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Zhu JW, Wong F, Szymiczek A, Ene GEV, Zhang S, May T, Narod SA, Kotsopoulos J, Akbari MR. Evaluating the Utility of ctDNA in Detecting Residual Cancer and Predicting Recurrence in Patients with Serous Ovarian Cancer. Int J Mol Sci 2023; 24:14388. [PMID: 37762691 PMCID: PMC10532395 DOI: 10.3390/ijms241814388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Ovarian cancer has a high case fatality rate, but patients who have no visible residual disease after surgery have a relatively good prognosis. The presence of any cancer cells left in the peritoneal cavity after treatment may precipitate a cancer recurrence. In many cases, these cells are occult and are not visible to the surgeon. Analysis of circulating tumour DNA in the blood (ctDNA) may offer a sensitive method to predict the presence of occult (non-visible) residual disease after surgery and may help predict disease recurrence. We assessed 48 women diagnosed with serous ovarian cancer (47 high-grade and 1 low-grade) for visible residual disease and for ctDNA. Plasma, formalin-fixed paraffin-embedded (FFPE) tumour tissue and white blood cells were used to extract circulating free DNA (cfDNA), tumour DNA and germline DNA, respectively. We sequenced DNA samples for 59 breast and ovarian cancer driver genes. The plasma sample was collected after surgery and before initiating chemotherapy. We compared survival in women with no residual disease, with and without a positive plasma ctDNA test. We found tumour-specific variants (TSVs) in cancer cells from 47 patients, and these variants were sought in ctDNA in their post-surgery plasma. Fifteen (31.9%) of the 47 patients had visible residual disease; of these, all 15 had detectable ctDNA. Thirty-one patients (65.9%) had no visible residual disease; of these, 24 (77.4%) patients had detectable ctDNA. Of the patients with no visible residual disease, those patients with detectable ctDNA had higher mortality (20 of 27 died) than those without detectable ctDNA (3 of 7 died) (HR 2.32; 95% CI: 0.67-8.05), although this difference was not statistically significant (p = 0.18). ctDNA in post-surgical serum samples may predict the presence of microscopic residual disease and may be a predictor of recurrence among women with ovarian cancer. Larger studies are necessary to validate these findings.
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Affiliation(s)
- Jie Wei Zhu
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8P 1H6, Canada
| | - Fabian Wong
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Agata Szymiczek
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
| | - Gabrielle E. V. Ene
- Division of Gynecologic Oncology, Department of Surgical Oncology, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Shiyu Zhang
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
| | - Taymaa May
- Division of Gynecologic Oncology, Department of Surgical Oncology, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2M9, Canada
- Division of Gynecologic Oncology, Department of Obstetric and Gynecology, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Steven A. Narod
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Joanne Kotsopoulos
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Mohammad R. Akbari
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
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Matsas A, Stefanoudakis D, Troupis T, Kontzoglou K, Eleftheriades M, Christopoulos P, Panoskaltsis T, Stamoula E, Iliopoulos DC. Tumor Markers and Their Diagnostic Significance in Ovarian Cancer. Life (Basel) 2023; 13:1689. [PMID: 37629546 PMCID: PMC10455076 DOI: 10.3390/life13081689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Ovarian cancer (OC) is characterized by silent progression and late-stage diagnosis. It is critical to detect and accurately diagnose the disease early to improve survival rates. Tumor markers have emerged as valuable tools in the diagnosis and management of OC, offering non-invasive and cost-effective options for screening, monitoring, and prognosis. PURPOSE This paper explores the diagnostic importance of various tumor markers including CA-125, CA15-3, CA 19-9, HE4,hCG, inhibin, AFP, and LDH, and their impact on disease monitoring and treatment response assessment. METHODS Article searches were performed on PubMed, Scopus, and Google Scholar. Keywords used for the searching process were "Ovarian cancer", "Cancer biomarkers", "Early detection", "Cancer diagnosis", "CA-125","CA 15-3","CA 19-9", "HE4","hCG", "inhibin", "AFP", "LDH", and others. RESULTS HE4, when combined with CA-125, shows improved sensitivity and specificity, particularly in early-stage detection. Additionally, hCG holds promise as a prognostic marker, aiding treatment response prediction and outcome assessment. Novel markers like microRNAs, DNA methylation patterns, and circulating tumor cells offer potential for enhanced diagnostic accuracy and personalized management. Integrating these markers into a comprehensive panel may improve sensitivity and specificity in ovarian cancer diagnosis. However, careful interpretation of tumor marker results is necessary, considering factors such as age, menopausal status, and comorbidities. Further research is needed to validate and refine diagnostic algorithms, optimizing the clinical significance of tumor markers in ovarian cancer management. In conclusion, tumor markers such as CA-125, CA15-3, CA 19-9, HE4, and hCG provide valuable insights into ovarian cancer diagnosis, monitoring, and prognosis, with the potential to enhance early detection.
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Affiliation(s)
- Alkis Matsas
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Stefanoudakis
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Theodore Troupis
- Department of Anatomy, Faculty of Health Sciences, Medical School, National and Kapodistrian University of Athens, MikrasAsias Str. 75, 11627 Athens, Greece
| | - Konstantinos Kontzoglou
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Makarios Eleftheriades
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Panagiotis Christopoulos
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Theodoros Panoskaltsis
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Eleni Stamoula
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, University Campus Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dimitrios C. Iliopoulos
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Abstract
The high fragmentation of nuclear circulating DNA (cirDNA) relies on chromatin organization and protection or packaging within mononucleosomes, the smallest and the most stabilized structure in the bloodstream. The detection of differing size patterns, termed fragmentomics, exploits information about the nucleosomal packing of DNA. Fragmentomics not only implies size pattern characterization but also considers the positioning and occupancy of nucleosomes, which result in cirDNA fragments being protected and persisting in the circulation. Fragmentomics can determine tissue of origin and distinguish cancer-derived cirDNA. The screening power of fragmentomics has been considerably strengthened in the omics era, as shown in the ongoing development of sophisticated technologies assisted by machine learning. Fragmentomics can thus be regarded as a strategy for characterizing cancer within individuals and offers an alternative or a synergistic supplement to mutation searches, methylation, or nucleosome positioning. As such, it offers potential for improving diagnostics and cancer screening.
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Affiliation(s)
- A.R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, and ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France,Corresponding author
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Höpke J, Brewer G, Dodsworth S, Ortiz E, Albach D. DNA extraction from old herbarium material of Veronica subgen. Pseudolysimachium (Plantaginaceae). UKRAINIAN BOTANICAL JOURNAL 2019. [DOI: 10.15407/ukrbotj75.06.564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Abstract
Early detection of ovarian cancer could reduce mortality by 10% to 30%. Effective screening requires high sensitivity (>75%) and extremely high specificity (99.7%). Clinical trials suggest the best specificity is achieved with 2-stage strategies in which increasing serum CA125 level triggers transvaginal sonography to detect a malignant pelvic mass, although evidence for such approaches improving overall survival has been limited. Screening may be improved by combining CA125 with novel biomarkers, such as autoantibodies, circulating tumor DNA, or microRNAs. In order to detect premetastatic ovarian cancers originating in the distal fallopian tube, more sensitive approaches to diagnostic imaging are required.
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Affiliation(s)
- Kevin M Elias
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
| | - Jing Guo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Gynecology and Obstetrics, Shanghai Tenth People's Hospital, Tongji University, 301 Yanchang Road, Jingan, Shanghai 200072, China
| | - Robert C Bast
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
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Castellanos-Rizaldos E, Richardson K, Lin R, Wu G, Makrigiorgos MG. Single-tube, highly parallel mutation enrichment in cancer gene panels by use of temperature-tolerant COLD-PCR. Clin Chem 2015; 61:267-77. [PMID: 25297854 PMCID: PMC4281501 DOI: 10.1373/clinchem.2014.228361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Multiplexed detection of low-level mutations presents a technical challenge for many technologies, including cancer gene panels used for targeted-resequencing. Analysis of mutations below approximately 2%-5% abundance in tumors with heterogeneity, samples with stromal contamination, or biofluids is problematic owing to increased noise from sequencing errors. Technologies that reduce noise via deep sequencing unavoidably reduce throughput and increase cost. Here we provide proof of principle that coamplification at lower denaturation temperature (COLD)-PCR technology enables multiplex low-level mutation detection in cancer gene panels while retaining throughput. METHODS We have developed a multiplex temperature-tolerant COLD-PCR (fast-TT-COLD-PCR) approach that uses cancer gene panels developed for massively parallel sequencing. After multiplex preamplification from genomic DNA, we attach tails to all amplicons and perform fast-TT-COLD-PCR. This approach gradually increases denaturation temperatures in a step-wise fashion, such that all possible denaturation temperatures are encompassed. By introducing modified nucleotides, fast-COLD-PCR is adapted to enrich for melting temperature (Tm)-increasing mutations over all amplicons, in a single tube. Therefore, in separate reactions, both Tm-decreasing and Tm-increasing mutations are enriched. RESULTS Using custom-made and commercial gene panels containing 8, 50, 190, or 16 000 amplicons, we demonstrate that fast-TT-COLD-PCR enriches mutations on all examined targets simultaneously. Incorporation of deoxyinosine triphosphate (dITP)/2,6-diaminopurine triphosphate (dDTP) in place of deoxyguanosine triphosphate (dGTP)/deoxyadenosine triphosphate (dATP) enables enrichment of Tm-increasing mutations. Serial dilution experiments demonstrate a limit of detection of approximately 0.01%-0.1% mutation abundance by use of Ion-Torrent and 0.1%-0.3% by use of Sanger sequencing. CONCLUSIONS Fast-TT-COLD-PCR improves the limit of detection of cancer gene panels by enabling mutation enrichment in multiplex, single-tube reactions. This novel adaptation of COLD-PCR converts subclonal mutations to clonal, thereby facilitating detection and subsequent mutation sequencing.
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Affiliation(s)
| | | | - Rui Lin
- Transgenomic Inc., Omaha, NE
| | | | - Mike G Makrigiorgos
- Division of DNA Repair and Genome Stability and Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA;
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Breitbach S, Tug S, Helmig S, Zahn D, Kubiak T, Michal M, Gori T, Ehlert T, Beiter T, Simon P. Direct quantification of cell-free, circulating DNA from unpurified plasma. PLoS One 2014; 9:e87838. [PMID: 24595313 PMCID: PMC3940427 DOI: 10.1371/journal.pone.0087838] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/30/2013] [Indexed: 02/06/2023] Open
Abstract
Cell-free DNA (cfDNA) in body tissues or fluids is extensively investigated in clinical medicine and other research fields. In this article we provide a direct quantitative real-time PCR (qPCR) as a sensitive tool for the measurement of cfDNA from plasma without previous DNA extraction, which is known to be accompanied by a reduction of DNA yield. The primer sets were designed to amplify a 90 and 222 bp multi-locus L1PA2 sequence. In the first module, cfDNA concentrations in unpurified plasma were compared to cfDNA concentrations in the eluate and the flow-through of the QIAamp DNA Blood Mini Kit and in the eluate of a phenol-chloroform isoamyl (PCI) based DNA extraction, to elucidate the DNA losses during extraction. The analyses revealed 2.79-fold higher cfDNA concentrations in unpurified plasma compared to the eluate of the QIAamp DNA Blood Mini Kit, while 36.7% of the total cfDNA were found in the flow-through. The PCI procedure only performed well on samples with high cfDNA concentrations, showing 87.4% of the concentrations measured in plasma. The DNA integrity strongly depended on the sample treatment. Further qualitative analyses indicated differing fractions of cfDNA fragment lengths in the eluate of both extraction methods. In the second module, cfDNA concentrations in the plasma of 74 coronary heart disease patients were compared to cfDNA concentrations of 74 healthy controls, using the direct L1PA2 qPCR for cfDNA quantification. The patient collective showed significantly higher cfDNA levels (mean (SD) 20.1 (23.8) ng/ml; range 5.1–183.0 ng/ml) compared to the healthy controls (9.7 (4.2) ng/ml; range 1.6–23.7 ng/ml). With our direct qPCR, we recommend a simple, economic and sensitive procedure for the quantification of cfDNA concentrations from plasma that might find broad applicability, if cfDNA became an established marker in the assessment of pathophysiological conditions.
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Affiliation(s)
- Sarah Breitbach
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Suzan Tug
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Susanne Helmig
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Daniela Zahn
- Department of Health Psychology, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Thomas Kubiak
- Department of Health Psychology, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Matthias Michal
- Department of Psychosomatic Medicine and Psychotherapy, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Tommaso Gori
- Department of Cardiology, Angiology and Internal Medicine, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Tobias Ehlert
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Thomas Beiter
- Department of Sports Medicine, Medical Clinic, Eberhard-Karls-University of Tuebingen, Tuebingen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
- * E-mail:
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Castellanos-Rizaldos E, Liu P, Milbury CA, Guha M, Brisci A, Cremonesi L, Ferrari M, Mamon H, Makrigiorgos GM. Temperature-tolerant COLD-PCR reduces temperature stringency and enables robust mutation enrichment. Clin Chem 2012; 58:1130-8. [PMID: 22587896 DOI: 10.1373/clinchem.2012.183095] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Low-level mutations in clinical tumor samples often reside below mutation detection limits, thus leading to false negatives that may impact clinical diagnosis and patient management. COLD-PCR (coamplification at lower denaturation temperature PCR) is a technology that magnifies unknown mutations during PCR, thus enabling downstream mutation detection. However, a practical difficulty in applying COLD-PCR has been the requirement for strict control of the denaturation temperature for a given sequence, to within ±0.3 °C. This requirement precludes simultaneous mutation enrichment in sequences of substantially different melting temperature (T(m)) and limits the technique to a single sequence at a time. We present a temperature-tolerant (TT) approach (TT-COLD-PCR) that reduces this obstacle. METHODS We describe thermocycling programs featuring a gradual increase of the denaturation temperature during COLD-PCR. This approach enabled enrichment of mutations when the cycling achieves the appropriate critical denaturation temperature of each DNA amplicon that is being amplified. Validation was provided for KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) and TP53 (tumor protein p53) exons 6-9 by use of dilutions of mutated DNA, clinical cancer samples, and plasma-circulating DNA. RESULTS A single thermocycling program with a denaturation-temperature window of 2.5-3.0 °C enriches mutations in all DNA amplicons simultaneously, despite their different T(m)s. Mutation enrichments of 6-9-fold were obtained with TT-full-COLD-PCR. Higher mutation enrichments were obtained for the other 2 forms of COLD-PCR, fast-COLD-PCR, and ice-COLD-PCR. CONCLUSIONS Low-level mutations in diverse amplicons with different T(m)s can be mutation enriched via TT-COLD-PCR provided that their T(m)s fall within the denaturation-temperature window applied during amplification. This approach enables simultaneous enrichment of mutations in several amplicons and increases significantly the versatility of COLD-PCR.
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Affiliation(s)
- E Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Mouliere F, Robert B, Arnau Peyrotte E, Del Rio M, Ychou M, Molina F, Gongora C, Thierry AR. High fragmentation characterizes tumour-derived circulating DNA. PLoS One 2011; 6:e23418. [PMID: 21909401 PMCID: PMC3167805 DOI: 10.1371/journal.pone.0023418] [Citation(s) in RCA: 381] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/16/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Circulating DNA (ctDNA) is acknowledged as a potential diagnostic tool for various cancers including colorectal cancer, especially when considering the detection of mutations. Certainly due to lack of normalization of the experimental conditions, previous reports present many discrepancies and contradictory data on the analysis of the concentration of total ctDNA and on the proportion of tumour-derived ctDNA fragments. METHODOLOGY In order to rigorously analyse ctDNA, we thoroughly investigated ctDNA size distribution. We used a highly specific Q-PCR assay and athymic nude mice xenografted with SW620 or HT29 human colon cancer cells, and we correlated our results by examining plasma from metastatic CRC patients. CONCLUSION/SIGNIFICANCE Fragmentation and concentration of tumour-derived ctDNA is positively correlated with tumour weight. CtDNA quantification by Q-PCR depends on the amplified target length and is optimal for 60-100 bp fragments. Q-PCR analysis of plasma samples from xenografted mice and cancer patients showed that tumour-derived ctDNA exhibits a specific amount profile based on ctDNA size and significant higher ctDNA fragmentation. Metastatic colorectal patients (n = 12) showed nearly 5-fold higher mean ctDNA fragmentation than healthy individuals (n = 16).
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Affiliation(s)
- Florent Mouliere
- SysDiag UMR3145 – CNRS, National Centre of the Scientific Research/BIO-RAD, Montpellier, France
| | - Bruno Robert
- U896 INSERM, National Institute of Health and Medical Research, University Montpellier1, IRCM, Institute of Oncological Research of Montpellier, Montpellier, France
| | - Erika Arnau Peyrotte
- SysDiag UMR3145 – CNRS, National Centre of the Scientific Research/BIO-RAD, Montpellier, France
| | - Maguy Del Rio
- U896 INSERM, National Institute of Health and Medical Research, University Montpellier1, IRCM, Institute of Oncological Research of Montpellier, Montpellier, France
| | - Marc Ychou
- CRLC, Regional Centre against Cancer, Val d'Aurelle-Paul Lamarque, Montpellier, France
| | - Franck Molina
- SysDiag UMR3145 – CNRS, National Centre of the Scientific Research/BIO-RAD, Montpellier, France
| | - Celine Gongora
- U896 INSERM, National Institute of Health and Medical Research, University Montpellier1, IRCM, Institute of Oncological Research of Montpellier, Montpellier, France
| | - Alain R. Thierry
- SysDiag UMR3145 – CNRS, National Centre of the Scientific Research/BIO-RAD, Montpellier, France
- * E-mail:
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Thierry AR, Mouliere F, Gongora C, Ollier J, Robert B, Ychou M, Del Rio M, Molina F. Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts. Nucleic Acids Res 2010; 38:6159-75. [PMID: 20494973 PMCID: PMC2952865 DOI: 10.1093/nar/gkq421] [Citation(s) in RCA: 222] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although circulating DNA (ctDNA) could be an attractive tool for early cancer detection, diagnosis, prognosis, monitoring or prediction of response to therapies, knowledge on its origin, form and rate of release is poor and often contradictory. Here, we describe an experimental system to systematically examine these aspects. Nude mice were xenografted with human HT29 or SW620 colorectal carcinoma (CRC) cells and ctDNA was analyzed by Q-PCR with highly specific and sensitive primer sets at different times post-graft. We could discriminate ctDNA from normal (murine) cells and from mutated and non-mutated tumor (human) cells by using species-specific KRAS or PSAT1 primers and by assessing the presence of the BRAF V600E mutation. The concentration of human (mutated and non-mutated) ctDNA increased significantly with tumor growth. Conversely, and differently from previous studies, low, constant level of mouse ctDNA was observed, thus facilitating the study of mutated and non-mutated tumor derived ctDNA. Finally, analysis of ctDNA fragmentation confirmed the predominance of low-size fragments among tumor ctDNA from mice with bigger tumors. Higher ctDNA fragmentation was also observed in plasma samples from three metastatic CRC patients in comparison to healthy individuals. Our data confirm the predominance of mononucleosome-derived fragments in plasma from xenografted animals and, as a consequence, of apoptosis as a source of ctDNA, in particular for tumor-derived ctDNA. Altogether, our results suggest that ctDNA features vary during CRC tumor development and our experimental system might be a useful tool to follow such variations.
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Affiliation(s)
- Alain R Thierry
- Sysdiag UMR3145 - CNRS/BIO-RAD, CAP DELTA 1682 Rue de la Valsière, 34184 Montpellier CEDEX 4, France.
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Kuang Y, Rogers A, Yeap BY, Wang L, Makrigiorgos M, Vetrand K, Thiede S, Distel RJ, Jänne PA. Noninvasive detection of EGFR T790M in gefitinib or erlotinib resistant non-small cell lung cancer. Clin Cancer Res 2009; 15:2630-6. [PMID: 19351754 DOI: 10.1158/1078-0432.ccr-08-2592] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE Tumors from 50% of epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer patients that develop resistance to gefitinib or erlotinib will contain a secondary EGFR T790M mutation. As most patients do not undergo repeated tumor biopsies we evaluated whether EGFR T790M could be detected using plasma DNA. EXPERIMENTAL DESIGN DNA from plasma of 54 patients with known clinical response to gefitinib or erlotinib was extracted and used to detect both EGFR-activating and EGFR T790M mutations. Forty-three (80%) of patients had tumor EGFR sequencing (EGFR mutant/wild type: 30/13) and seven patients also had EGFR T790M gefitinib/erlotinib-resistant tumors. EGFR mutations were detected using two methods, the Scorpion Amplification Refractory Mutation System and the WAVE/Surveyor, combined with whole genome amplification. RESULTS Both EGFR-activating and EGFR T790M were identified in 70% of patients with known tumor EGFR-activating (21 of 30) or T790M (5 of 7) mutations. EGFR T790M was identified from plasma DNA in 54% (15 of 28) of patients with prior clinical response to gefitinib/erlotinib, 29% (4 of 14) with prior stable disease, and in 0% (0 of 12) that had primary progressive disease or were untreated with gefitinib/erlotinib. CONCLUSIONS EGFR T790M can be detected using plasma DNA from gefitinib- or erlotinib-resistant patients. This noninvasive method may aid in monitoring drug resistance and in directing the course of subsequent therapy.
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Affiliation(s)
- Yanan Kuang
- Translational Research Laboratory, Center for Clinical and Translational Research, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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