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Benesova L, Ptackova R, Halkova T, Semyakina A, Svaton M, Fiala O, Pesek M, Minarik M. Detection and Quantification of ctDNA for Longitudinal Monitoring of Treatment in Non-Small Cell Lung Cancer Patients Using a Universal Mutant Detection Assay by Denaturing Capillary Electrophoresis. Pathol Oncol Res 2022; 28:1610308. [PMID: 35837614 PMCID: PMC9274771 DOI: 10.3389/pore.2022.1610308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022]
Abstract
Background: Observation of anticancer therapy effect by monitoring of minimal residual disease (MRD) is becoming an important tool in management of non-small cell lung cancer (NSCLC). The approach is based on periodic detection and quantification of tumor-specific somatic DNA mutation in circulating tumor DNA (ctDNA) extracted from patient plasma. For such repetitive testing, complex liquid-biopsy techniques relying on ultra-deep NGS sequencing are impractical. There are other, cost-effective, methods for ctDNA analysis, typically based on quantitative PCR or digital PCR, which are applicable for detecting specific individual mutations in hotspots. While such methods are routinely used in NSCLC therapy prediction, however, extension to cover broader spectrum of mutations (e.g., in tumor suppressor genes) is required for universal longitudinal MRD monitoring. Methods: For a set of tissue samples from 81 NSCLC patients we have applied a denaturing capillary electrophoresis (DCE) for initial detection of somatic mutations within 8 predesigned PCR amplicons covering oncogenes and tumor suppressor genes. Mutation-negative samples were then subjected to a large panel NGS sequencing. For each patient mutation found in tissue was then traced over time in ctDNA by DCE. Results: In total we have detected a somatic mutation in tissue of 63 patients. For those we have then prospectively analyzed ctDNA from collected plasma samples over a period of up to 2 years. The dynamics of ctDNA during the initial chemotherapy therapy cycles as well as in the long-term follow-up matched the clinically observed response. Conclusion: Detection and quantification of tumor-specific mutations in ctDNA represents a viable complement to MRD monitoring during therapy of NSCLC patients. The presented approach relying on initial tissue mutation detection by DCE combined with NGS and a subsequent ctDNA mutation testing by DCE only represents a cost-effective approach for its routine implementation.
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Affiliation(s)
- Lucie Benesova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Renata Ptackova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Tereza Halkova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Anastasiya Semyakina
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Martin Svaton
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Ondrej Fiala
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Milos Pesek
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Marek Minarik
- Elphogene, Prague, Czechia
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Marek Minarik,
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Hálková T, Ptáčková R, Semyakina A, Suchánek Š, Traboulsi E, Ngo O, Hejcmanová K, Májek O, Bureš J, Zavoral M, Minárik M, Benešová L. Somatic Mutations in Exon 7 of the TP53 Gene in Index Colorectal Lesions Are Associated with the Early Occurrence of Metachronous Adenoma. Cancers (Basel) 2022; 14:cancers14122823. [PMID: 35740488 PMCID: PMC9221022 DOI: 10.3390/cancers14122823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Identifying patients with an increased risk of early recurrence of colorectal lesions is still a problem. In our study, we focused on improving this identification by determining the mutation profile of index lesions. We found a statistically significant association between the mutation in exon 7 of the TP53 gene in the index lesion and the risk of early metachronous adenoma. Abstract (1) Background: this prospective study was focused on detailed analysis of the mutation heterogeneity in colorectal lesions removed during baseline (index) colonoscopy to identify patients at high risk of early occurrence of metachronous adenomas. (2) Methods: a total of 120 patients after endoscopic therapy of advanced colorectal neoplasia size ≥10 mm (index lesion) with subsequent surveillance colonoscopy after 10–18 months were included. In total, 143 index lesions and 84 synchronous lesions in paraffin blocks were divided into up to 30 samples. In each of them, the detection of somatic mutations in 11 hot spot gene loci was performed. Statistical analysis to correlate the mutation profiles and the degree of heterogeneity of the lesions with the risk of metachronous adenoma occurrence was undertaken. (3) Results: mutation in exon 7 of the TP53 gene found in the index lesion significantly correlated with the early occurrence of metachronous adenoma (log-rank test p = 0.003, hazard ratio 2.73, 95% confidence interval 1.14–6.56). We did not find an association between the risk of metachronous adenomas and other markers monitored. (4) Conclusions: the findings of this study could lead to an adjustment of existing recommendations for surveillance colonoscopies in a specific group of patients with mutations in exon 7 of the TP53 gene in an index lesion, where a shortening of surveillance interval may be warranted.
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Affiliation(s)
- Tereza Hálková
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Renata Ptáčková
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Anastasiya Semyakina
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Štěpán Suchánek
- Department of Medicine, 1st Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Correspondence:
| | - Eva Traboulsi
- Department of Pathology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Ondřej Ngo
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Kateřina Hejcmanová
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Ondřej Májek
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Jan Bureš
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Miroslav Zavoral
- Department of Medicine, 1st Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Marek Minárik
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
- Elphogene, Drnovská 1112/60, 161 00 Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 00 Prague, Czech Republic
| | - Lucie Benešová
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
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Fiala O, Baxa J, Svaton M, Benesova L, Ptackova R, Halkova T, Minarik M, Hosek P, Buresova M, Finek J, Ferda J, Pesek M. Combination of Circulating Tumour DNA and 18F-FDG PET/CT for Precision Monitoring of Therapy Response in Patients With Advanced Non-small Cell Lung Cancer: A Prospective Study. Cancer Genomics Proteomics 2022; 19:270-281. [PMID: 35181593 DOI: 10.21873/cgp.20319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Circulating tumour DNA (ctDNA) represents an emerging biomarker in non-small cell lung cancer (NSCLC). We focused on the combination of ctDNA and positron emission tomography/computed tomography (PET/CT) in the follow-up monitoring of advanced-stage NSCLC patients treated with chemotherapy. PATIENTS AND METHODS Eighty-four patients were enrolled in this study. 18F-fluorodeoxyglucose PET/CT and ctDNA assessments were performed at baseline and after two cycles of chemotherapy (follow-up). RESULTS There was a correlation of ctDNA with metabolic tumour volume (MTV), total lesion glycolysis (TLG), and iodine concentration (IC) at baseline (p=0.001, p=0.001, p=0.003) and at follow-up (p=0.006, p=0.002, p=0.001). The objective response was associated with follow-up ctDNA (p<0.001) and the change of all PET/CT parameters. ROC analyses showed that the combination of follow-up ctDNA with changes in SUVmax is very promising for the estimation of objective response and progression-free survival. CONCLUSION The combination of ctDNA assessment with PET/CT is a promising approach for the follow-up monitoring of therapy response and prognosis estimation of advanced-stage NSCLC patients.
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Affiliation(s)
- Ondrej Fiala
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic; .,Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jan Baxa
- Department of Imaging Methods, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Martin Svaton
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Lucie Benesova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czech Republic
| | - Renata Ptackova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czech Republic
| | - Tereza Halkova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czech Republic
| | - Marek Minarik
- Elphogene, Prague, Czech Republic.,Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Hosek
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Marcela Buresova
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jindrich Finek
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jiri Ferda
- Department of Imaging Methods, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Milos Pesek
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
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Benešová L, Hálková T, Ptáčková R, Semyakina A, Menclová K, Pudil J, Ryska M, Levý M, Šimša J, Pazdírek F, Hoch J, Blaha M, Minárik M. Significance of postoperative follow-up of patients with metastatic colorectal cancer using circulating tumor DNA. World J Gastroenterol 2019; 25:6939-6948. [PMID: 31908397 PMCID: PMC6938726 DOI: 10.3748/wjg.v25.i48.6939] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/05/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND One of the most notable applications for circulating tumor DNA (ctDNA) detection in peripheral blood of patients with metastatic colorectal cancer (mCRC) is a long-term postoperative follow-up. Sometimes referred to as a “liquid (re)biopsy” it is a minimally invasive procedure and can be performed repeatedly at relatively short intervals (months or even weeks). The presence of the disease and the actual extent of the tumor burden (tumor mass) within the patient’s body can be monitored. This is of particular importance, especially when evaluating radicality of surgical treatment as well as for early detection of disease progression or recurrence.
AIM To confirm the radicality of surgery using ctDNA and compare available methods for detection of recurrence in metastatic colorectal cancer.
METHODS A total of 47 patients with detected ctDNA and indications for resection of mCRC were enrolled in the multicenter study involving three surgical centers. Standard postoperative follow-ups using imaging techniques and the determination of tumor markers were supplemented by ctDNA sampling. In addition to the baseline ctDNA testing prior to surgery, a postoperative observation was conducted by evaluating ctDNA presence up to a week after surgery and subsequently at approximately three-month intervals. The presence of ctDNA was correlated with radicality of surgical treatment and the actual clinical status of the patient.
RESULTS Among the monitored patients, the R0 (curative) resection correlated with postoperative ctDNA negativity in 26 out of 28 cases of surgical procedures (26/28, 93%). In the remaining cases of R0 surgeries that displayed ctDNA, both patients were diagnosed with a recurrence of the disease after 6 months. In 7 patients who underwent an R1 resection, 4 ctDNA positivities (4/7, 57%) were detected after surgery and associated with the confirmation of early disease recurrence (after 3 to 7 months). All 15 patients (15/15, 100%) undergoing R2 resection remained constantly ctDNA positive during the entire follow-up period. In 22 cases of recurrence, ctDNA positivity was detected 22 times (22/22, 100%) compared to 16 positives (16/22, 73%) by imaging methods and 15 cases (15/22, 68%) of elevated tumor markers.
CONCLUSION ctDNA detection in patients with mCRC is a viable tool for early detection of disease recurrence as well as for confirmation of the radicality of surgical treatment.
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Affiliation(s)
- Lucie Benešová
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
| | - Tereza Hálková
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
| | - Renata Ptáčková
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
| | - Anastasiya Semyakina
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
| | - Kateřina Menclová
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Military University Hospital, Prague CZ 169 02, Czech Republic
| | - Jiří Pudil
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Military University Hospital, Prague CZ 169 02, Czech Republic
| | - Miroslav Ryska
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Military University Hospital, Prague CZ 169 02, Czech Republic
| | - Miroslav Levý
- Surgery Department, 1st Faculty of Medicine, Charles University Prague and Thomayer Hospital, Prague CZ 140 59, Czech Republic
| | - Jaromír Šimša
- Surgery Department, 1st Faculty of Medicine, Charles University Prague and Thomayer Hospital, Prague CZ 140 59, Czech Republic
| | - Filip Pazdírek
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Motol University Hospital, Prague CZ 150 06, Czech Republic
| | - Jiří Hoch
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Motol University Hospital, Prague CZ 150 06, Czech Republic
| | - Milan Blaha
- Institute of Biostatistics and Analyses of the Masaryk University, Brno CZ 625 00, Czech Republic
| | - Marek Minárik
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
- Elphogene, Prague CZ 161 00, Czech Republic
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