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Panet F, Papakonstantinou A, Borrell M, Vivancos J, Vivancos A, Oliveira M. Use of ctDNA in early breast cancer: analytical validity and clinical potential. NPJ Breast Cancer 2024; 10:50. [PMID: 38898045 PMCID: PMC11187121 DOI: 10.1038/s41523-024-00653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Circulating free tumor DNA (ctDNA) analysis is gaining popularity in precision oncology, particularly in metastatic breast cancer, as it provides non-invasive, real-time tumor information to complement tissue biopsies, allowing for tailored treatment strategies and improved patient selection in clinical trials. Its use in early breast cancer has been limited so far, due to the relatively low sensitivity of available techniques in a setting characterized by lower levels of ctDNA shedding. However, advances in sequencing and bioinformatics, as well as the use of methylome profiles, have led to an increasing interest in the application of ctDNA analysis in early breast cancer, from screening to curative treatment evaluation and minimal residual disease (MRD) detection. With multiple prospective clinical trials in this setting, ctDNA evaluation may become useful in clinical practice. This article reviews the data regarding the analytical validity of the currently available tests for ctDNA detection and the clinical potential of ctDNA analysis in early breast cancer.
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Affiliation(s)
- François Panet
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada
| | - Andri Papakonstantinou
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Breast, Endocrine Tumors and Sarcomas, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Borrell
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain
| | - Joan Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mafalda Oliveira
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain.
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Tung PH, Chiu TH, Huang ACC, Ju JS, Huang CH, Wang CC, Ko HW, Chung FT, Hsu PC, Fang YF, Guo YK, Kuo CHS, Yang CT. Differential prognostic value of tumor and plasma T790M mutations in EGFR TKI-treated advanced NSCLC. Ther Adv Med Oncol 2024; 16:17588359231222604. [PMID: 38249338 PMCID: PMC10799606 DOI: 10.1177/17588359231222604] [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: 02/22/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024] Open
Abstract
Background Substitution of methionine for threonine at codon 790 (T790M) of epidermal growth factor receptor (EGFR) represents the major mechanism of resistance to EGFR tyrosine kinase inhibitors (TKIs) in EGFR-mutant non-small-cell lung cancer. We determined the prognostic impact and association of secondary T790M mutations with the outcomes of osimertinib and chemotherapy. Methods Patients (n = 460) progressing from first-line EGFR-TKI treatment were assessed. Tissue and/or liquid biopsies were used to determine T790M status; post-progression overall survival (OS) was analyzed. Results Overall, 143 (31.1%) patients were T790M positive, 95 (20.7%) were T790M negative, and 222 (48.2%) had unknown T790M status. T790M status [T790M positive versus T790M negative: hazard ratio (HR) 0.48 (95% confidence interval (CI), 0.32-0.70); p < 0.001, T790M unknown versus T790M negative: HR 1.97 (95% CI, 1.47-2.64); p < 0.001] was significantly associated with post-progression OS. T790M positivity rates were similar for tissue (90/168, 53.6%) and liquid (53/90, 58.9%) biopsies (Fisher's exact test, p = 0.433). Tumor T790M-positive patients had significantly longer post-progression OS than tumor T790M-negative patients (34.1 versus 17.1 months; log-rank test, p = 8 × 10-5). Post-progression OS was similar between plasma T790M-positive and -negative patients (17.4 versus not reached; log-rank test, p = 0.600). In tumor T790M-positive patients, post-progression OS was similar after osimertinib and chemotherapy [34.1 versus 29.1 months; log-rank test, p = 0.900; HR 1.06 (95% CI, 0.44-2.57); p = 0.897]. Conclusion T790M positivity predicts better post-progression OS than T790M negativity; tumor T790M positivity has a stronger prognostic impact than plasma T790M positivity. Osimertinib and chemotherapy provide similar OS benefits in patients with T790M-positive tumors.
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Affiliation(s)
- Pi-Hung Tung
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Tzu-Hsuan Chiu
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Allen Chung-Cheng Huang
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Jia-Shiuan Ju
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Chi-Hsien Huang
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Chin-Chou Wang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - How-Wen Ko
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Fu-Tsai Chung
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Ping-Chih Hsu
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Yueh-Fu Fang
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
| | - Yi-Ke Guo
- Data Science Institute, Department of Computing, Imperial College London, London, UK
| | - Chih-Hsi Scott Kuo
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, No. 199, Tun-Hwa North Road, Taipei 333, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center
- Data Science Institute, Department of Computing, Imperial College London, London, UK
| | - Cheng-Ta Yang
- Division of Thoracic Oncology, Department of Thoracic Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan
- Thoracic Oncology Unit, Chang Gung Memorial Hospital Cancer Center, Taipei, Taiwan
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Heredia D, Bolaño-Guerra L, Valencia-Velarde A, Santoyo EV, Lara-Mejía L, Cárdenas-Fernández D, Orozco M, Cruz-Rico G, Arrieta O. Liquid biopsy in clinical outcomes and detection of T790M mutation in metastatic non-small cell lung cancer after progression to EGFR-TKI. Cancer Biomark 2023:CBM230124. [PMID: 38108344 DOI: 10.3233/cbm-230124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
BACKGROUND Liquid biopsy (LB) is used to detect epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) and has been demonstrated to have prognostic and predictive value. OBJECTIVE To associate the rates of EGFR and T790M mutations detected by LB during disease progression after first- or second-generation EGFR-TKIs with clinical characteristics and survival outcomes. METHODS From January 2018 to December 2021, 295 patients with advanced EGFR mutant (EGFRm) NSCLC treated with first- or second-generation EGFR-TKIs were retrospectively analyzed. LB was collected at the time of progression. The frequency of EGFRT790M mutations, overall survival (OS), and the clinical characteristics associated with LB positivity were determined. RESULTS The prevalence of EGFRT790M mutation detected using LB was 44%. In patients with negative vs. positive LB, the median OS was 45.0 months vs. 25.0 months (p= 0.0001), respectively. Patients with a T790M mutation receiving osimertinib had a median OS of 44 months (95% CI [33.05-54.99]). Clinical characteristics associated with positive LB at progression extra-thoracic involvement, > 3 metastatic sites, and bone metastases. CONCLUSIONS Our findings showed that LB positivity was associated with worse survival outcomes and specific clinical characteristics. This study also confirmed the feasibility and detection rate of T790M mutation in a Latin American population.
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Affiliation(s)
- David Heredia
- Thoracic Oncology Unit, Department of Thoracic Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | - Angel Valencia-Velarde
- Thoracic Oncology Unit, Department of Thoracic Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Edgar Varela Santoyo
- Medical Oncology Department, Centro Oncológico Estatal, ISSSEMyN, Toluca, Mexico
| | - Luis Lara-Mejía
- Thoracic Oncology Unit, Department of Thoracic Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Daniela Cárdenas-Fernández
- Thoracic Oncology Unit, Department of Thoracic Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Mario Orozco
- Neuroimmunology Laboratory, Instituto Nacional de Neurología y Neurocirugía, Mexico City, Mexico
| | - Graciela Cruz-Rico
- Thoracic Oncology Unit, Department of Thoracic Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Oscar Arrieta
- Thoracic Oncology Unit, Department of Thoracic Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
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Venkataram R, Shetty V, Prasad K, Kille S, Srinivas T, Chakraborty A. Detection of clinically-relevant <em>EGFR</em> variations in <em>de novo</em> small cell lung carcinoma by droplet digital PCR. Monaldi Arch Chest Dis 2022; 93. [PMID: 36062504 DOI: 10.4081/monaldi.2022.2280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Targeted therapy that utilizes tyrosine kinase inhibitors (TKIs), specific to epidermal growth factor receptors (EGFR) has changed the landscape of treatment of non-small cell lung cancer (NSCLC). The success or failure of this approach depends on presence of certain variations in the tyrosine kinase domain of EGFR gene. Generally, patients diagnosed with Small cell lung cancer (SCLC) are considered ineligible for TKI therapy owing to the absence of EGFR variations. . However, there is evidence of these variations being detected in SCLCs, both in de-novo and in transformed SCLCs (TKI-treated adenocarcinomas). Despite the presence of clinically-relevant EGFR variations in SCLCs, the response to TKIs has been inconsistent. Liquid biopsy is a well-established approach in lung cancer management with proven diagnostic, prognostic and predictive applications. It relies on detection of circulating tumor-derived nucleic acids present in plasma of the patient. In this study, a liquid biopsy approach was utilized to screen 118 consecutive lung cancer patients for four clinically-relevant variations in EGFR gene, which included three activating/sensitizing variations (Ex18 G719S, Ex19del E746-A750 and Ex21 L858R) and one acquired/resistance (Ex20 T790M, de novo) variation by droplet digital PCR, the most advanced third generation PCR technique. As expected, clinically-relevant EGFR variations were found in majority of the non-small cell lung cancer cases. However, among the handful of small cell lung cancer samples screened, sensitizing variations (Ex18 G719S and Ex21 L858R) were seen in almost all of them. Interestingly, Ex20 T790M variation was not detected in any of the cases screened. The results of our study indicate that EGFR variations are present in SCLCs and highly sensitive liquid biopsy techniques like ddPCR can be effectively utilized for this purpose of screening EGFR variations in such samples.
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Affiliation(s)
- Rajesh Venkataram
- Department of Pulmonary Medicine, KS Hegde Medical Academy, Nitte (Deemed to Be University), Mangalore.
| | - Vijith Shetty
- Department of Medical Oncology, KS Hegde Medical Academy, Nitte (Deemed to Be University), Mangalore.
| | - Kishan Prasad
- Department of Pathology, KS Hegde Medical Academy, Nitte (Deemed to Be University), Mangalore.
| | - Sonam Kille
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to Be University), Mangalore.
| | - Teerthanath Srinivas
- Department of Pathology, KS Hegde Medical Academy, Nitte (Deemed to Be University), Mangalore.
| | - Anirban Chakraborty
- Dean Faculty of Biological Sciences, Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to Be University), Mangalore.
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Hassan S, Shehzad A, Khan SA, Miran W, Khan S, Lee YS. Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management. Biomedicines 2022; 10:biomedicines10082047. [PMID: 36009594 PMCID: PMC9405989 DOI: 10.3390/biomedicines10082047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 11/20/2022] Open
Abstract
Over time, molecular biology and genomics techniques have been developed to speed up the early diagnosis and clinical management of cancer. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. Important advances in applying molecular testing involve circulating-free DNA (cfDNA)- and cell-free RNA (cfRNA)-based liquid biopsies for the diagnosis, prognosis, prediction, and treatment of cancer. Both cfDNA and cfRNA are sensitive and specific biomarkers for cancer detection, which have been clinically proven through multiple randomized and prospective trials. These help in cancer management based on the noninvasive evaluation of size, quantity, and point mutations, as well as copy number alterations at the tumor site. Moreover, personalized detection of ctDNA helps in adjuvant therapeutics and predicts the chances of recurrence of cancer and resistance to cancer therapy. Despite the controversial diagnostic values of cfDNA and cfRNA, many clinical trials have been completed, and the Food and Drug Administration has approved many multigene assays to detect genetic alterations in the cfDNA of cancer patients. In this review, we underpin the recent advances in the physiological roles of cfDNA and cfRNA, as well as their roles in cancer detection by highlighting recent clinical trials and their roles as prognostic and predictive markers in cancer management.
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Affiliation(s)
- Sadia Hassan
- Department of Biomedical Engineering and Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Adeeb Shehzad
- Department of Biomedical Engineering and Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
- Correspondence: (A.S.); (Y.-S.L.)
| | - Shahid Ali Khan
- Department of Chemistry, School of Natural Sciences (SNS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Waheed Miran
- Department of Chemical Engineering, School of Chemical and Materials Engineering National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Salman Khan
- Department of pharmacy, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Young-Sup Lee
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea
- Correspondence: (A.S.); (Y.-S.L.)
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Maggi R, Breitschwerdt EB, Qurollo B, Miller JC. Development of a Multiplex Droplet Digital PCR Assay for the Detection of Babesia, Bartonella, and Borrelia Species. Pathogens 2021; 10:pathogens10111462. [PMID: 34832618 PMCID: PMC8620149 DOI: 10.3390/pathogens10111462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
We describe the development, optimization, and validation of a multiplex droplet digital PCR (ddPCR) assay for the simultaneous detection of Babesia, Bartonella, and Borrelia spp. DNA from several sample matrices, including clinical blood samples from animals and humans, vectors, in-vitro infected human and animal cell lines, and tissues obtained from animal models (infected with Bartonella and/or B. burgdorferi). The multiplex ddPCR assay was able to detect 31 Bartonella, 13 Borrelia, and 24 Babesia species, including Theileria equi, T. cervi, and Cytauxzoon felis. No amplification of Treponema or Leptospira spp. was observed. Sensitivity of 0.2-5 genome equivalent DNA copies per microliter was achieved for different members of the Bartonella and Borrelia genus, depending on the species or matrix type (water or spiked blood DNA) tested. The ddPCR assay facilitated the simultaneous detection of co-infections with two and three vector-borne pathogens comprising four different genera (Babesia, Bartonella, Borrelia, and Theileria) from clinical and other sample sources.
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Affiliation(s)
- Ricardo Maggi
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
- Correspondence:
| | - Edward B. Breitschwerdt
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
| | - Barbara Qurollo
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
| | - Jennifer C. Miller
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
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Venkataram R, Arjuna S, Hosmane GB, Chakraborty A. Quantitative analysis of cell-free DNA by droplet digital PCR reveals the presence of EGFR mutations in non-malignant lung pathologies. Monaldi Arch Chest Dis 2021; 91. [PMID: 33960186 DOI: 10.4081/monaldi.2021.1748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/18/2021] [Indexed: 11/23/2022] Open
Abstract
Tyrosine kinase inhibitors (TKIs) targeting epidermal growth factor receptor (EGFR) are effectively used in treatment of non-small cell lung cancer (NSCLC). Mutation profile of tyrosine kinase domain of EGFR determines the eligibility of the patients for tyrosine kinase inhibitor (TKI) therapy. Liquid biopsy, which relies on circulating tumor-derived nucleic acids, has emerged as an effective tool in lung cancer management with proven diagnostic, prognostic and predictive applications. We screened 100 subjects, suspected to have lung malignancy, for four hotspot mutations including three activating (G719S, Ex19del E746-A750 and L858R) and one acquired (T790M, de novo) in EGFR gene by droplet digital PCR (ddPCR). While 97 subjects were subsequently confirmed to have lung malignancy based on histo/cytopathological studies, three cases turned out to be non-malignant lung pathologies that were completely cured by antibiotic therapy. Intriguingly, ddPCR revealed the presence of EGFR mutations in these non-malignant subjects. Two cases showed the presence of G719S and T790M mutations respectively and another had compound mutations (T790M and L858R). The detection of EGFR mutations in non-malignant pulmonary conditions opens up a new area of research.
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Affiliation(s)
- Rajesh Venkataram
- Department of Pulmonary Medicine, KS Hegde Medical Academy (Deemed to be University), Nitte, Mangalore .
| | - Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre For Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangalore .
| | - Giridhar Belur Hosmane
- Department of Pulmonary Medicine, KS Hegde Medical Academy (Deemed to be University), Nitte, Mangalore.
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre For Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangalore .
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Can Quantitative Measures of T790M Allelic Fraction Predict Survival Outcomes in Patients Receiving Osimertinib? Observations From an Early Access Programme. Clin Oncol (R Coll Radiol) 2021; 33:e305-e314. [PMID: 33589348 DOI: 10.1016/j.clon.2021.01.011] [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: 11/06/2020] [Revised: 01/08/2021] [Accepted: 01/26/2021] [Indexed: 11/24/2022]
Abstract
AIMS Multiple studies have shown conflicting results on the correlation between the EGFR T790M quantitative level and survival outcomes in osimertinib-treated patients. We sought to validate such correlations using data from an osimertinib early access programme (EAP) providing access for metastatic non-small cell lung cancer patients with limited treatment options. PATIENTS AND METHODS This observational, multicentre, retrospective analysis included EAP participants who received osimertinib until disease progression, intolerable toxicities or death. Digital droplet polymerase chain reaction-based quantitative plasma genotyping was carried out upon disease progression and data were analysed to explore the relationships between T790M mutant allele fraction (MAF), T790M copy number, MAF ratio and post-osimertinib overall survival. Real-world treatment outcomes and safety were also evaluated. RESULTS Data from 156 EAP participants were analysed (median follow-up 37.7 months). The median age was 62 years, 62.2% were women, 79.5% were never-smokers, 60.9% had Eastern Cooperative Oncology Group performance status 0/1. In patients with available plasma data (n = 114), T790M MAF (%) showed no significant relationships with overall survival (hazard ratio 1.02; 95% confidence interval 0.99-1.04) or time to treatment discontinuation (TTD) (hazard ratio 1.01; 95% confidence interval 0.98-1.04). Absolute T790M copy number and T790M to activating EGFR mutation MAF ratio also showed no prognostic value. The investigator-assessed response rate was 42.3% and the disease control rate was 85.5%. The median TTD was 15.8 (95% confidence interval 12.5-18.5) months and the median overall survival was 22.3 (95% confidence interval 18.6-26.1) months. CONCLUSION T790M MAF did not correlate with TTD or overall survival in this EAP cohort but limitations should not be overlooked. Observed survival outcomes and the toxicity profile were consistent with data from other real-world series.
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Cecchini MJ, Yi ES. Liquid biopsy is a valuable tool in the diagnosis and management of lung cancer. J Thorac Dis 2020; 12:7048-7056. [PMID: 33282410 PMCID: PMC7711358 DOI: 10.21037/jtd.2020.04.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the use of various body fluids to test for circulating biological elements derived from the tumor. Liquid biopsy has taken on an increasingly important role in lung cancer diagnosis, molecular characterization, surveillance, monitoring, and determining mechanisms of resistance. These assays can utilize various sources of cell-free DNA (cfDNA) including blood, pleural fluid, urine, and others to detect tumor associated alterations. With the increasing power of next-generation sequencing technologies and the development of assays such as digital droplet PCR, rare tumor alleles can be detected in cfDNA to determine key characteristics of the tumor. Current assays, while effective, are still challenged by limited sensitivity and capacity to single genes or small panels of genes, though this is rapidly expanding. Nevertheless, testing of cfDNA has been shown to be valuable in detecting resistance to targeted inhibitors, particularly for detection of T790M in EGFR and monitoring response to therapy. With the continued development of more powerful and sensitive assays, these techniques will empower clinicians to better characterize early stage disease and can be used in the screening of high-risk patients, which may eliminate the requirement for tissue diagnosis in some settings. That said, since the majority of these alterations are not specific to lung cancer, there will continue to be a need for tissue in at least the initial diagnosis. Used in conjugation with tissue sampling, these assays will assist the treating clinician and the pathologist to better characterize individual tumors, even in the setting of limited tissue.
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Affiliation(s)
- Matthew J Cecchini
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Eunhee S Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
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Arjuna S, Venkataram R, Dechamma PN, Chakraborty G, Babu N, D'Cruz A, Hosmane GB, Chakraborty A. Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP). Sci Rep 2020; 10:17559. [PMID: 33067539 PMCID: PMC7568567 DOI: 10.1038/s41598-020-74689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 11/17/2022] Open
Abstract
Targeting epidermal growth factor receptor (EGFR) through tyrosine kinase inhibitors (TKI) is a successful therapeutic strategy in non-small cell lung cancer. However, the response to TKI therapy depends on specific activating and acquired mutations in the tyrosine kinase domain of the EGFR gene. Therefore, confirming the EGFR status of patients is crucial, not only for determining the eligibility, but also for monitoring the emergence of mutations in patients under TKI therapy. In this study, our aim was to develop a cost effective, yet sensitive, technique that allows the detection of therapeutically-relevant EGFR hotspot mutations at isothermal conditions in a non-invasive manner. Previously, we developed an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for screening germline and somatic de novo T790M EGFR mutation in lung cancer patients. In this study, we used cell free DNA as a template in AS-LAMP assay (CF-LAMP) for non-invasive detection of two hotspot EGFR mutations (T790M, and L858R) and compared its efficiency with ultrasensitive droplet digital PCR (ddPCR) assay. The results of CF-LAMP assay were consistent with those obtained in ddPCR assay, indicating the robustness of the method. CF-LAMP may serve as a valuable and cost-effective alternative for liquid biopsy techniques used in molecular diagnosis of non-small cell lung cancer.
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Affiliation(s)
- Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Rajesh Venkataram
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Pandyanda Nanjappa Dechamma
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Gunimala Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Audrey D'Cruz
- Department of Health Dentistry, A B Shetty Memorial Institute of Dental Sciences, Nitte (Deemed to be University), Mangaluru, India
| | - Giridhar Belur Hosmane
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India.
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Manoharan A, Sambandam R, Bhat V. Recent technologies enhancing the clinical utility of circulating tumor DNA. Clin Chim Acta 2020; 510:498-506. [PMID: 32795543 DOI: 10.1016/j.cca.2020.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
Circulating tumor DNA (ctDNA) is a promising blood based biomarker that is set to revolutionize cancer management. Non-invasive biopsy takes precedence over tissue biopsy for enabling longitudinal monitoring, providing a comprehensive profile of tumor heterogeneity and the ease of repeated sampling. Advanced genomic technologies enable real-time disease monitoring, detect minimal residual disease and recurrence at the earliest stages, the potential time points when treatment significantly reduces morbidity and mortality and enable tailored and personalized therapy. The review highlights evidence from literature that make ctDNA a potential liquid biopsy marker and the clinical utility of the recent techniques that leverage up on ctDNA.
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Affiliation(s)
- Aarthi Manoharan
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India
| | - Ravikumar Sambandam
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India.
| | - Vishnu Bhat
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India
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12
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Maggi RG, Richardson T, Breitschwerdt EB, Miller JC. Development and validation of a droplet digital PCR assay for the detection and quantification of Bartonella species within human clinical samples. J Microbiol Methods 2020; 176:106022. [PMID: 32795640 DOI: 10.1016/j.mimet.2020.106022] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022]
Abstract
This report describes the development, optimization, and validation of a ddPCR assay for the detection of Bartonella spp. DNA within several sample matrices, including clinical blood samples from patients with or without documented Bartonella spp. bacteremia. The Bartonella spp. ddPCR assay was developed based upon previously published TaqMan-based qPCR assays that can amplify DNA of over 25 Bartonella spp. Host DNA (housekeeping gene) amplification serves as a reference target to facilitate quantification. The efficiency, sensitivity, and specificity of the Bartonella spp. ddPCR assay was assessed by direct comparison with the current qPCR methods used by the Intracellular Pathogens Research Laboratory (North Carolina State University, North Carolina, USA), and Galaxy Diagnostics (Research Triangle Park, North Carolina, USA). Bartonella spp. ddPCR assay parameters were successfully optimized to detect Bartonella concentrations equivalent to 0.5 bacterial genome copies per microliter of blood (0.001 pg/ul of bacterial DNA). The number of droplets detected (resolution) for each concentration was consistent across each of four assessed time points. The Bartonella spp. ddPCR assay detected 16 species/strains including B. henselae; B. quintana; B. vinsonii subsp. berkhoffii (genotypes I, II, III and IV); B. vinsonii subsp. vinsonii; B. melophagi; B. volans; B. monaki; B. alsatica; B. bovis; B. elizabethae; B. clarridgeiae; and B. koehlerae. Bartonella DNA was detected in only one previously negative patient sample (119/120 negative; 99% specificity). The ddPCR sensitivity (53/112) was significantly better than qPCR (6/112) when testing patient blood and enrichment blood culture samples. The development of commercial ddPCR systems with integrated technologies has significantly streamlined the DNA detection process, making it more efficient and standardized for clinical diagnostic testing. The assay described in this work is the first step toward the development of a multiplex ddPCR assay (i.e., using the QX One from Bio-Rad) for the simultaneous detection and absolute quantification of multiple vector-borne pathogens (such as Babesia, Bartonella and Borrelia) within clinical samples.
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Affiliation(s)
- Ricardo G Maggi
- Galaxy Diagnostics, Inc, 7020 Kit Creek Rd #130, Research Triangle Park, NC 27709, USA; Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA
| | - Toni Richardson
- Galaxy Diagnostics, Inc, 7020 Kit Creek Rd #130, Research Triangle Park, NC 27709, USA
| | - Edward B Breitschwerdt
- Galaxy Diagnostics, Inc, 7020 Kit Creek Rd #130, Research Triangle Park, NC 27709, USA; Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA
| | - Jennifer C Miller
- Galaxy Diagnostics, Inc, 7020 Kit Creek Rd #130, Research Triangle Park, NC 27709, USA.
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13
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Wehrle J, Philipp U, Jolic M, Follo M, Hussung S, Waldeck S, Deuter M, Rassner M, Braune J, Rawluk J, Greil C, Waller CF, Becker H, Duque-Afonso J, Illert AL, Fritsch RM, Meiss F, Duyster J, von Bubnoff N, Scherer F. Personalized Treatment Selection and Disease Monitoring Using Circulating Tumor DNA Profiling in Real-World Cancer Patient Management. Diagnostics (Basel) 2020; 10:E550. [PMID: 32748806 PMCID: PMC7459590 DOI: 10.3390/diagnostics10080550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) in the blood plasma of cancer patients is an emerging biomarker used across oncology, facilitating noninvasive disease monitoring and genetic profiling at various disease milestones. Digital droplet PCR (ddPCR) technologies have demonstrated high sensitivity and specificity for robust ctDNA detection at relatively low costs. Yet, their value for ctDNA-based management of a broad population of cancer patients beyond clinical trials remains elusive. METHODS We developed mutation-specific ddPCR assays that were optimized for their use in real-world cancer management, covering 12 genetic aberrations in common cancer genes, such as EGFR, BRAF, KIT, KRAS, and NRAS. We assessed the limit of detection (LOD) and the limit of blank (LOB) for each assay and validated their performance for ctDNA detection using matched tumor sequencing. RESULTS We applied our custom ddPCR assays to 352 plasma samples from 96 patients with solid tumors. Mutation detection in plasma was highly concordant with tumor sequencing, demonstrating high sensitivity and specificity across all assays. In 20 cases, radiographic cancer progression was mirrored by an increase of ctDNA concentrations or the occurrence of novel mutations in plasma. Moreover, ctDNA profiling at diagnosis and during disease progression reflected personalized treatment selection through the identification of actionable gene targets in 20 cases. CONCLUSION Collectively, our work highlights the potential of ctDNA assessment by sensitive ddPCR for accurate disease monitoring, robust identification of resistance mutations, and upfront treatment selection in patients with solid tumors. We envision an increasing future role for ctDNA profiling within personalized cancer management in daily clinical routine.
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Affiliation(s)
- Julius Wehrle
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Ulrike Philipp
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Martina Jolic
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Marie Follo
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Saskia Hussung
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
- Department of Medical Oncology and Hematology, Zurich University Hospital, 8091 Zurich, Switzerland
| | - Silvia Waldeck
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Max Deuter
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Michael Rassner
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Jan Braune
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Justyna Rawluk
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Christine Greil
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Cornelius F. Waller
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Heiko Becker
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Jesús Duque-Afonso
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Anna L. Illert
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Ralph M. Fritsch
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
- Department of Medical Oncology and Hematology, Zurich University Hospital, 8091 Zurich, Switzerland
| | - Frank Meiss
- Department of Dermatology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
| | - Justus Duyster
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
| | - Nikolas von Bubnoff
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
- Department of Hematology and Oncology, University Hospital Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
| | - Florian Scherer
- Department Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (J.W.); (U.P.); (M.J.); (M.F.); (S.H.); (S.W.); (M.D.); (M.R.); (J.B.); (J.R.); (C.G.); (C.F.W.); (H.B.); (J.D.-A.); (A.L.I.); (R.M.F.); (J.D.)
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Lee SH, Kim EY, Kim A, Chang YS. Clinical implication and usefulness of de novo EGFR T790M mutation in lung adenocarcinoma with EGFR-tyrosine kinase inhibitor sensitizing mutation. Cancer Biol Ther 2020; 21:741-748. [PMID: 32543264 DOI: 10.1080/15384047.2020.1776579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In total, 102 cases diagnosed as lung adenocarcinoma with EGFR-tyrosine kinase inhibitor (TKI) sensitizing mutations (mEGFR) and had been treated with 1st ~ 2nd generation EGFR-TKI alone were enrolled for this study. De novo T790 M status was tested using the tissues at the initial diagnosis and positivity was defined as the ratio of T790 M/wild-type copies over 0.00294 by ddPCR. Seventy patients (68.6%) harbored the de novo T790 M. De novo T790 M was more frequently detected in cases with EGFR L858 R mutation than those with EGFR exon 19 deletion (E19d) mutations (P = 0.024). Forty-three patients underwent rebiopsy due to disease progression. The cases who experienced progression due to acquired T790 M were more likely to have E19d at initial diagnosis and the presence of de novo T790 M and the ratio of T790 M/wild-type copies did not relate to the emergence of acquired T790 M. On the other hand, the cases with a longer duration of disease-control by EGFR-TKI had higher change to get acquired T790 M mutation (P-value = 0.040). The presence of de novo T790 M has limitation in predicting disease progression by acquired T790 M, suggesting that identifying de novo T790 M through the ultrasensitive methods may not be necessary identifying patients who would be beneficial by 3rd-generation EGFR-TKI as the 1st line treatment.
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Affiliation(s)
- Sang Hoon Lee
- Department of Internal Medicine, Yonsei University College of Medicine , Seoul, Republic of Korea
| | - Eun Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine , Seoul, Republic of Korea
| | - Arum Kim
- Department of Internal Medicine, Yonsei University College of Medicine , Seoul, Republic of Korea
| | - Yoon Soo Chang
- Department of Internal Medicine, Yonsei University College of Medicine , Seoul, Republic of Korea
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Lei J, Huang Y, Zhong W, Xiao D, Zhou C. Early Monitoring Drug Resistant Mutation T790M with a Two-Dimensional Simultaneous Discrimination Nanopore Strategy. Anal Chem 2020; 92:8867-8873. [PMID: 32452671 DOI: 10.1021/acs.analchem.0c00575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
With the aim of detecting low frequency of drug resistant mutation T790M against wild-type sequences, we reported a two-dimensional signal analysis strategy by combining a three locked nucleic acids (LNAs)-modified probe (LP15-3t) and an α-HL nanopore. The specific hybridization of the LP15-3t probe with the T790M generated unique long two-level signals, including characteristic blocking current and characteristic dwell time. Due to the significant dwell time difference (114.2-fold) and the blocking current difference ranging from 81% to 96%, this two-dimensional signal analysis strategy can simultaneously distinguish T790M sequences with a sensitivity of 0.0001% against wild-type sequences. The LOD of T790M was 0.1 pM. This high discrimination capability would have great potential in the detection of rare mutation sequences and the early monitoring of clinical outcome of NSCLC patients with TKI drug resistance.
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Affiliation(s)
- Jing Lei
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Yuqin Huang
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Wenjun Zhong
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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Chatterjee T, Li Z, Khanna K, Montoya K, Tewari M, Walter NG, Johnson-Buck A. Ultraspecific analyte detection by direct kinetic fingerprinting of single molecules. Trends Analyt Chem 2020; 123:115764. [PMID: 32863484 PMCID: PMC7451408 DOI: 10.1016/j.trac.2019.115764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The detection and quantification of biomarkers have numerous applications in biological research and medicine. The most widely used methods to detect nucleic acids require amplification via the polymerase chain reaction (PCR). However, errors arising from the imperfect copying fidelity of DNA polymerases, limited specificity of primers, and heat-induced damage reduce the specificity of PCR-based methods, particularly for single-nucleotide variants. Furthermore, not all analytes can be amplified efficiently. While amplification-free methods avoid these pitfalls, the specificity of most such methods is strictly constrained by probe binding thermodynamics, which for example hampers detection of rare somatic mutations. In contrast, single-molecule recognition through equilibrium Poisson sampling (SiMREPS) provides ultraspecific detection with single-molecule and single-nucleotide sensitivity by monitoring the repetitive interactions of a fluorescent probe with surface-immobilized targets. In this review, we discuss SiMREPS in comparison with other analytical approaches, and describe its utility in quantifying a range of nucleic acids and other analytes.
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Affiliation(s)
- Tanmay Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zi Li
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kunal Khanna
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Karen Montoya
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Preoperative detection of KRAS G12D mutation in ctDNA is a powerful predictor for early recurrence of resectable PDAC patients. Br J Cancer 2020; 122:857-867. [PMID: 31969677 PMCID: PMC7078253 DOI: 10.1038/s41416-019-0704-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/30/2019] [Accepted: 12/10/2019] [Indexed: 02/07/2023] Open
Abstract
Background About 25–37% of resectable pancreatic ductal adenocarcinoma (PDAC) had a great chance of early recurrence after radical resection, which is mainly due to preoperative micrometastasis. We herein demonstrated the profiles of ctDNA in resectable PDAC and use of ctDNA to identify patients with potential micrometastasis. Methods A total of 113 and 44 resectable PDACs were enrolled in discovery and validation cohorts, separately. A panel containing 50 genes was used to screen ctDNA by an NGS-based assessment with high specificity. Results In the discovery cohort, the overall detection rate was 38.05% (43/113). Among positive ctDNA, KRAS mutation had the highest detection rate (23.01%, 26/113), while the others were <5%. Survival analysis showed that plasma KRAS mutations, especially KRAS G12D mutation, had significant association with OS and RFS of resectable PDAC. Plasma KRAS G12D mutation showed a strong correlation with early distant metastasis. In the validation cohort, survival analysis showed similar association between plasma KRAS G12D mutation and poor outcomes. Conclusions This study demonstrated that plasma KRAS mutations, especially KRAS G12D mutation, served as a useful predictive biomarker for prognosis of resectable PDAC. More importantly, due to high correlation with micrometastasis, preoperative detection of plasma KRAS G12D mutation helps in optimising surgical selection of resectable PDAC.
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Kurtz DM. Prognostication with circulating tumor DNA: is it ready for prime time? HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2019; 2019:47-52. [PMID: 31808836 PMCID: PMC6913479 DOI: 10.1182/hematology.2019000013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Emerging methods to detect tumor-derived DNA in the blood plasma of patients with lymphomas-so-called "circulating tumor DNA" (ctDNA)-have the potential to change the way in which lymphoma is diagnosed and managed in the clinic. The possible applications for ctDNA are numerous, including mutation genotyping, response monitoring, and detection of minimal residual disease during a time of radiographic remission. This article discusses the methodology for detecting ctDNA in aggressive B-cell lymphomas, including digital polymerase chain reaction, targeted sequencing of immunoglobulin receptors, and targeted next-generation sequencing. The advantages of each of these methods are also compared, with a focus on promising clinical applications. These include identification of molecular subtypes (eg, cell-of-origin and double-hit lymphomas) from pretreatment plasma, molecular response prediction after an initial course of therapy, and early detection of relapsing disease prior to clinical relapse. Finally, this article discusses the challenges in implementing ctDNA assays in the clinic today, including possible solutions to these challenges.
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Affiliation(s)
- David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
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19
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Liao Y, Chen Y, Kou X, Xiao Y, Ye J, Wu A. Diagnostic test accuracy of droplet digital PCR for the detection of EGFR mutation (T790M) in plasma: Systematic review and meta-analysis. Clin Chim Acta 2019; 503:190-196. [PMID: 31805270 DOI: 10.1016/j.cca.2019.11.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/04/2019] [Accepted: 11/16/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND T790M mutation was a primary lead cause in the acquired resistance to EGFR-TKIs confirmed in earlier studies. Since the shortcomings of tumor tissue detection are well known, the liquid biopsy is more appropriate to track T790M status. We assessed the accuracy and clinical significance of the droplet digital PCR (ddPCR) detection of T790M mutation in plasma. METHODS We retrieved PubMed, Embase, Cochrane, and Web of science with no limitation of language and publication year. Summary sensitivity and specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and diagnostic odds ratio of detection of EGFR T790M status were calculated from extracted data from included articles. The summary receiver operating curve (SROC), diagnostic odds ratio (DOR), and the area under the summary receiver operating curve (AUC) was used to assess the overall diagnostic accuracy. I2 and meta-regression were used to evaluate heterogeneity and the source of heterogeneity, respectively. RESULT We identified 15 studies in the total search of 1364 reports, including 427 paired tissue and plasma samples. The pooled sensitivity and the pooled specificity were 0.68 (95% CI 0.61-0.75) and 0.85 (95% CI 0.75-0.91) by the bivariate model, respectively. The AUC and the pooled DOR were 0.78 (95% CI 0.74-0.81) and 12 (95% CI 7-22), respectively. None of the cofactors could account for the heterogeneity. CONCLUSION The plasma analysis is of a promising performance to screen EGFR-T790M mutation status by ddPCR.
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Affiliation(s)
- Yingyin Liao
- KingMed School of Laboratory Medicine of Guangzhou Medical University, No. 195 Dongfengxi Road, Guangzhou, Guangdong, China
| | - Yuan Chen
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, No. 151 Yanjiangxi Road, Guangzhou, Guangdong, China
| | - Xiaoxia Kou
- KingMed School of Laboratory Medicine of Guangzhou Medical University, No. 195 Dongfengxi Road, Guangzhou, Guangdong, China
| | - Yi Xiao
- The Fifth Affiliated Hospital of Guangzhou Medical University, No. 621 Gangwan Road, Guangzhou, Guangdong, China
| | - Junkai Ye
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, No. 151 Yanjiangxi Road, Guangzhou, Guangdong, China
| | - Aiwu Wu
- KingMed School of Laboratory Medicine of Guangzhou Medical University, No. 195 Dongfengxi Road, Guangzhou, Guangdong, China.
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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: 46] [Impact Index Per Article: 9.2] [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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Multiplex ddPCR assay for screening copy number variations in BRCA1 gene. Breast Cancer Res Treat 2019; 178:545-555. [PMID: 31482362 DOI: 10.1007/s10549-019-05425-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/27/2019] [Indexed: 12/16/2022]
Abstract
PURPOSE Germinal and somatic rearrangements in BRCA1 gene play a significant role in carcinogenesis of breast and ovarian cancer. The present study is dedicated to the development of multiplex droplet digital PCR (ddPCR) assay for detecting large deletions and duplications in the BRCA1 gene. METHODS In-house tetraplex ddPCR assay for BRCA1 gene analysis was used for testing of DNA samples with BRCA1 status. RESULTS DNA specimens were purified from 24 individuals. The presence of BRCA1 rearrangements in samples was confirmed by a commercial MLPA-based kit. An amplitude-based multiplex ddPCR assay was developed: 8 multiplexes, each containing primers and probes to amplify 3 BRCA1 exons and 1 reference gene (ALB or RPP30). A novel assay demonstrated 100% concordance with the commercial MLPA-based kit, identifying 9 specimens with different deletions in BRCA1, 1 with duplication, and 14 with the wild-type BRCA1. CONCLUSIONS We have designed a simple, precise, and cost-effective assay for BRCA1 rearrangement testing, based on ddPCR. The developed assay is the first multiplex ddPCR-based test that provides results in accordance with MLPA and can be used for routine clinical screening.
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Dvorská D, Škovierová H, Braný D, Halašová E, Danková Z. Liquid Biopsy as a Tool for Differentiation of Leiomyomas and Sarcomas of Corpus Uteri. Int J Mol Sci 2019; 20:E3825. [PMID: 31387281 PMCID: PMC6695893 DOI: 10.3390/ijms20153825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 01/10/2023] Open
Abstract
Utilization of liquid biopsy in the management of cancerous diseases is becoming more attractive. This method can overcome typical limitations of tissue biopsies, especially invasiveness, no repeatability, and the inability to monitor responses to medication during treatment as well as condition during follow-up. Liquid biopsy also provides greater possibility of early prediction of cancer presence. Corpus uteri mesenchymal tumors are comprised of benign variants, which are mostly leiomyomas, but also a heterogenous group of malignant sarcomas. Pre-surgical differentiation between these tumors is very difficult and the final description of tumor characteristics usually requires excision and histological examination. The leiomyomas and malignant leiomyosarcomas are especially difficult to distinguish and can, therefore, be easily misdiagnosed. Because of the very aggressive character of sarcomas, liquid biopsy based on early diagnosis and differentiation of these tumors would be extremely helpful. Moreover, after excision of the tumor, liquid biopsy can contribute to an increased knowledge of sarcoma behavior at the molecular level, especially on the formation of metastases which is still not well understood. In this review, we summarize the most important knowledge of mesenchymal uterine tumors, the possibilities and benefits of liquid biopsy utilization, the types of molecules and cells that can be analyzed with this approach, and the possibility of their isolation and capture. Finally, we review the typical abnormalities of leiomyomas and sarcomas that can be searched and analyzed in liquid biopsy samples with the final aim to pre-surgically differentiate between benign and malignant mesenchymal tumors.
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Affiliation(s)
- Dana Dvorská
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Henrieta Škovierová
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dušan Braný
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia.
| | - Erika Halašová
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Danková
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
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The Role of Circulating Tumor DNA in Lung Cancer: Mutational Analysis, Diagnosis, and Surveillance Now and into the Future. Curr Treat Options Oncol 2019; 20:61. [DOI: 10.1007/s11864-019-0653-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Kaumaya M, Halmos B. Expanding the gamut of circulating tumor DNA applications. J Thorac Dis 2019; 10:S4151-S4155. [PMID: 30631579 DOI: 10.21037/jtd.2018.10.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Meghan Kaumaya
- Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Balazs Halmos
- Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
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Pandey A, Dutt S, Singh A, Kumar A, Singh S. Outcomes with liquid biopsy to determine the EGFR mutation status in poor performance status, biopsy-ineligible, advanced NSCLC patients. CANCER RESEARCH, STATISTICS, AND TREATMENT 2019. [DOI: 10.4103/crst.crst_60_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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26
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Microarray-based measurement of microRNA-449c-5p levels in hepatocellular carcinoma and bioinformatic analysis of potential signaling pathways. Pathol Res Pract 2018; 215:68-81. [PMID: 30389318 DOI: 10.1016/j.prp.2018.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/15/2018] [Accepted: 10/17/2018] [Indexed: 12/15/2022]
Abstract
The clinical role and potential molecular mechanisms of microRNA-449c-5p (miR-449c-5p) in hepatocellular carcinoma (HCC) tissues remains unclear. Combining multiple bioinformatic tools, we studied the miR-449c-5p expression levels in HCC tissues and explored possible target genes and related signaling pathways. First, miR-449c-5p expression data from microarrays provided by publicly available sources were mined and analyzed using various meta-analysis methods. Next, genes that were downregulated after miR-449c-5p mimic transfection into HCC cells were identified, and in silico methods were used to predict potential target genes. Several bioinformatic assessments were also performed to evaluate the possible signaling pathways of miR-449c-5p in HCC. Five microarrays were included in the current study, including GSE98269, GSE64632, GSE74618, GSE40744 and GSE57555. The standard mean difference was 0.44 (0.07-0.80), and the area under the curve was 0.68 (0.63-0.72), as assessed by meta-analyses, which consistently indicated the upregulation of miR-449c-5p in HCC tissues. A total of 2244 genes were downregulated after miR-449c-5p mimic transfection into an HCC cell line, while 5217 target genes were predicted by in silico methods. The overlap of these two gene pools led to a final group of 428 potential target genes of miR-449c-5p. These 428 potential target genes were primarily enriched in the homologous recombination pathway, which includes DNA Polymerase Delta 3 (POLD3). Data mining with Oncomine and the Human Protein Atlas showed a decreasing trend in POLD3 mRNA and protein levels in HCC tissue samples. This evidence suggests that miR-449c-5p could play an essential role in HCC through various pathways and that POLD3 could be a potential miR-449c-5p target. However, these in silico findings should be validated with further experiments.
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