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Ezzeldin N, El-Lebedy D, Hassan M, Shalaby AO, Hussein SAM, Gharib AM, Hamdy G, Mohammed AM, Ramadan A, Sobeih ME. Evaluating circulating cell-free DNA and DNA integrity index as biomarkers in non-small cell lung cancer. J Egypt Natl Canc Inst 2024; 36:21. [PMID: 38880832 DOI: 10.1186/s43046-024-00219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/23/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND Analysis of free DNA molecules shed from tumour cells in plasma of patients referred as circulating tumour DNA (ctDNA) with reference to physiological circulating cell-free DNA (cfDNA) is nowadays exploited as liquid biopsy and is considered a new emerging promising biomarker for diagnosis, selection of proper treatment, and prognosis of cancer. DNA integrity index (DII) is assessed by calculating the ratio between the concentration of long cfDNA strands released from tumour cells (ALU247) and the short strands released from normal cells (ALU115). The aim of the current study was to evaluate DII as a potential diagnostic and prognostic biomarker of NSCLC. METHODS Our study included 48 NSCLC patients diagnosed as primary NSCLC before starting treatment, 30 COPD patients diagnosed clinically, radiologically, and subjected to chest high-resolution computerized tomography, and 40 healthy controls. cfDNA concentration and DII were measured by quantitative real-time polymerase chain reaction (qPCR). RESULTS ALU115, ALU247, and DII were significantly higher in NSCLC compared to COPD patients (p < 0.0001) and controls (p < 0.0001) and in COPD patients compared to control subjects (p < 0.0001). DII positively correlated with the stage of tumour (p = 0.01), tumour metastasis (p = 0.004), and with adenocarcinoma compared to other histopathological types (p = 0.02). To evaluate clinical utility of DII in NSCLC, ROC curve analysis demonstrated an AUC of 0.91 at a cut-off value of 0.44 with total accuracy = 85.6%, sensitivity = 90%, specificity = 83%, PPV = 78.1%, and NPV = 92.1%. CONCLUSION cfDNA and DII represent a promising diagnostic and prognostic tool in NSCLC. This type of noninvasive liquid biopsy revealed its chance in the screening, early diagnosis, and monitoring of NSCLC.
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Affiliation(s)
- Nada Ezzeldin
- Chest Diseases, National Research Centre, Cairo, Egypt
| | - Dalia El-Lebedy
- Clinical Pathology department, Medical Research and Clinical Studies Institute, National Research Centre, Cairo, Egypt
| | - Mirhane Hassan
- Clinical Pathology department, Medical Research and Clinical Studies Institute, National Research Centre, Cairo, Egypt.
| | | | | | | | - Gehan Hamdy
- Chest Diseases, National Research Centre, Cairo, Egypt
| | - Asmaa Mahmoud Mohammed
- Department of Environmental and Occupational Medicine, National Research Centre, Cairo, Egypt
| | - Abeer Ramadan
- Molecular Genetics and Enzymology Department, Human Genetics and Genomics Research Institute, National Research Centre, Cairo, Egypt
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Sultana GNN, Akter F, Israfil SMH, Ray UC, Jahan RA, Ali MS, Din SA, Rahman S, Halim R, Alam MS. Quantitative analysis of serum cell-free DNA as a predictive and prognostic marker in breast cancer patients. Front Oncol 2023; 13:1171412. [PMID: 37427131 PMCID: PMC10324030 DOI: 10.3389/fonc.2023.1171412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/23/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction According to the GLOBOCAN (Global Cancer Observatory) 2020 report, 13,028 new cases of breast cancer (19%) were diagnosed in the United States, and 6,783 of them succumbed to the disease, making it the most common cancer among women. The clinical stage at the time of diagnosis is one of the most significant survival predictors in breast cancer. With delayed illness detection comes a lower survival rate. The prognosis of breast cancer may be predicted using circulating cell-free DNA (cfDNA), a non-invasive diagnosis technique. Objective This study aimed to determine the most sensitive and effective method for detecting changes in cfDNA levels and for using cfDNA as a diagnostic and prognostic marker of breast cancer. Methods The potential function of serum cfDNA levels as a marker for early breast cancer diagnosis was investigated using UV spectrophotometric, fluorometric, and real-time qPCR assays. Results This research suggests that the most successful way to measure the amount of cfDNA described decades ago could be used as a "liquid biopsy" to track cancer in real time. The RT-qPCR (ALU115) method produced the most statistically significant results (p=0.000). At the threshold concentration of 395.65 ng/ml of cfDNA, the ROC curve reflects the maximum AUC= 0.7607, with a sensitivity of 0.65 and specificity of 0.80. Conclusion For a preliminary assessment of total circulating cfDNA, a combination of all of the above techniques will be most efficacious. Based on our results, we conclude that the RT-qPCR technique combined with fluorometric measurement can identify a statistically significant difference in cfDNA levels between cohorts of breast cancer patients and healthy controls.
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Affiliation(s)
| | - Ferdowsi Akter
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - S. M. Hasan Israfil
- Department of Pharmaceutical Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Utpal Chandra Ray
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Rumana Akther Jahan
- Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Shawkat Ali
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Salim Al Din
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Shafiqur Rahman
- Institute of Statistical Research and Training, University of Dhaka, Dhaka, Bangladesh
| | - Rezaul Halim
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Mohammad Sahajadul Alam
- Department of Surgical Oncology, National Institute of Cancer Research and Hospital, Dhaka, Bangladesh
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Eastley N, Sommer A, Ottolini B, Neumann R, Luo JL, Hastings RK, McCulloch T, Esler CP, Shaw JA, Ashford RU, Royle NJ. The Circulating Nucleic Acid Characteristics of Non-Metastatic Soft Tissue Sarcoma Patients. Int J Mol Sci 2020; 21:ijms21124483. [PMID: 32599895 PMCID: PMC7349923 DOI: 10.3390/ijms21124483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Soft tissue sarcomas (STS) are rare, malignant tumours with a generally poor prognosis. Our aim was to explore the potential of cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) analysis to track non-metastatic STS patients undergoing attempted curative treatment. The analysed cohort (n = 29) contained multiple STS subtypes including myxofibrosarcomas, undifferentiated pleomorphic sarcomas, leiomyosarcomas, and dedifferentiated liposarcomas amongst others. Perioperative cfDNA levels trended towards being elevated in patients (p = 0.07), although did not correlate with tumour size, grade, recurrence or subtype, suggesting a limited diagnostic or prognostic role. To characterise ctDNA, an amplicon panel covering three genes commonly mutated in STSs was first trialled on serial plasma collected from nine patients throughout follow-up. This approach only identified ctDNA in 2.5% (one in 40) of the analysed samples. Next custom-designed droplet digital PCR assays and Ion AmpliSeq™ panels were developed to track single nucleotide variants identified in patients’ STSs by whole exome sequencing (1–6 per patient). These approaches identified ctDNA in 17% of patients. Although ctDNA was identified before radiologically detectable recurrence in two cases, the absence of demonstrable ctDNA in 83% of cases highlights the need for much work before circulating nucleic acids can become a useful means to track STS patients.
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Affiliation(s)
- Nicholas Eastley
- Trauma and Orthopaedics, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK;
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
- Correspondence:
| | - Aurore Sommer
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Barbara Ottolini
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Rita Neumann
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Jin-Li Luo
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Robert K. Hastings
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Thomas McCulloch
- Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK; (T.M.); (C.P.E.)
| | - Claire P. Esler
- Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK; (T.M.); (C.P.E.)
| | - Jacqueline A. Shaw
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Robert U. Ashford
- Trauma and Orthopaedics, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK;
- Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK; (T.M.); (C.P.E.)
| | - Nicola J. Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
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Thakur S, Tobey A, Daley B, Auh S, Walter M, Patel D, Nilubol N, Kebebew E, Patel A, Jensen K, Vasko V, Klubo-Gwiezdzinska J. Limited Utility of Circulating Cell-Free DNA Integrity as a Diagnostic Tool for Differentiating Between Malignant and Benign Thyroid Nodules With Indeterminate Cytology (Bethesda Category III). Front Oncol 2019; 9:905. [PMID: 31620364 PMCID: PMC6759775 DOI: 10.3389/fonc.2019.00905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/30/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Analysis of plasma circulating cell-free DNA integrity (cfDI) has emerged as a promising tool in the diagnosis of malignant vs. benign tumors. There is limited data on the role of cfDI in thyroid cancer. The goal of this study was to analyze cfDI as a biomarker of malignancy in patients with cytologically indeterminate thyroid nodules. Methods: The cfDI was measured in the plasma of patients with cytologically indeterminate thyroid nodules. All patients underwent plasma collection within 24–72 h before surgical treatment for thyroid nodules. Additionally, samples were collected from seven patients via the vein draining the thyroid and peripheral vein during surgery. Quantitative real-time PCR was performed on the isolated cell-free DNA using two different primer sets (115 and 247 bp) to amplify consensus ALU sequences. The cfDI was calculated as the ratio of ALU247 to ALU115. Results: All data are given as median [25th−75th percentile]. The study group consisted of 67 patients with 100 nodules, 80.6% (54/67) women, aged 43 [33-60] years. There was no difference in cfDI between 29 patients with benign nodules (0.49 [0.41–0.59]) and 38 patients with malignant lesions (0.45 [0.36–0.57], p = 0.19). There was no difference in cfDI in the vein draining the thyroid (0.47 [0.24–1.05]) and peripheral vein (0.48 [0.36–0.56], p = 0.44). In comparison to thyroid cancer patients, patients with benign nodules were characterized by significantly higher concentrations of ALU115 (1,064 [529–2,960] vs. 411 [27–1,049] ng/ml; p = 0.002) and ALU247 (548 [276–1,894] vs. 170 [17-540] ng/ml; p = 0.0005), most likely because benign tumors were larger (3, [1.8–4.1 cm]) than malignant lesions (0.7 [0.23–1.45], p < 0.0001). Women had significantly lower cfDI (0.45 [0.27–0.54]) than men (0.56 [0.44–0.8], p = 0.011). Conclusion: The cfDI measured in the vein draining the thyroid is similar to the cfDI measured in the antecubital vein, validating cfDI measurements by peripheral liquid biopsy. Analysis of cfDI needs to be stratified by patients gender. In contrast to its diagnostic utility in aggressive cancers, cfDI has limited utility as a biomarker of malignancy in cytologically indeterminate thyroid nodules.
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Affiliation(s)
- Shilpa Thakur
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew Tobey
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Brianna Daley
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sungyoung Auh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mary Walter
- Core for Clinical Laboratory Services, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Dhaval Patel
- Cancer Center - Froedtert Hospital, Milwaukee, WI, United States
| | - Naris Nilubol
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Electron Kebebew
- Division of General Surgery, Endocrine Oncology Research Laboratory, Department of Surgery, Stanford Medicine, School of Medicine, Stanford, CA, United States
| | - Aneeta Patel
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Kirk Jensen
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Vasyl Vasko
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Joanna Klubo-Gwiezdzinska
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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Temilola DO, Wium M, Coulidiati TH, Adeola HA, Carbone GM, Catapano CV, Zerbini LF. The Prospect and Challenges to the Flow of Liquid Biopsy in Africa. Cells 2019; 8:E862. [PMID: 31404988 PMCID: PMC6721679 DOI: 10.3390/cells8080862] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/30/2019] [Accepted: 08/03/2019] [Indexed: 12/24/2022] Open
Abstract
Liquid biopsy technologies have the potential to transform cancer patient management as it offers non-invasive diagnosis and real-time monitoring of disease progression and treatment responses. The use of liquid biopsy for non-invasive cancer diagnosis can have pivotal importance for the African continent where access to medical infrastructures is limited, as it eliminates the need for surgical biopsies. To apply liquid biopsy technologies in the African setting, the influence of environmental and population genetic factors must be known. In this review, we discuss the use of circulating tumor cells, cell-free nucleic acids, extracellular vesicles, protein, and other biomolecules in liquid biopsy technology for cancer management with special focus on African studies. We discussed the prospect, barriers, and other aspects that pose challenges to the use of liquid biopsy in the African continent.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
| | - Tangbadioa Herve Coulidiati
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Training and Research unit in Sciences and Technology, University Norbert Zongo, P.O. Box 376, Koudougou 376, Burkina Faso
| | - Henry Ademola Adeola
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town 7925, South Africa
| | - Giuseppina Maria Carbone
- Institute of Oncology Research, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Carlo Vittorio Catapano
- Institute of Oncology Research, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa.
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Rushton JG, Ertl R, Klein D, Tichy A, Nell B. Circulating cell-free DNA does not harbour a diagnostic benefit in cats with feline diffuse iris melanomas. J Feline Med Surg 2019; 21:124-132. [PMID: 29529957 PMCID: PMC10814613 DOI: 10.1177/1098612x18762017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Feline diffuse iris melanoma (FDIM) is the most common malignant primary intraocular tumour in cats, with reported metastases rates between 19% and 63%. Currently, the only available diagnostic tool for a tentative diagnosis is histopathological examination of the enucleated eye. Therefore, the veterinary ophthalmologist is often faced with the dilemma of whether to enucleate an oftentimes visual eye or to continue monitoring, with the risk of metastases developing. In the past, cell-free DNA (cfDNA) gained more attention in human medicine, especially in the field of oncology. Prior studies have shown the use of cfDNA as diagnostic or prognostic markers in canine and human cancer patients. Therefore, the aim of this study was to investigate cfDNA concentration and integrity in cats with FDIMs compared with cats with benign iris naevi and without ocular abnormalities. METHODS cfDNA from plasma of cats with iris melanoma (n = 34), iris naevus (n = 30) and without ocular abnormalities (n = 32) were extracted. Primer and probes for feline amyloid beta precursor protein ( APP) and beta actin ( ACTB) were designed for amplicons of various lengths and quantitative PCRs of extracted cfDNA were performed to measure cfDNA concentration and integrity of the plasma samples. Differences of cfDNA concentrations and integrity levels between the three groups (iris melanoma, iris naevi and controls) were analysed using the Mann-Whitney U-test. RESULTS cfDNA concentration and integrity analysis revealed no significant differences between the cats with iris melanoma, iris naevus or the control group ( P >0.01). Cats with metastases showed similar cfDNA concentration and integrity to cats without metastases. CONCLUSIONS AND RELEVANCE cfDNA concentration and integrity seem to be insufficient as a diagnostic or prognostic marker in cats with FDIMs.
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Affiliation(s)
- Jessica G Rushton
- Department for Companion Animals and Horses, Vetmeduni Vienna, Vienna, Austria
| | - Reinhard Ertl
- VetCore Facility for Research, Vetmeduni Vienna, Vienna, Austria
| | - Dieter Klein
- VetCore Facility for Research, Vetmeduni Vienna, Vienna, Austria
| | - Alexander Tichy
- Department of Biomedical Sciences, Vetmeduni Vienna, Vienna, Austria
| | - Barbara Nell
- Department for Companion Animals and Horses, Vetmeduni Vienna, Vienna, Austria
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7
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Soliman SES, Alhanafy AM, Habib MSED, Hagag M, Ibrahem RAL. Serum circulating cell free DNA as potential diagnostic and prognostic biomarker in non small cell lung cancer. Biochem Biophys Rep 2018; 15:45-51. [PMID: 29984326 PMCID: PMC6031238 DOI: 10.1016/j.bbrep.2018.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is leading cause of cancer related death and the survival rate for patients with NSCLC remain poor so early diagnosis of NSCLC represents the best opportunity for cure. Cell-free DNA (cf-DNA) is extracellular nucleic acids found in cell-free plasma/serum of humans, given the recent approval of a liquid biopsy in lung cancer, the use of circulating tumor DNA as a novel non-invasive diagnostic and prognostic biomarker is promising. Objectives Studying whether the concentrations of circulating Cell Free DNA in serum can be used as a diagnostic and prognostic biomarker for NSCLC patients. Method This study was carried out on 140 subjects included 60 patients with non small cell lung cancer,40 patients with Chronic Obstructive Pulmonary Disease (COPD) and 40 healthy controls. Quantitative analysis of serum circulating cf-DNA was done b y AlU-based quantitative real time PCR. Serum level of CEA was measured by ELISA. Results NSCLC patients demonstrated significantly higher values of each of ALU 215, ALU 247, and DNA integrity than both COPD patients and controls. On ROC curve analysis, the total accuracy of ALU 247, ALU 115, DNA integrity (92.1%, 83.6%, 56.4%) at cutoff points (325, 565 & 0.48) respectively. On combining both DNA integrity and CEA, improved sensitivity to 93.3% was noted. For NSCLC patients, ALU 115 & ALU 247 increased significantly with more advanced stage and highest level was noticed in metastatic patients. Regarding survival there was better overall survival among patients with low DNA integrity. Conclusion Serum cf-DNA concentrations and integrity index may be valuable tool in early diagnosis of NSCLC and prediction of prognosis of those patients.
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Affiliation(s)
- Shimaa El-Shafey Soliman
- Department of Medical Biochemistry &Molecular biology, Faculty of Medicine, Menoufia University, Shebin El-Kom, Menoufia Postal Code: 32511, Egypt
| | - Alshimaa Mahmoud Alhanafy
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Menoufia University, Egypt
| | - Mona Salah El-Din Habib
- Department of Medical Biochemistry &Molecular biology, Faculty of Medicine, Menoufia University, Shebin El-Kom, Menoufia Postal Code: 32511, Egypt
| | - Mohamed Hagag
- Department of Cardiothoracic Surgery, Faculty of Medicine, Menoufia University, Egypt
| | - Reda Abdel Latif Ibrahem
- Department of Public Health and Community Medicine, Faculty of Medicine, Menoufia University, Egypt
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Cabanero M, Tsao MS. Circulating tumour DNA in EGFR-mutant non-small-cell lung cancer. ACTA ACUST UNITED AC 2018; 25:S38-S44. [PMID: 29910646 DOI: 10.3747/co.25.3761] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The advent of targeted therapy in non-small-cell lung cancer (nsclc) has made the routine molecular diagnosis of EGFR mutations crucial for optimal patient management. Obtaining tumour tissue for biomarker testing, especially in the setting of re-biopsy, can present many challenges. A potential alternative source of tumour dna is circulating cell-free tumour-derived dna (ctdna). Although ctdna is present in low quantities in plasma, the convenience of sample acquisition and the increasing reliability of detection methods make this approach a promising one. The various performance characteristics of both digital and nondigital platforms are still variable, and a standardized approach is needed that will make those platforms reliable clinical tools for the detection of EGFR sensitizing mutations and resistance mutations, including the T790M resistance mutation. Information derived from ctdna can be used to assess tumour burden, to identify genomic-based resistance mechanisms, and to track dynamic changes during therapy.
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Affiliation(s)
- M Cabanero
- Princess Margaret Cancer Centre, University Health Network, and.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
| | - M S Tsao
- Princess Margaret Cancer Centre, University Health Network, and.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
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Kostyuk SV, Porokhovnik LN, Ershova ES, Malinovskaya EM, Konkova MS, Kameneva LV, Dolgikh OA, Veiko VP, Pisarev VM, Martynov AV, Sergeeva VA, Kaliyanov AA, Filev AD, Chudakova JM, Abramova MS, Kutsev SI, Izhevskaya VL, Veiko NN. Changes of KEAP1/NRF2 and IKB/NF- κB Expression Levels Induced by Cell-Free DNA in Different Cell Types. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1052413. [PMID: 29743966 PMCID: PMC5883976 DOI: 10.1155/2018/1052413] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/31/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022]
Abstract
Cell-free DNA (cfDNA) is a circulating DNA of nuclear and mitochondrial origin mainly derived from dying cells. Recent studies have shown that cfDNA is a stress signaling DAMP (damage-associated molecular pattern) molecule. We report here that the expression profiles of cfDNA-induced factors NRF2 and NF-κB are distinct depending on the target cell's type and the GC-content and oxidation rate of the cfDNA. Stem cells (MSC) have shown higher expression of NRF2 without inflammation in response to cfDNA. In contrast, inflammatory response launched by NF-κB was dominant in differentiated cells HUVEC, MCF7, and fibroblasts, with a possibility of transition to massive apoptosis. In each cell type examined, the response for oxidized cfDNA was more acute with higher peak intensity and faster resolution than that for nonoxidized cfDNA. GC-rich nonoxidized cfDNA evoked a weaker and prolonged response with proinflammatory component (NF-κB) as predominant. The exploration of apoptosis rates after adding cfDNA showed that cfDNA with moderately increased GC-content and lightly oxidized DNA promoted cell survival in a hormetic manner. Novel potential therapeutic approaches are proposed, which depend on the current cfDNA content: either preconditioning with low doses of cfDNA before a planned adverse impact or eliminating (binding, etc.) cfDNA when its content has already become high.
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Affiliation(s)
| | - Lev N. Porokhovnik
- Research Centre for Medical Genetics (RCMG), Moscow 115478, Russia
- V. A. Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow 107031, Russia
| | - Elizaveta S. Ershova
- Research Centre for Medical Genetics (RCMG), Moscow 115478, Russia
- V. A. Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow 107031, Russia
| | | | | | | | - Olga A. Dolgikh
- Research Centre for Medical Genetics (RCMG), Moscow 115478, Russia
| | - Vladimir P. Veiko
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia
| | - Vladimir M. Pisarev
- V. A. Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow 107031, Russia
| | | | | | | | - Anton D. Filev
- Research Centre for Medical Genetics (RCMG), Moscow 115478, Russia
- V. A. Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow 107031, Russia
| | | | - Margarita S. Abramova
- Research Centre for Medical Genetics (RCMG), Moscow 115478, Russia
- N. I. Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Serguey I. Kutsev
- Research Centre for Medical Genetics (RCMG), Moscow 115478, Russia
- N. I. Pirogov Russian National Research Medical University, Moscow 117997, Russia
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Wang H, Liu Z, Xie J, Wang Z, Zhou X, Fang Y, Pan H, Han W. Quantitation of cell-free DNA in blood is a potential screening and diagnostic maker of breast cancer: a meta-analysis. Oncotarget 2017; 8:102336-102345. [PMID: 29254249 PMCID: PMC5731959 DOI: 10.18632/oncotarget.21827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/22/2017] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION Increased cell-free DNA (cfDNA) levels in circulating blood have been associated with higher possibility of breast cancer, however, researchers have not reached an agreement on its analysis. MATERIALS AND METHODS We conducted a meta-analysis of 12 retrospective studies to clarify the value of cfDNA quantification in screening and diagnosis of breast cancer. PubMed, EMBASE, Web of Science and Cochrane library were searched from January, 2000 to October, 2016. Pooled analyses were estimated using a random effects model. RESULTS In total, 1003 primary breast cancer patients, 283 cases with benign breast disease and 575 healthy individuals were included. Pooled diagnostic odds ratio (DOR) was 27.63 (95% confidence interval [CI]: 10.96~69.61, I2 = 86.2%, P < 0.001) in discriminating between breast cancer and healthy controls; the area under the summary receiver operating characteristic (SROC) curve measured 0.91 (95% CI: 0.17~1.00). Analysis of available data in distinguishing breast cancer and benign breast disease showed a pooled DOR of 35.30 (95% CI: 7.58~164.39, I2 = 79.9%, P = 0.002) with an area under SROC of 0.91 (95% CI: 0.89~0.93). Ethnic group distribution based geographical factors suggested by meta-regression and subgroup analyses explained most of the heterogeneity. CONCLUSIONS Quantification of cfDNA is a promising test in screening and diagnostic of breast cancer, but population-based standardization of test methods require completion prior to clinical use.
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Affiliation(s)
- Huadi Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Liu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiansheng Xie
- Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhanggui Wang
- Department of Radiotherapy, The Second People's Hospital of Anhui Province, Hefei, Anhui, China
| | - Xiaoyun Zhou
- Department of Medical Oncology, Xiasha Campus, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yong Fang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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11
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Cree IA, Uttley L, Buckley Woods H, Kikuchi H, Reiman A, Harnan S, Whiteman BL, Philips ST, Messenger M, Cox A, Teare D, Sheils O, Shaw J. The evidence base for circulating tumour DNA blood-based biomarkers for the early detection of cancer: a systematic mapping review. BMC Cancer 2017; 17:697. [PMID: 29061138 PMCID: PMC5654013 DOI: 10.1186/s12885-017-3693-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/18/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The presence of circulating cell-free DNA from tumours in blood (ctDNA) is of major importance to those interested in early cancer detection, as well as to those wishing to monitor tumour progression or diagnose the presence of activating mutations to guide treatment. In 2014, the UK Early Cancer Detection Consortium undertook a systematic mapping review of the literature to identify blood-based biomarkers with potential for the development of a non-invasive blood test for cancer screening, and which identified this as a major area of interest. This review builds on the mapping review to expand the ctDNA dataset to examine the best options for the detection of multiple cancer types. METHODS The original mapping review was based on comprehensive searches of the electronic databases Medline, Embase, CINAHL, the Cochrane library, and Biosis to obtain relevant literature on blood-based biomarkers for cancer detection in humans (PROSPERO no. CRD42014010827). The abstracts for each paper were reviewed to determine whether validation data were reported, and then examined in full. Publications concentrating on monitoring of disease burden or mutations were excluded. RESULTS The search identified 94 ctDNA studies meeting the criteria for review. All but 5 studies examined one cancer type, with breast, colorectal and lung cancers representing 60% of studies. The size and design of the studies varied widely. Controls were included in 77% of publications. The largest study included 640 patients, but the median study size was 65 cases and 35 controls, and the bulk of studies (71%) included less than 100 patients. Studies either estimated cfDNA levels non-specifically or tested for cancer-specific mutations or methylation changes (the majority using PCR-based methods). CONCLUSION We have systematically reviewed ctDNA blood biomarkers for the early detection of cancer. Pre-analytical, analytical, and post-analytical considerations were identified which need to be addressed before such biomarkers enter clinical practice. The value of small studies with no comparison between methods, or even the inclusion of controls is highly questionable, and larger validation studies will be required before such methods can be considered for early cancer detection.
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Affiliation(s)
- Ian A. Cree
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
| | - Lesley Uttley
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Helen Buckley Woods
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Hugh Kikuchi
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
| | - Anne Reiman
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
| | - Susan Harnan
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Becky L. Whiteman
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
| | | | - Michael Messenger
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
| | - Angela Cox
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
| | - Dawn Teare
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Orla Sheils
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
| | - Jacqui Shaw
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
| | - For the UK Early Cancer Detection Consortium
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
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12
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Kamel AM, Teama S, Fawzy A, El Deftar M. Plasma DNA integrity index as a potential molecular diagnostic marker for breast cancer. Tumour Biol 2016; 37:7565-72. [PMID: 26684805 DOI: 10.1007/s13277-015-4624-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/10/2015] [Indexed: 12/11/2022] Open
Abstract
Plasma DNA integrity index is increased in various malignancies including breast cancer, the most common cancer in women worldwide; early detection is crucial for successful treatment. Current screening methods fail to detect many cases of breast cancer at an early stage. In this study, we evaluated the level of plasma DNA integrity index in 260 females (95 with breast cancer, 95 with benign breast lesions, and 70 healthy controls) to verify its potential value in discriminating malignant from benign breast lesions. The criteria of the American Joint Committee on Cancer were used for staging of breast cancer patients. DNA integrity index was measured by real-time PCR. DNA integrity index was significantly higher in breast cancer than in benign breast patients and healthy subjects (P = <0.001). DNA integrity index is correlated with TNM stage. Given 100 % specificity, the highest sensitivity achieved in detecting cancer group was 85.3 % at 0.55 DNA integrity index cutoff. In conclusion, the plasma DNA integrity index may be a promising molecular diagnostic marker of malignancy in breast lesions.
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MESH Headings
- Adult
- Aged
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Breast/metabolism
- Breast/pathology
- Breast Neoplasms/blood
- Breast Neoplasms/diagnosis
- Breast Neoplasms/genetics
- Carcinoma, Ductal, Breast/blood
- Carcinoma, Ductal, Breast/diagnosis
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Lobular/blood
- Carcinoma, Lobular/diagnosis
- Carcinoma, Lobular/genetics
- Case-Control Studies
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Female
- Follow-Up Studies
- Humans
- Middle Aged
- Neoplasm Grading
- Neoplasm Staging
- Plasma/chemistry
- Prognosis
- ROC Curve
- Real-Time Polymerase Chain Reaction
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Affiliation(s)
- Azza M Kamel
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Fom El-Khalig Square, Kasr El-Aini Street, 11796, Cairo, Egypt.
| | - Salwa Teama
- Medical Research Center, Molecular Biology Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Amal Fawzy
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Fom El-Khalig Square, Kasr El-Aini Street, 11796, Cairo, Egypt
| | - Mervat El Deftar
- Department of Pathology, Tissue culture & Cytogenetic unit, National Cancer Institute, Cairo University, Cairo, Egypt
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