig AFM, Borchmann S, Kurtz DM. Liquid biopsy in lymphoma: Molecular methods and clinical applications. Cancer Treat Rev 2020; 91:102106. [PMID: 33049623 PMCID: PMC8043056 DOI: 10.1016/j.ctrv.2020.102106] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/31/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
In this article, we broadly review the application of cfDNA analysis to the diagnosis and management of lymphoma. We introduce the advantages of cfDNA measurement over conventional tissue biopsy and describe how cfDNA may be utilized for both genotyping and detection of minimal residual disease. First, we discuss genotyping, beginning with differences in identifying mutations from the blood plasma vs. from circulating cells. We review the technical distinctions between PCR- and NGS-based assays and describe two important applications of NGS-based cfDNA tests, namely the identification of resistance mutations and classification of disease subtype. We discuss difficulties in genotyping diseases with low burden of tumor cells and the application of cfDNA assays in these contexts. Second, we describe the utility of ctDNA measurement in assessing MRD. We cover recent advances in the assessment of pre-treatment disease burden as a prognostic biomarker, detection of molecular response to therapy, and early detection of relapsing disease. Third, we explore select emerging areas of research in ctDNA technologies that show promise in boosting the performance of existing ctDNA-based assays. These include cell-free DNA fragment structure analysis or 'fragmentomics', epigenetic modifications, and novel circulating analytes such as tumor-educated platelets and extracellular vesicular DNA. We also discuss alternative analytes to blood plasma for tumor detection, such as urine, saliva, and stool. Finally, we present a case that highlights potential applications of ctDNA approaches to the management of patients with lymphoma, while also defining important prerequisite advances before this can be fully realized. We close with a look to the future of cfDNA applications, outlining one potential timeline and path forward towards routine clinical application.
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Affiliation(s)
- Melita Cirillo
- Royal Perth Hospital, Perth, Australia; University of Western Australia, Perth, Australia
| | - Alexander F M Craig
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Sven Borchmann
- University of Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Hodgkin Study Group, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital of Cologne, Center for Molecular Medicine, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital of Cologne, Else Kröner Forschungskolleg Clonal Evolution in Cancer, Cologne, Germany.
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
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69
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Exploration of cell-free DNA (cfDNA) recovery for touch deposits. Forensic Sci Int Genet 2020; 51:102431. [PMID: 33260058 DOI: 10.1016/j.fsigen.2020.102431] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/15/2022]
Abstract
Although touch deposit DNA is widely used in forensic casework, its cellular and acellular contents and their biological origins are poorly understood. There is evidence that the cell-free component of DNA deposited by handling may contribute substantial genetic information; however, most research into touch DNA recovery does not separate cellular and cell-free fractions or seek to characterize their contents. This work is an important early step in developing methods to isolate the cfDNA from biological material deposited by handling. Size-filtration as a separation technique was determined to be prone to DNA loss, even on optimized control samples of pure ladder DNA. Centrifugal separation was optimized to determine minimum speed and time required to reliably remove all cellular debris from the material collected by rinsing donor hands. To determine if the centrifugal force risked rupturing shed corneocyte cells and releasing cellular DNA into the supernatant, DNA levels were measured, and cells were visualized microscopically before and after centrifugation of hand rinses. Heated buccal cells were used as a positive control to demonstrate cell rupture would be detected with these methods. Following the determination of a suitable separation technique, an investigation into purification methods for cfDNA was conducted. DNA recovery using three kits for plasma cfDNA, one for PCR clean-up and one for genomic DNA were assessed on both ladder DNA to simulate cfDNA fragments and on collected hand deposit supernatants from both unwashed and washed hands. Purification methods designed for recovery of short DNA fragments from plasma yielded the highest recovery percentage across sample types, with BioChain cfPure performing the best. Donors' hands were shown to shed high levels of cfDNA, which were better recovered with a method for short fragments than with a traditional genomic technique often used on touch DNA samples.
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70
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Bronkhorst AJ, Ungerer V, Diehl F, Anker P, Dor Y, Fleischhacker M, Gahan PB, Hui L, Holdenrieder S, Thierry AR. Towards systematic nomenclature for cell-free DNA. Hum Genet 2020; 140:565-578. [PMID: 33123832 PMCID: PMC7981329 DOI: 10.1007/s00439-020-02227-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023]
Abstract
Cell-free DNA (cfDNA) has become widely recognized as a promising candidate biomarker for minimally invasive characterization of various genomic disorders and other clinical scenarios. However, among the obstacles that currently challenge the general progression of the research field, there remains an unmet need for unambiguous universal cfDNA nomenclature. To address this shortcoming, we classify in this report the different types of cfDNA molecules that occur in the human body based on its origin, genetic traits, and locality. We proceed by assigning existing terms to each of these cfDNA subtypes, while proposing new terms and abbreviations where clarity is lacking and more precise stratification would be beneficial. We then suggest the proper usage of these terms within different contexts and scenarios, focusing mainly on the nomenclature as it relates to the domains of oncology, prenatal testing, and post-transplant surgery surveillance. We hope that these recommendations will serve as useful considerations towards the establishment of universal cfDNA nomenclature in the future. In addition, it is conceivable that many of these recommendations can be transposed to cell-free RNA nomenclature by simply exchanging “DNA” with “RNA” in each acronym/abbreviation. Similarly, when describing DNA and RNA collectively, the suffix can be replaced with “NAs” to indicate nucleic acids.
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Affiliation(s)
- Abel J Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Frank Diehl
- Thrive Earlier Detection Corp., Cambridge, MA, USA
| | - Philippe Anker
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- University of Montpellier, Montpellier, France
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Michael Fleischhacker
- DRK Kliniken Berlin Mitte, Klinik für Innere Medizin, Pneumologie und Schlafmedizin, Drontheimer Str. 39-40, 13359, Berlin, Germany
| | - Peter B Gahan
- Fondazione "Enrico Puccinelli" Onlus, 06126, Perugia, Italy
| | - Lisa Hui
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, VIC, Australia
- Department of Obstetrics and Gynaecology, The Northern Hospital, Epping, VIC, Australia
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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71
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Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms. Int J Mol Sci 2020; 21:ijms21218062. [PMID: 33137955 PMCID: PMC7662960 DOI: 10.3390/ijms21218062] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.
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72
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Godsey JH, Silvestro A, Barrett JC, Bramlett K, Chudova D, Deras I, Dickey J, Hicks J, Johann DJ, Leary R, Lee JSH, McMullen J, McShane L, Nakamura K, Richardson AO, Ryder M, Simmons J, Tanzella K, Yee L, Leiman LC. Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC's Analytical Variables Working Group. Clin Chem 2020; 66:1156-1166. [PMID: 32870995 PMCID: PMC7462123 DOI: 10.1093/clinchem/hvaa164] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC's Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors' presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.
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Affiliation(s)
| | | | | | | | | | | | | | - James Hicks
- University of Southern California, Los Angeles, CA
| | | | | | | | | | - Lisa McShane
- National Cancer Institute at the National Institutes of Health (NIH/NCI), Rockville, MD
| | | | | | | | | | | | - Laura Yee
- National Cancer Institute at the National Institutes of Health (NIH/NCI), Rockville, MD
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73
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Elzanowska J, Semira C, Costa-Silva B. DNA in extracellular vesicles: biological and clinical aspects. Mol Oncol 2020; 15:1701-1714. [PMID: 32767659 PMCID: PMC8169445 DOI: 10.1002/1878-0261.12777] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
The study of extracellular vesicles (EVs), especially in the liquid biopsy field, has rapidly evolved in recent years. However, most EV studies have focused on RNA or protein content and DNA in EVs (EV‐DNA) has largely been unnoticed. In this review, we compile current evidence regarding EV‐DNA and provide an extensive discussion on EV‐DNA biology. We look into EV‐DNA biogenesis and mechanisms of DNA loading into EVs, as well as describe the particularly significant function of DNA‐carrying EVs in the maintenance of cellular homeostasis, intracellular communication, and immune response modulation. We also examine the current role of EV‐DNA in the clinical setting, specifically in cancer, infections, pregnancy, and prenatal diagnosis.
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Affiliation(s)
- Julia Elzanowska
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Christine Semira
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Bruno Costa-Silva
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
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74
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Magkouta SF, Pappas AG, Vaitsi PC, Agioutantis PC, Pateras IS, Moschos CA, Iliopoulou MP, Kosti CN, Loutrari HV, Gorgoulis VG, Kalomenidis IT. MTH1 favors mesothelioma progression and mediates paracrine rescue of bystander endothelium from oxidative damage. JCI Insight 2020; 5:134885. [PMID: 32554927 DOI: 10.1172/jci.insight.134885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/20/2020] [Indexed: 01/08/2023] Open
Abstract
Oxidative stress and inadequate redox homeostasis is crucial for tumor initiation and progression. MTH1 (NUDT1) enzyme prevents incorporation of oxidized dNTPs by sanitizing the deoxynucleoside triphosphate (dNTP) pool and is therefore vital for the survival of tumor cells. MTH1 inhibition has been found to inhibit the growth of several experimental tumors, but its role in mesothelioma progression remained elusive. Moreover, although MTH1 is nonessential to normal cells, its role in survival of host cells in tumor milieu, especially tumor endothelium, is unclear. We validated a clinically relevant MTH1 inhibitor (Karonudib) in mesothelioma treatment using human xenografts and syngeneic murine models. We show that MTH1 inhibition impedes mesothelioma progression and that inherent tumoral MTH1 levels are associated with a tumor's response. We also identified tumor endothelial cells as selective targets of Karonudib and propose a model of intercellular signaling among tumor cells and bystander tumor endothelium. We finally determined the major biological processes associated with elevated MTH1 gene expression in human mesotheliomas.
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Affiliation(s)
- Sophia F Magkouta
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
| | - Apostolos G Pappas
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
| | - Photene C Vaitsi
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
| | - Panagiotis C Agioutantis
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
| | - Ioannis S Pateras
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, Athens, Greece
| | - Charalampos A Moschos
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
| | - Marianthi P Iliopoulou
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
| | - Chrysavgi N Kosti
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
| | - Heleni V Loutrari
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, Athens, Greece.,Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Ioannis T Kalomenidis
- "Marianthi Simou Laboratory", 1st Department of Critical Care and Pulmonary Medicine, National and Kapodistrian University of Athens, School of Medicine, Evangelismos Hospital, Athens, Greece
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75
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Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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76
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Comparison of methods for the isolation of cell-free DNA from cell culture supernatant. Tumour Biol 2020; 42:1010428320916314. [PMID: 32338581 DOI: 10.1177/1010428320916314] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In vitro characterization of cell-free DNA using two-dimensional cell culture models is emerging as an important step toward an improved understanding of the physical and biological characteristics of cell-free DNA in human biology. However, precise measurement of the cell-free DNA in cell culture medium is highly dependent on the efficacy of the method used for DNA purification, and is often a juncture of experimental confusion. Therefore, in this study, we compared six commercially available cell-free DNA isolation kits for the recovery of cell-free DNA from the cell culture supernatant of a human bone cancer cell line (143B), including two magnetic bead-based manual kits, one automated magnetic bead-based extraction method, and three manual spin-column kits. Based on cell-free DNA quantitation and sizing, using the Qubit dsDNA HS assay and Bioanalyzer HS DNA assay, respectively, the different methods showed significant variability concerning recovery, reproducibility, and size discrimination. These findings highlight the importance of selecting a cell-free DNA extraction method that is appropriate for the aims of a study. For example, mutational analysis of cell-free DNA may be enhanced by a method that favors a high yield or is biased toward the isolation of short cell-free DNA fragments. In contrast, quantitative analysis of cell-free DNA in a comparative setting (e.g. measuring the fluctuation of cell-free DNA levels over time) may require the selection of a cell-free DNA isolation method that forgoes a high recovery for high reproducibility and minimal size bias.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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77
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Zvereva M, Roberti G, Durand G, Voegele C, Nguyen MD, Delhomme TM, Chopard P, Fabianova E, Adamcakova Z, Holcatova I, Foretova L, Janout V, Brennan P, Foll M, Byrnes GB, McKay JD, Scelo G, Le Calvez-Kelm F. Circulating tumour-derived KRAS mutations in pancreatic cancer cases are predominantly carried by very short fragments of cell-free DNA. EBioMedicine 2020; 55:102462. [PMID: 32249202 PMCID: PMC7251242 DOI: 10.1016/j.ebiom.2019.09.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/13/2019] [Accepted: 09/22/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The DNA released into the bloodstream by malignant tumours· called circulating tumour DNA (ctDNA), is often a small fraction of total cell-free DNA shed predominantly by hematopoietic cells and is therefore challenging to detect. Understanding the biological properties of ctDNA is key to the investigation of its clinical relevance as a non-invasive marker for cancer detection and monitoring. METHODS We selected 40 plasma DNA samples of pancreatic cancer cases previously reported to carry a KRAS mutation at the 'hotspot' codon 12 and re-screened the cell-free DNA using a 4-size amplicons strategy (57 bp, 79 bp, 167 bp and 218 bp) combined with ultra-deep sequencing in order to investigate whether amplicon lengths could impact on the capacity of detection of ctDNA, which in turn could provide inference of ctDNA and non-malignant cell-free DNA size distribution. FINDINGS Higher KRAS amplicon size (167 bp and 218 bp) was associated with lower detectable cell-free DNA mutant allelic fractions (p < 0·0001), with up to 4·6-fold (95% CI: 2·6-8·1) difference on average when comparing the 218bp- and the 57bp-amplicons. The proportion of cases with detectable KRAS mutations was also hampered with increased amplicon lengths, with only half of the cases having detectable ctDNA using the 218 bp assay relative to those detected with amplicons less than 80 bp. INTERPRETATION Tumour-derived mutations are carried by shorter cell-free DNA fragments than fragments of wild-type allele. Targeting short amplicons increases the sensitivity of cell-free DNA assays for pancreatic cancer and should be taken into account for optimized assay design and for evaluating their clinical performance. FUNDING IARC; MH CZ - DRO; MH SK; exchange program between IARC and Sao Paulo medical Sciences; French Cancer League.
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Affiliation(s)
- Maria Zvereva
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Gabriel Roberti
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France; Santa Casa de Sao Paulo of medical Sciences, Sao Paulo, Brazil
| | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Catherine Voegele
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Minh Dao Nguyen
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Tiffany M Delhomme
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Priscilia Chopard
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Eleonora Fabianova
- Regional Authority of Public Health, Banska Bystrica, and Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Zora Adamcakova
- Regional Authority of Public Health, Banska Bystrica, and Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Ivana Holcatova
- First Faculty of Medicine, Charles University of Prague, Institute of Hygiene and Epidemiology, Prague, Czechia
| | - Lenka Foretova
- Masaryk Memorial Cancer Institute and Medical Faculty of Masaryk University, Brno, Czechia
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czechia
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Graham B Byrnes
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - James D McKay
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Florence Le Calvez-Kelm
- International Agency for Research on Cancer (IARC), Genetic Cancer Susceptibility group, 150 Cours Albert Thomas, 69372 Lyon, France.
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Abstract
Abstract
It is well documented that in the chain from sample to the result in a clinical laboratory, the pre-analytical phase is the weakest and most vulnerable link. This also holds for the use and analysis of extracellular nucleic acids. In this short review, we will summarize and critically evaluate the most important steps of the pre-analytical phase, i.e. the choice of the best control population for the patients to be analyzed, the actual blood draw, the choice of tubes for blood drawing, the impact of delayed processing of blood samples, the best method for getting rid of cells and debris, the choice of matrix, i.e. plasma vs. serum vs. other body fluids, and the impact of long-term storage of cell-free liquids on the outcome. Even if the analysis of cell-free nucleic acids has already become a routine application in the area of non-invasive prenatal screening (NIPS) and in the care of cancer patients (search for resistance mutations in the EGFR gene), there are still many unresolved issues of the pre-analytical phase which need to be urgently tackled.
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Affiliation(s)
- Michael Fleischhacker
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Drontheimer Str. 39 – 40 , 13359 Berlin , Germany
| | - Bernd Schmidt
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Berlin , Germany
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79
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Andersson D, Fagman H, Dalin MG, Ståhlberg A. Circulating cell-free tumor DNA analysis in pediatric cancers. Mol Aspects Med 2020; 72:100819. [DOI: 10.1016/j.mam.2019.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/06/2019] [Accepted: 09/12/2019] [Indexed: 12/18/2022]
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80
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Grabuschnig S, Soh J, Heidinger P, Bachler T, Hirschböck E, Rosales Rodriguez I, Schwendenwein D, Sensen CW. Circulating cell-free DNA is predominantly composed of retrotransposable elements and non-telomeric satellite DNA. J Biotechnol 2020; 313:48-56. [DOI: 10.1016/j.jbiotec.2020.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 12/19/2022]
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81
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Otandault A, Anker P, Al Amir Dache Z, Guillaumon V, Meddeb R, Pastor B, Pisareva E, Sanchez C, Tanos R, Tousch G, Schwarzenbach H, Thierry AR. Recent advances in circulating nucleic acids in oncology. Ann Oncol 2020; 30:374-384. [PMID: 30753271 DOI: 10.1093/annonc/mdz031] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) is one of the fastest growing and most exciting areas in oncology in recent years. Its potential clinical uses cover now each phase of cancer patient management care (predictive information, detection of the minimal residual disease, early detection of resistance, treatment monitoring, recurrence surveillance, and cancer early detection/screening). This review relates the recent advances in the application of circulating DNA or RNA in oncology building on unpublished or initial findings/work presented at the 10th international symposium on circulating nucleic acids in plasma and serum held in Montpellier from the 20th to the 22nd of September 2017. This year, presenters revealed their latest data and crucial observations notably in relation to (i) the circulating cell-free (cfDNA) structure and implications regarding their optimal detection; (ii) their role in the metastatic or immunological processes; (iii) evaluation of miRNA panels for cancer patient follow up; (iv) the detection of the minimal residual disease; (v) the evaluation of a screening tests for cancer using cfDNA analysis; and (vi) elements of preanalytical guidelines. This work reviews the recent progresses in the field brought to light in the meeting, as well as in the most important reports from the literature, past and present. It proposes a broader picture of the basic research and its potential, and of the implementation and current challenges in the use of circulating nucleic acids in oncology.
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Affiliation(s)
- A Otandault
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - P Anker
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - Z Al Amir Dache
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - V Guillaumon
- Regional Institute of Cancer of Montpellier, Montpellier; SIRIC, Integrated Cancer Research Site, Montpellier, France
| | - R Meddeb
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - B Pastor
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - E Pisareva
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - C Sanchez
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - R Tanos
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - G Tousch
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - H Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - A R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier.
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82
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Jagelkova M, Zelinova K, Laucekova Z, Bobrovska M, Dankova Z, Grendar M, Dokus K. Comparison of Somatic Mutation Profiles Between Formalin-Fixed Paraffin Embedded Tissues and Plasma Cell-Free DNA from Ovarian Cancer Patients Before and After Surgery. Biores Open Access 2020; 9:73-79. [PMID: 32219013 PMCID: PMC7097678 DOI: 10.1089/biores.2019.0031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ovarian carcinogenesis can be induced by a large number of somatic gene mutations. Circulating tumor DNA (ctDNA) released into peripheral blood can provide insights into the genomic landscape of cancer cells and monitor their dynamics. Our aim was to detect and compare the genetic profiles in tumor tissue and plasma before and after tumor resection in ovarian cancer patients. All three samples were collected from each patient. In this study, we used a commercial cancer panel to identify somatic mutations in 26 genes in seven selected patients through next-generation sequencing on the Illumina platform. Overall, 16 variants with pathogenic effect were identified in the TP53, PIK3CA, PTEN, APC, NRAS, KRAS, GNAS, and MET genes involved in important signaling pathways. The genetic alterations found in the presurgical plasma in six of seven ovarian cancer patients were no longer present in the plasma after tumor surgical removal. Identical variants in formalin-fixed paraffin embedded (FFPE) tissues and preoperative plasma specimens were observed in only two cases. These findings suggest that the detected presurgical pathogenic variants absent in postsurgery plasma are associated with the primary ovarian tumor. Finally, the low-identified concordance between FFPE and plasma can be due to various factors, but most likely to high tumor heterogeneity and low ctDNA level.
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Affiliation(s)
- Marianna Jagelkova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Martin, Slovakia
- Clinic of Gynecology and Obstetrics, Martin University Hospital (MUH) and JFM CU, Martin, Slovakia
| | - Katarina Zelinova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Martin, Slovakia
- Clinic of Gynecology and Obstetrics, Martin University Hospital (MUH) and JFM CU, Martin, Slovakia
| | - Zuzana Laucekova
- Clinic of Gynecology and Obstetrics, Martin University Hospital (MUH) and JFM CU, Martin, Slovakia
| | - Martina Bobrovska
- Department of Pathological Anatomy, MUH and JFM CU, Martin, Slovakia
| | - Zuzana Dankova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Martin, Slovakia
| | - Marian Grendar
- Department of Bioinformatics, Biomedical Center Martin JFM CU, Martin, Slovakia
| | - Karol Dokus
- Clinic of Gynecology and Obstetrics, Martin University Hospital (MUH) and JFM CU, Martin, Slovakia
- 2nd Department of Gynecology and Obstetrics, Faculty Hospital with Policlinic of F. D. Roosevelt, Slovak Medical University, Banska Bystrica, Slovakia
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83
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Otandault A, Abraham JD, Al Amir Dache Z, Khalyfa A, Jariel-Encontre I, Forné T, Prévostel C, Chouaib S, Gozal D, Thierry AR. Hypoxia differently modulates the release of mitochondrial and nuclear DNA. Br J Cancer 2020; 122:715-725. [PMID: 31929518 PMCID: PMC7054557 DOI: 10.1038/s41416-019-0716-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/29/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND We investigated the influence of hypoxia on the concentration of mitochondrial and nuclear cell-free DNA (McfDNA and NcfDNA, respectively). METHOD By an ultra-sensitive quantitative PCR-based assay, McfDNA and NcfDNA were measured in the supernatants of different colorectal cell lines, and in the plasma of C57/Bl6 mice engrafted with TC1 tumour cells, in normoxic or hypoxic conditions. RESULTS Our data when setting cell culture conditions highlighted the higher stability of McfDNA as compared to NcfDNA and revealed that cancer cells released amounts of nuclear DNA equivalent to the mass of a chromosome over a 6-h duration of incubation. In cell model, hypoxia induced a great increase in NcfDNA and McfDNA concentrations within the first 24 h. After this period, cfDNA total concentrations remained stable in hypoxia consecutive to a decrease of nuclear DNA release, and noteworthy, to a complete inhibition of daily mitochondrial DNA release. In TC1-engrafted mice submitted to intermittent hypoxia, plasma NcfDNA levels are much higher than in mice bred in normoxia, unlike plasma McfDNA concentration that is not impacted by hypoxia. CONCLUSION This study suggests that hypoxia negatively modulates nuclear and, particularly, mitochondrial DNA releases in long-term hypoxia, and revealed that the underlying mechanisms are differently regulated.
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Affiliation(s)
- Amaelle Otandault
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Jean-Daniel Abraham
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Zahra Al Amir Dache
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Abdelnaby Khalyfa
- Department of Child Health and Child Health Research Institute, University of Missouri School of Medicine, Columbia, MO, 65201, USA
| | - Isabelle Jariel-Encontre
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Thierry Forné
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Corinne Prévostel
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Salem Chouaib
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Fac. de médecine-Univ. Paris-Sud, University Paris-Saclay, Villejuif, 94805, France
- TRIPM, Gulf Medical University, Ajman, UAE
| | - David Gozal
- Department of Child Health and Child Health Research Institute, University of Missouri School of Medicine, Columbia, MO, 65201, USA
| | - Alain R Thierry
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France.
- Université de Montpellier, Montpellier, 34090, France.
- Institut régional du cancer de Montpellier, Montpellier, 34298, France.
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84
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McGuire AL, Hughesman CB, McConechy MK, Melosky B, Lam S, Myers R, Yee J, Tang E, Yip S. Optimizing molecular residual disease detection using liquid biopsy postoperatively in early stage lung cancer. Lung Cancer Manag 2020; 9:LMT24. [PMID: 32346401 PMCID: PMC7186850 DOI: 10.2217/lmt-2019-0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Anna L McGuire
- Department of Surgery, Division of Thoracic Surgery, Vancouver General Hospital, University of British Columbia, Vancouver V5Z1M9, BC, Canada
| | - Curtis B Hughesman
- Department of Pathology and Laboratory Medicine, BC Cancer, Cancer Genetics & Genomics Laboratory, Vancouver, BC, Canada
| | | | - Barb Melosky
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Vancouver, BC, Canada.,Medical Oncology, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Vancouver, BC, Canada.,Department of Medicine, Divisions of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Renelle Myers
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Vancouver, BC, Canada.,Department of Medicine, Divisions of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - John Yee
- Department of Surgery, Division of Thoracic Surgery, Vancouver General Hospital, University of British Columbia, Vancouver V5Z1M9, BC, Canada
| | - Ernest Tang
- Department of Surgery, Division of Thoracic Surgery, Vancouver General Hospital, University of British Columbia, Vancouver V5Z1M9, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, BC Cancer, Cancer Genetics & Genomics Laboratory, Vancouver, BC, Canada.,Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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85
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Duforestel M, Briand J, Bougras-Cartron G, Heymann D, Frenel JS, Vallette FM, Cartron PF. Cell-free circulating epimarks in cancer monitoring. Epigenomics 2020; 12:145-155. [DOI: 10.2217/epi-2019-0170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer numbers increasing, cases heterogeneity and the drug resistance emergence have pushed scientists to search for innovative solutions for patients and epimutations can be one. Methylated DNA, modified nucleosomes and noncoding RNAs are found in all cells, including tumor cells. They are intracellular actors but also have intercellular communication roles, being released in extracellular environment and in different body fluids. Here, we reviewed current literature on the use of these blood circulating epimarks in cancer monitoring. What stands out is that epimarkers must be considered as ‘real time’ images of the tumor, and can be isolated without invasive methods. In the future, the real challenge lies in the development of specific, sensitive, fast and clinically applicable detection and analysis methods of epimarkers.
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Affiliation(s)
- Manon Duforestel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Joséphine Briand
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Gwenola Bougras-Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Dominique Heymann
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
| | - Jean-Sébastien Frenel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- Department of Medical Oncology, Institut de Cancérologie de l'Ouest Site René Gauducheau, Saint Herblain, France
| | - François M Vallette
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
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86
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations. Crit Rev Clin Lab Sci 2019:1-17. [PMID: 31865831 DOI: 10.1080/10408363.2019.1700902] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early diagnosis of cancer improves the efficacy of curative therapies. However, due to the difficulties involved in distinguishing between small early-stage tumors and normal biological variation, early detection of cancer is an extremely challenging task and there are currently no clinically validated biomarkers for a pan-cancer screening test. It is thus of particular significance that increasing evidence indicates the potential of circulating tumor DNA (ctDNA) molecules, which are fragmented segments of DNA shed from tumor cells into adjacent body fluids and the circulatory system, to serve as molecular markers for early cancer detection and thereby allow early intervention and improvement of therapeutic and survival outcomes. This is possible because ctDNA molecules bear cancer-specific fragmentation patterns, nucleosome depletion motifs, and genetic and epigenetic alterations, as distinct from plasma DNA originating from non-cancerous tissues/cells. Compared to traditional biomarkers, ctDNA analysis therefore presents the distinctive advantage of detecting tumor-specific alterations. However, based on a thorough survey of the literature, theoretical and empirical evidence suggests that current ctDNA analysis strategies, which are mainly based on DNA mutation detection, do not demonstrate the necessary diagnostic sensitivity and specificity that is required for broad clinical implementation in a screening context. Therefore, in this review we explain the biological, physiological, and analytical challenges toward the development of clinically meaningful ctDNA tests. In addition, we explore some approaches that can be implemented in order to increase the sensitivity and specificity of ctDNA assays.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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87
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Willis J, Lefterova MI, Artyomenko A, Kasi PM, Nakamura Y, Mody K, Catenacci DVT, Fakih M, Barbacioru C, Zhao J, Sikora M, Fairclough SR, Lee H, Kim KM, Kim ST, Kim J, Gavino D, Benavides M, Peled N, Nguyen T, Cusnir M, Eskander RN, Azzi G, Yoshino T, Banks KC, Raymond VM, Lanman RB, Chudova DI, Talasaz A, Kopetz S, Lee J, Odegaard JI. Validation of Microsatellite Instability Detection Using a Comprehensive Plasma-Based Genotyping Panel. Clin Cancer Res 2019; 25:7035-7045. [PMID: 31383735 DOI: 10.1158/1078-0432.ccr-19-1324] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/15/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022]
Abstract
PURPOSE To analytically and clinically validate microsatellite instability (MSI) detection using cell-free DNA (cfDNA) sequencing. EXPERIMENTAL DESIGN Pan-cancer MSI detection using Guardant360 was analytically validated according to established guidelines and clinically validated using 1,145 cfDNA samples for which tissue MSI status based on standard-of-care tissue testing was available. The landscape of cfDNA-based MSI across solid tumor types was investigated in a cohort of 28,459 clinical plasma samples. Clinical outcomes for 16 patients with cfDNA MSI-H gastric cancer treated with immunotherapy were evaluated. RESULTS cfDNA MSI evaluation was shown to have high specificity, precision, and sensitivity, with a limit of detection of 0.1% tumor content. In evaluable patients, cfDNA testing accurately detected 87% (71/82) of tissue MSI-H and 99.5% of tissue microsatellite stable (863/867) for an overall accuracy of 98.4% (934/949) and a positive predictive value of 95% (71/75). Concordance of cfDNA MSI with tissue PCR and next-generation sequencing was significantly higher than IHC. Prevalence of cfDNA MSI for major cancer types was consistent with those reported for tissue. Finally, robust clinical activity of immunotherapy treatment was seen in patients with advanced gastric cancer positive for MSI by cfDNA, with 63% (10/16) of patients achieving complete or partial remission with sustained clinical benefit. CONCLUSIONS cfDNA-based MSI detection using Guardant360 is highly concordant with tissue-based testing, enabling highly accurate detection of MSI status concurrent with comprehensive genomic profiling and expanding access to immunotherapy for patients with advanced cancer for whom current testing practices are inadequate.See related commentary by Wang and Ajani, p. 6887.
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Affiliation(s)
- Jason Willis
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Pashtoon Murtaza Kasi
- Division of Oncology/Hematology, Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kabir Mody
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, Florida
| | | | - Marwan Fakih
- Medical Oncology, City of Hope, Duarte, California
| | | | - Jing Zhao
- Guardant Health, Redwood City, California
| | | | | | - Hyuk Lee
- Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyoung-Mee Kim
- Division of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jinchul Kim
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | | | - Manuel Benavides
- Medical Oncology, Hospital Universitario Virgen de la Victoria, Malaga, Spain
| | - Nir Peled
- Division of Medical Oncology, Rabin Medical Center, Petach Tiqea, Israel
| | - Timmy Nguyen
- Hematology/Oncology, Cleveland Clinic Foundation, Weston, Florida
| | - Mike Cusnir
- Comprehensive Cancer Center, Mount Sinai Medical Center, Miami Beach, Florida
| | - Ramez N Eskander
- Center for Personalized Cancer Therapy, Division of Gynecologic Oncology, University of California San Diego Health Moores Cancer Center, La Jolla, California
| | - Georges Azzi
- Medical Oncology, Holy Cross Michael & Dianne Bienes Comprehensive Cancer Center, Fort Lauderdale, Florida
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | | | | | | | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeeyun Lee
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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88
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Tuaeva NO, Falzone L, Porozov YB, Nosyrev AE, Trukhan VM, Kovatsi L, Spandidos DA, Drakoulis N, Kalogeraki A, Mamoulakis C, Tzanakakis G, Libra M, Tsatsakis A. Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. Cells 2019; 8:E1251. [PMID: 31615102 PMCID: PMC6829588 DOI: 10.3390/cells8101251] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients' prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients' samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.
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Affiliation(s)
- Natalia O Tuaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Luca Falzone
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy.
| | - Yuri B Porozov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- ITMO University, Saint Petersburg 197101, Russia.
| | - Alexander E Nosyrev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54248 Thessaloniki, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Zografou, Greece.
| | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, Medical School, Heraklion, 70013 Crete, Greece.
| | - George Tzanakakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Massimo Libra
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| | - Aristides Tsatsakis
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, 71003 Crete, Greece.
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89
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van der Pol Y, Mouliere F. Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA. Cancer Cell 2019; 36:350-368. [PMID: 31614115 DOI: 10.1016/j.ccell.2019.09.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022]
Abstract
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic alterations, but only a minor fraction of tumor-derived cell-free DNA (cfDNA) fragments exhibit mutations. The cellular processes occurring in cancer development mark the chromatin. These epigenetic marks are reflected by modifications in the cfDNA methylation, fragment size, and structure. In this review, we describe how going beyond DNA sequence information alone, by analyzing cfDNA epigenetic and immune signatures, boosts the potential of liquid biopsy for the early detection of cancer.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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90
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Rice A, Del Rio Hernandez A. The Mutational Landscape of Pancreatic and Liver Cancers, as Represented by Circulating Tumor DNA. Front Oncol 2019; 9:952. [PMID: 31608239 PMCID: PMC6769086 DOI: 10.3389/fonc.2019.00952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
The mutational landscapes of pancreatic and liver cancers share many common genetic alterations which drive cancer progression. However, these mutations do not occur in all cases of these diseases, and this tumoral heterogeneity impedes diagnosis, prognosis, and therapeutic development. One minimally invasive method for the evaluation of tumor mutations is the analysis of circulating tumor DNA (ctDNA), released through apoptosis, necrosis, and active secretion by tumor cells into various body fluids. By observing mutations in those genes which promote transformation by controlling the cell cycle and oncogenic signaling pathways, a representation of the mutational profile of the tumor is revealed. The analysis of ctDNA is a promising technique for investigating these two gastrointestinal cancers, as many studies have reported on the accuracy of ctDNA assessment for diagnosis and prognosis using a variety of techniques.
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Affiliation(s)
- Alistair Rice
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Armando Del Rio Hernandez
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
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91
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Abstract
Several studies have proposed that cell-free DNA (cfDNA) is a potential biomarker present in follicular fluid (FF) for oocyte quality. Recently we reported that mitochondria-derived cfDNA (mt-cfDNA) closely reflects the amount of cfDNA in FFs. The present study investigated the mechanism regulating mt-cfDNA secretion from porcine granulosa cells. Oocytes and cumulus cell complexes or granulosa cells (GCs) were cultured in maturation medium for 24 or 48 h respectively. Then, nuclear-derived cell-free DNA (n-cfDNA) or mt-cfDNA contents in the spent medium were examined using real-time polymerase chain reaction. When 10 μM of MG132, a proteasome inhibitor, was added to the culture medium, cellular viability of both COCs and GCs decreased and n-cfDNA significantly increased in the culture medium, whereas mt-cfDNA significantly decreased. Supplementation of the culture medium with GW4869, an inhibitor of intracellular vesicle formation, significantly decreased the mt-cfDNA, whereas no effect was observed on n-cfDNA in the medium of both COCs and GCs. Furthermore, the addition of bafilomycin, an inhibitor of autophagy to the culture medium significantly increased mt-cfDNA in the culture medium. After filtration (0.22 μm) and centrifugation (23,000 g), the mt-cfDNA content of the medium decreased significantly. In conclusion, the proteasomal mitochondrial quality control system is upstream of mt-cfDNA secretion and autophagy plays a role in cellular digestion of mitochondrial DNA in the cytoplasm. It is further suggested that dsDNA is enclosed in certain vesicles or associated with small molecules and secreted into the medium.
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92
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Comparison of methods for the quantification of cell-free DNA isolated from cell culture supernatant. Tumour Biol 2019; 41:1010428319866369. [DOI: 10.1177/1010428319866369] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gaining a better understanding of the biological properties of cell-free DNA constitutes an important step in the development of clinically meaningful cell-free DNA–based tests. Since the in vivo characterization of cell-free DNA is complicated by the immense heterogeneity of blood samples, an increasing number of in vitro cell culture experiments, which offer a greater level of control, are being conducted. However, cell culture studies are currently faced with three notable caveats. First, the concentration of cell-free DNA in vitro is relatively low. Second, the median amount and size of cell-free DNA in culture medium varies greatly between cell types. Third, the amount and size of cell-free DNA in the culture medium of a single cell line fluctuates over time. Although these are interesting findings, it can also be a great source of experimental confusion and emphasizes the importance of method optimization and standardization. Therefore, in this study, we compared five commonly used cell-free DNA quantification methods, including quantitative polymerase chain reaction, Qubit Double-Stranded DNA High Sensitivity assay, Quant-iT PicoGreen Assay, Bioanalyzer High Sensitivity DNA assay, and NanoDrop Onec. Analysis of the resulting data, along with an interpretation of theoretical values (i.e. the theoretical detection and quantification limits of the respective methods), enables the calculation of optimal conditions for several important preanalytical steps pertaining to each quantification method and different cell types, including the (1) time-point at which culture medium should be collected for cell-free DNA extraction, (2) amount of cell culture supernatant from which to isolate cell-free DNA, (3) volume of elution buffer, and (4) volume of cell-free DNA sample to use for quantification.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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93
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Application of digital PCR for assessing DNA fragmentation in cytotoxicity response. Biochim Biophys Acta Gen Subj 2019; 1863:1235-1242. [DOI: 10.1016/j.bbagen.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/04/2019] [Accepted: 05/02/2019] [Indexed: 12/18/2022]
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94
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Fujihara J, Takinami Y, Ueki M, Kimura-Kataoka K, Yasuda T, Takeshita H. Circulating cell-free DNA fragment analysis by microchip electrophoresis and its relationship with DNase I in cardiac diseases. Clin Chim Acta 2019; 497:61-66. [PMID: 31302100 DOI: 10.1016/j.cca.2019.07.014] [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] [Received: 04/25/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 11/29/2022]
Abstract
Circulating cell-free DNA (cfDNA) has been directly related to cancer, diabetes, stroke, systemic lupus erythematosus, trauma, rheumatoid arthritis, inflammation, infection, and myocardial infarction (MI). In this study, plasma cfDNA was extracted from the plasma of cardiac disease patients and the cfDNA fragment distribution as well as the relationships between cfDNA concentration and deoxyribonuclease I (DNase I) activity enzyme implicated in double-stranded DNA processing were examined. Results revealed that the cfDNA concentrations in patients with MI and cardiac angina were significantly higher than that in healthy control subjects. Microchip electrophoresis of plasma cfDNA revealed a single fragment (150-200 bp) in some healthy control subjects and three fragments (150-200 bp, 300-400 bp, and 500-600 bp) in all cardiac patient samples. Moreover, a cfDNA ratio of 150-200 bp/500-600 bp was significantly more prevalent in MI patients than in patients with other cardiac diseases (chest pain, cardiac angina, atrial fibrillation and cardiac failure). In addition, a positive correlation between DNase I activity and cfDNA concentration was observed. These results suggest that the plasma cfDNA in cardiac disease patients may originate from apoptosis and that the 150-200 bp/500-600 bp ratio for cfDNA may be a novel diagnostic indicator for MI.
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Affiliation(s)
- Junko Fujihara
- Department of Legal Medicine, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane 693-8501, Japan.
| | - Yoshikazu Takinami
- Department of Emergency and Critical Care Medicine, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane 693-8501, Japan
| | - Misuzu Ueki
- Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Kaori Kimura-Kataoka
- Department of Legal Medicine, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane 693-8501, Japan
| | - Toshihiro Yasuda
- Organization for Life Science Advancement Programs, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Haruo Takeshita
- Department of Legal Medicine, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane 693-8501, Japan
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95
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Parackal S, Zou D, Day R, Black M, Guilford P. Comparison of Roche Cell-Free DNA collection Tubes ® to Streck Cell-Free DNA BCT ® s for sample stability using healthy volunteers. Pract Lab Med 2019; 16:e00125. [PMID: 31289732 PMCID: PMC6593214 DOI: 10.1016/j.plabm.2019.e00125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 05/08/2019] [Accepted: 06/04/2019] [Indexed: 12/15/2022] Open
Abstract
Objectives To compare the Roche Cell-Free DNA Collection Tubes® against the Streck Cell-Free DNA BCT®s for sample stability using Cell Free DNA (cfDNA) from healthy volunteers (n = 20). Design & methods Whole blood was drawn into five Roche and five Streck tubes per volunteer, stored at room temperature and processed at five different time points (Days 0, 4, 7, 10 and 14). One volunteer had blood drawn into ×10 K3EDTA tubes to observe the effect of no preservation buffer on White Blood Cell (WBC) lysis. DNA was extracted from the plasma and the concentration (ng/μL) measured using the Qubit Fluorometer® at each time point. The eluted DNA was further analysed by capillary electrophoresis to determine the proportion of cfDNA and gDNA contamination in the samples over the 14 days. Results There was no difference in individual (p = 0.097) and median paired (p = 0.26) DNA concentration across the five time points between the two tubes. However, a difference was observed for samples in the Roche tubes for pair days 0-7 (p = 0.01), 0 to 10 (p = 0.046) and 0 to 14 (p = 0.0016) in contrast to the Streck tubes after adjustment for multiple testing. Conclusion The findings of this study indicate that the Roche Cell-Free DNA Collection Tubes® are a suitable alternative for sample collection and storage at room temperature, albeit for a duration of less than 7 days.
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96
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Chin RI, Chen K, Usmani A, Chua C, Harris PK, Binkley MS, Azad TD, Dudley JC, Chaudhuri AA. Detection of Solid Tumor Molecular Residual Disease (MRD) Using Circulating Tumor DNA (ctDNA). Mol Diagn Ther 2019; 23:311-331. [PMID: 30941670 PMCID: PMC6561896 DOI: 10.1007/s40291-019-00390-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Circulating tumor DNA (ctDNA) is a component of cell-free DNA that is shed by malignant tumors into the bloodstream and other bodily fluids. Levels of ctDNA are typically low, particularly in patients with localized disease, requiring highly sophisticated methods for detection and quantification. Multiple liquid biopsy methods have been developed for ctDNA analysis in solid tumor malignancies and are now enabling detection and assessment of earlier stages of disease, post-treatment molecular residual disease (MRD), resistance to targeted systemic therapy, and tumor mutational burden. Understanding ctDNA biology, mechanisms of release, and clearance and size characteristics, in conjunction with the application of molecular barcoding and targeted error correction, have increased the sensitivity and specificity of ctDNA detection techniques. Combinatorial approaches including integration of ctDNA data with circulating protein biomarkers may further improve assay sensitivity and broaden the scope of ctDNA applications. Circulating viral DNA may be utilized to monitor disease in some virally induced malignancies. In spite of increasingly accurate methods of ctDNA detection, results need to be interpreted with caution given that somatic mosaicisms such as clonal hematopoiesis of indeterminate potential (CHIP) may give rise to genetic variants in the bloodstream unrelated to solid tumors, and the limited concordance observed between different commercial platforms. Overall, highly precise ctDNA detection and quantification methods have the potential to transform clinical practice via non-invasive monitoring of solid tumor malignancies, residual disease detection at earlier timepoints than standard clinical and/or imaging surveillance, and treatment personalization based on real-time assessment of the tumor genomic landscape.
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Affiliation(s)
- Re-I Chin
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kevin Chen
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abul Usmani
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chanelle Chua
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter K Harris
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tej D Azad
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan C Dudley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA.
- Alvin J. Siteman Cancer Center, Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA.
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97
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Shi W, Xu X, Huang R, Yu Q, Zhang P, Xie S, Zheng H, Lu R. Plasma C-MYC level manifesting as an indicator in progression of breast cancer. Biomark Med 2019; 13:917-929. [PMID: 31144531 DOI: 10.2217/bmm-2019-0073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aim: To investigate whether plasma C-MYC level could be an indicator in clinical progression of breast cancer. Materials & methods: Plasma level of C-MYC expression was detected by quantitative real time PCR and the level of c-myc protein in breast cancer tissues was detected by immunohistochemistry. The expression level of C-MYC mRNA in supernatant of cancer cells culture was measured compared with the nonbreast cancer cells. Results: Plasma C-MYC level was significantly higher in patients with breast cancer than that in the controls, which associated with clinical stages, lymph node status, etc. Receiver operating characteristic curve analysis showed the sensitivity and specificity of plasma C-MYC level for diagnosis of breast cancer were 63.6 and 81.8%, respectively. The expression of c-myc protein in breast cancer tissues was associated with plasma C-MYC level, even C-MYC level in supernatant of cancer cells was elevated. Conclusion: Plasma C-MYC level might be a potential indicator in progression of breast cancer.
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Affiliation(s)
- Weizhong Shi
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Xiaofeng Xu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China
| | - Ren Huang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China
| | - Qi Yu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China
| | - Peiru Zhang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China
| | - Suhong Xie
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Hui Zheng
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Renquan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
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98
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Kustanovich A, Schwartz R, Peretz T, Grinshpun A. Life and death of circulating cell-free DNA. Cancer Biol Ther 2019; 20:1057-1067. [PMID: 30990132 PMCID: PMC6606043 DOI: 10.1080/15384047.2019.1598759] [Citation(s) in RCA: 305] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/24/2019] [Accepted: 03/12/2019] [Indexed: 12/18/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA in liquid biopsies is a promising source of biomarkers for minimally invasive serial monitoring of treatment responses in cancer management. We will review the current understanding of the origin of circulating cell-free DNA and different forms of DNA release (including various types of cell death and active secretion processes) and clearance routes. The dynamics of extracellular DNA in blood during therapy and the role of circulating DNA in pathophysiological processes (tumor-associated inflammation, NETosis, and pre-metastatic niche development) provide insights into the mechanisms that contribute to tumor development and metastases formation. Better knowledge of circulating tumor-specific cell-free DNA could facilitate the development of new therapeutic and diagnostic options for cancer management.
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Affiliation(s)
- Anatoli Kustanovich
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ruth Schwartz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Albert Grinshpun
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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99
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Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100087. [PMID: 30923679 PMCID: PMC6425120 DOI: 10.1016/j.bdq.2019.100087] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.
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Affiliation(s)
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße. 36, D-80636, Munich, Germany
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100
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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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