1
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Ren S, Yu C, Huang Q. Diagnostic value of combined detection of plasma cfDNA concentration and integrity in NSCLC. Lung Cancer Manag 2024; 13:LMT64. [PMID: 38812772 PMCID: PMC11131340 DOI: 10.2217/lmt-2023-0009] [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: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 05/31/2024] Open
Abstract
Aim: To evaluate the value of combined detection of plasma cfDNA concentration and integrity in the early diagnosis of NSCLC. Methods: Real-time fluorescence quantitative PCR was used to determine the concentration and integrity of plasma cfDNA in 71 NSCLC patients and 53 healthy people. Results: Combined detection of plasma cfDNA concentration and integrity had higher diagnostic power in differentiating NSCLC patients with stage I/II from healthy people than detection of plasma cfDNA concentration alone or integrity alone. The AUC, sensitivity and specificity of the combined detection of plasma cfDNA concentration and integrity were 0.781, 0.62 and 0.85. Conclusion: Combined detection of plasma cfDNA concentration and integrity could improve the diagnostic value in NSCLC detection.
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Affiliation(s)
- Sai Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
- Department of Laboratory Medicine, People's Hospital of Chongqing Liang Jiang New Area, Chongqing, 401121, PR China
| | - Chunli Yu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
- Department of Laboratory Medicine, Chengdu Xinhua Hospital, Chengdu, 610055, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
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2
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He G, Wang W, Zhou Y, Zhao G, Liao J. Ampholytic ion-exchange magnetic beads: a promising tool for selecting short fragments in circulating cell-free DNA analysis. Front Oncol 2024; 14:1397680. [PMID: 38779084 PMCID: PMC11109406 DOI: 10.3389/fonc.2024.1397680] [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: 03/08/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Objective For liquid biopsy of cancer, the extraction of circulating cell-free DNA (cfDNA) from plasma is required. We evaluated the efficacy of use of magnetic submicron particles coated with abundant small zwitterions (MSP-ZEWBs) for extracting short fragments of cfDNA. Methods We developed and optimized an MSP-ZEWB-based cfDNA extraction method using ampholytic ion-exchange materials and compared its results with those using a control kit. We measured the cfDNA concentration by quantitative polymerase-chain-reaction and using the Qubit method and analyzed cfDNA fragmentation patterns using a bioanalyzer. Results The fragment size of cfDNA isolated from glycine hydrochloric acid at a pH of 2.2 exhibited a better alignment with the DNA marker. The highest DNA intensity was observed at the final concentration of 0.8% polyethylene glycol 8000. The intensity of cfDNA decreased significantly when isolated from plasma with DNA marker using MSP-ZEWBs with an adsorption buffer containing guanidine hydrochloride or isothiocyanoguanidine. All fragments were successfully extracted using MSP-ZEWBs from both plasma and phosphate-buffered saline. Notably, the intensity of short cfDNA fragments isolated using MSP-ZEWBs remained consistent for recovery of long DNA fragments. indicating a potential selective of small fragments. Conclusion The extraction of plasma cfDNA with MSP-ZEWBs requires no protein denaturation, shows resistance to cells remaining in plasma, and demonstrates higher overall efficiency and better reproducibility than other extraction methods. Use of MSP-ZEWBs may greatly enhance liquid biopsy of cancers through the analysis of plasma cfDNA in clinical practice.
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Affiliation(s)
- Gan He
- Gastrointestinal Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Weixuan Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Yongxia Zhou
- Department of Radiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Center Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Guowei Zhao
- Gastrointestinal Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Liao
- Center Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Geriatric Disease Clinical Research Center, Chongqing, China
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Shan MA, Ishtiaq W, Kanwal S, Khan MU, Iftikhar A, Khan S. Cell-free DNA as a potential diagnostic biomarker in academic stress: A case-control study in young adults. Saudi J Biol Sci 2024; 31:103933. [PMID: 38304540 PMCID: PMC10831250 DOI: 10.1016/j.sjbs.2024.103933] [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: 07/26/2023] [Revised: 01/01/2024] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Background Stress is a pervasive issue in modern life, affecting both physical and mental health. Identifying biomarkers like cell-free DNA (cfDNA) could provide insights into stress response and help detect individuals at risk for stress-related disorders. Objective The aim of this study is to investigate the potential use of cfDNA as a diagnostic biomarker in individuals experiencing stress. Methodology A case-control analysis was conducted using convenient sampling on university participants (N = 285 cases, N = 500 controls) aged 18-24. The study assessed haematological and lipid profile parameters using the Sysmex XP-300TM automated analyzer and an automated biochemistry analyzer, and cfDNA was extracted using a standardized in house developed Phenol-Chloroform protocol and estimated using Agarose Gel Electrophoresis and Nanodrop. Statistical analysis was performed using SPSS ver. 21.0. Results The results indicated a significant difference between stressed individuals and healthy controls in demographic, haematological and biochemical parameters. Specifically, stressed cases had significantly higher levels of cholesterol, LDL cholesterol, triglycerides, glucose, VLDL cholesterol, and lower levels of HDL compared to healthy controls. Stressed cases also showed significantly elevated levels of circulating cfDNA relative to healthy controls. Conclusion These findings suggest that cfDNA may have potential as a diagnostic biomarker for stress.
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Affiliation(s)
| | - Warda Ishtiaq
- Center for Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shamsa Kanwal
- Muhammad Ali Jinnah University Karachi, Karachi, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Ayesha Iftikhar
- Lahore Business School, The University of Lahore, Lahore, Pakistan
| | - Samiullah Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
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Canu GL, Cappellacci F, Abdallah A, Elzahaby I, Figueroa-Bohorquez D, Lori E, Miller JA, Pavia SZ, Pinillos P, Pongtippan A, Saleh SS, Sorrenti S, Sriphrapradang C, Calò PG, Medas F. Surgical Management of Indeterminate Thyroid Nodules across Different World Regions: Results from a Retrospective Multicentric (the MAIN-NODE) Study. Cancers (Basel) 2023; 15:3996. [PMID: 37568811 PMCID: PMC10416924 DOI: 10.3390/cancers15153996] [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: 06/07/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Indeterminate thyroid nodules (ITNs) are characterized by an expected malignancy ranging from 5% to 30%, with most patients undergoing a diagnostic, rather than therapeutic, operation. The aim of our study was to compare the approach to ITNs across different regions of the world. In this retrospective, multicentric, international study, according to the WHO classification, we identified the South East Asian Region (SEAR), the Americas Region (AMR), the Eastern Mediterranean Region (EMR), the Europe Region (EUR), and the Western Pacific Region (WPR). One high-volume thyroid centre was included for each region. Demographic, preoperative, and pathologic data were compared among the different regions. Overall, 5737 patients from five high-volume thyroid centres were included in this study. We found that the proportion of ITNs over the global activity for thyroid disease was higher in the EUR (37.6%) than in the other regions (21.1-23.6%). In the EMR, the patients were significantly younger (with a mean of 43.1 years) than in the other regions (range, 48.8-57.4 years). The proportion of lobectomy was significantly higher in the WPR, where 83.2% (114/137) of patients received this treatment, than in the other regions, where lobectomies were performed in 44.1-58.1% of patients. The pathological diagnosis of malignancy was significantly higher in the SEAR centre, being over 60%, than in centres of the other regions, where it ranged from 26.3% to 41.3%. The occurrence of lymph node metastases was higher in the WPR (27.8%), AMR (26.9%), and EMR (20%) centres than in the EUR and SEAR centres, where it was lower than 10%. In summary, we found in our study different approaches and outcomes in the diagnosis and treatment of ITNs among countries. Overall, almost 60% of patients with ITNs who underwent surgery actually presented a benign disease, potentially undergoing an unnecessary operation.
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Affiliation(s)
- Gian Luigi Canu
- Department of Surgical Sciences, University of Cagliari, 09124 Cagliari, Italy; (G.L.C.); (F.C.); (P.G.C.)
| | - Federico Cappellacci
- Department of Surgical Sciences, University of Cagliari, 09124 Cagliari, Italy; (G.L.C.); (F.C.); (P.G.C.)
| | - Ahmed Abdallah
- Surgical Oncology, Mansoura University, Mansoura 35516, Egypt; (A.A.); (I.E.); (S.S.S.)
| | - Islam Elzahaby
- Surgical Oncology, Mansoura University, Mansoura 35516, Egypt; (A.A.); (I.E.); (S.S.S.)
| | - David Figueroa-Bohorquez
- Head and Neck Surgery, Hospital Universitario Nacional de Colombia, Bogotá 250247, Colombia; (D.F.-B.); (S.Z.P.); (P.P.)
| | - Eleonora Lori
- Department of Surgery, “Sapienza” University of Rome, 00185 Rome, Italy; (E.L.); (S.S.)
| | - Julie A. Miller
- The Royal Melbourne Hospital and Epworth Hospital, Melbourne, VIC 3121, Australia;
| | - Sergio Zúñiga Pavia
- Head and Neck Surgery, Hospital Universitario Nacional de Colombia, Bogotá 250247, Colombia; (D.F.-B.); (S.Z.P.); (P.P.)
| | - Pilar Pinillos
- Head and Neck Surgery, Hospital Universitario Nacional de Colombia, Bogotá 250247, Colombia; (D.F.-B.); (S.Z.P.); (P.P.)
| | - Atcharaporn Pongtippan
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Saleh Saleh Saleh
- Surgical Oncology, Mansoura University, Mansoura 35516, Egypt; (A.A.); (I.E.); (S.S.S.)
| | - Salvatore Sorrenti
- Department of Surgery, “Sapienza” University of Rome, 00185 Rome, Italy; (E.L.); (S.S.)
| | - Chutintorn Sriphrapradang
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Pietro Giorgio Calò
- Department of Surgical Sciences, University of Cagliari, 09124 Cagliari, Italy; (G.L.C.); (F.C.); (P.G.C.)
| | - Fabio Medas
- Department of Surgical Sciences, University of Cagliari, 09124 Cagliari, Italy; (G.L.C.); (F.C.); (P.G.C.)
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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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Armakolas A, Kotsari M, Koskinas J. Liquid Biopsies, Novel Approaches and Future Directions. Cancers (Basel) 2023; 15:1579. [PMID: 36900369 PMCID: PMC10000663 DOI: 10.3390/cancers15051579] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Cancer is among the leading causes of death worldwide. Early diagnosis and prognosis are vital to improve patients' outcomes. The gold standard of tumor characterization leading to tumor diagnosis and prognosis is tissue biopsy. Amongst the constraints of tissue biopsy collection is the sampling frequency and the incomplete representation of the entire tumor bulk. Liquid biopsy approaches, including the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs), as well as certain protein signatures that are released in the circulation from primary tumors and their metastatic sites, present a promising and more potent candidate for patient diagnosis and follow up monitoring. The minimally invasive nature of liquid biopsies, allowing frequent collection, can be used in the monitoring of therapy response in real time, allowing the development of novel approaches in the therapeutic management of cancer patients. In this review we will describe recent advances in the field of liquid biopsy markers focusing on their advantages and disadvantages.
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Affiliation(s)
- Athanasios Armakolas
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Maria Kotsari
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - John Koskinas
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
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Hou F, Sun XD, Deng ZY. Diagnostic value of cell-free DNA in thyroid cancer: A systematic review and meta-analysis. Medicine (Baltimore) 2023; 102:e32928. [PMID: 36800605 PMCID: PMC9935987 DOI: 10.1097/md.0000000000032928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
OBJECTIVE An increasing number of studies have shown the potential diagnostic value of cell-free DNA (cfDNA) as a new biomarker in the management of thyroid cancer (TC); however, the accuracy of research results is inconsistent. This meta-analysis is the first to synthesize published results and evaluate the application value of circulating cfDNA in the diagnosis of TC. METHODS A search strategy was developed according to PICO (P: Patient; I: Intervention; C: Comparison; O: Outcome) principles. We searched 5 databases until October 2022. Original studies that examined cfDNA for the diagnosis of TC and used pathology as the gold standard were included in this meta-analysis. A random-effects model was used to pool the data extracted from individual studies, including the number of patients and the numbers of true positives, false positives, true negatives, and false negatives. RESULTS A total of 622 patients with TC, 547 patients with benign thyroid nodules, and 98 healthy individuals were included in 20 studies reported in 14 articles. The types of cfDNA included in the research include specific mutations of cfDNA, methylation of cfDNA, the content of cfDNA, and cfDNA index. After rigorous statistical analysis, the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the summary receiver operating characteristic curve were 0.76 (95% confidence interval [CI] 0.62-0.85), 0.87 (95% CI 0.78-0.93), 5.08 (95% CI 3.3-10.3), 0.28 (95% CI 0.17-0.46), 21 (95% CI 9-49), and 0.89 (95% CI 0.86-0.91), respectively. The meta-regression results showed that the number of cfDNAs, cfDNA methylation status, and sample size were the sources of heterogeneity in the specificity of the study. A subgroup analysis showed that the quantitative analysis group (cfDNA level) had a higher diagnostic accuracy than that of the qualitative analysis group (cfDNA methylation, mutation, or integrity index), with a sensitivity of 0.84, specificity of 0.89, and area under the curve of 0.91. CONCLUSIONS The results of this meta-analysis suggest that cfDNA has value as an adjunct for the diagnosis of TC. Quantitative detection of cfDNA can achieve relatively high diagnostic accuracy. However, due to heterogeneity, the test results based on cfDNA for TC should be interpreted with caution.
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Affiliation(s)
- Fei Hou
- Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
| | - Xiao-Dan Sun
- Publicity Department, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
| | - Zhi-Yong Deng
- Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
- * Correspondence: Zhi-Yong Deng, Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming 650118, China (e-mail: )
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8
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Dutta S, Tarafdar S, Mukhopadhyay P, Bhattacharyya NP, Ghosh S. Detection of driver mutations in plasma cell-free nucleic acids in differentiated thyroid neoplasm. Eur J Endocrinol 2023; 188:6976051. [PMID: 36744987 DOI: 10.1093/ejendo/lvac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/15/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
IMPORTANCE This proof-of-concept paper demonstrates that driver mutations can be detected in plasma in differentiated thyroid tumors, and we were able to detect mutations in upto 80% malignant thyroid nodules. Additionally, cancer subtypes could also be predicted using a 8-gene panel. In almost 90% follicular adenoma, rat sarcoma virus (RAS) mutations were detectable. There was a strong agreement between driver mutations found in plasma samples, FNAC materials, and histopathology samples. This has potential as a noninvasive, preoperative diagnostic tool (particularly of clinical importance in indeterminate nodules) and may help in detection of residual tumor after surgery. Future research is warranted to test the role of this tool to detect tumor recurrence. OBJECTIVE Ultrasonographic (USG) evaluation and fine-needle aspiration (FNA) are cornerstone for evaluation of thyroid neoplasm. Molecular technique including detection of driver mutation from FNA cytology (FNAC) material is an established modality. In this study, we explored the feasibility of using plasma cell-free nucleic acids to identify known driver mutations in differentiated thyroid neoplasm. DESIGN Patients presenting with thyroid nodules underwent USG with Thyroid Image Reporting and Data Systems scoring and FNAC (Bethesda classification). All patients in Bethesda 3, 4, 5, 6 underwent surgery and histopathological confirmation. Patients in Bethesda 2 (cosmetic concerns, compressive symptoms) underwent surgery, and rest were presumed benign on the basis of USG, FNAC features, and clinical followup.). SETTING Endocrinology clinic. PARTICIPANTS Subjects with thyroid nodule. INTERVENTION(S) OR EXPOSURE(S) None. MAIN OUTCOME(S) AND MEASURE(S) Plasma sample, FNA, and histopathology material were evaluated for driver mutations (8-gene panel comprising BRAF-V600E, RET/PTC3, RET/PTC1, TERT promoter, HRAS, NRAS, KRAS, and PAX8-PPARG). RESULTS A total of 223 subjects were recruited; of these 154 were benign and 69 had differentiated thyroid cancer. We were able to detect driver mutation from plasma in 55 subjects (79.71%) of all malignant patients, and 11 patients in benign category had RAS mutation (follicular adenoma). Rest of the benign nodules did not have any detectable driver mutations. CONCLUSIONS AND RELEVANCE Plasma might be a viable noninvasive alternative source for detection of driver mutations (8-gene panel) in subjects with differentiated thyroid tumors and may have significant clinical utility.
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Affiliation(s)
- Susmita Dutta
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Soham Tarafdar
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Pradip Mukhopadhyay
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Nitai P Bhattacharyya
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Sujoy Ghosh
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
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Marotta V, Cennamo M, La Civita E, Vitale M, Terracciano D. Cell-Free DNA Analysis within the Challenges of Thyroid Cancer Management. Cancers (Basel) 2022; 14:cancers14215370. [PMID: 36358788 PMCID: PMC9654679 DOI: 10.3390/cancers14215370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary Liquid biopsy is a minimally invasive method that emerged as a new promising tool for improving diagnosis, risk stratification, follow-up, and treatment of cancer patients. To date, the majority of the research in the area of liquid biopsy has focused on plasma-based cell-free DNA as a potential surrogate for tumor DNA obtained from a tissue biopsy. In the last decades, breakthrough advancements have been performed in the knowledge of thyroid cancer genetics, and the role of molecular characterization in clinical decision-making is continuously rising, from diagnosis completion to the personalization of treatment approach. Hence, it is expectable for cell-free DNA to be applicable in thyroid cancer management. This review aims to investigate the cell-free DNA utility for thyroid cancer patients’ care. Abstract Thyroid cancer is the most frequent endocrine malignancy with an increasing incidence trend during the past forty years and a concomitant rise in cancer-related mortality. The circulating cell-free DNA (cfDNA) analysis is a patient’s friendly and repeatable procedure allowing to obtain surrogate information about the genetics and epigenetics of the tumor. The aim of the present review was to address the suitability of cfDNA testing in different forms of thyroid cancer, and the potential clinical applications, as referred to the clinical weaknesses. Despite being limited by the absence of standardization and by reproducibility and validity issues, cfDNA assessment has great potential for the improvement of thyroid cancer management. cfDNA may support the pre-surgical definition of thyroid nodules by complementing invasive thyroid fine needle aspiration cytology. In addition, it may empower risk stratification and could be used as a biomarker for monitoring the post-surgical disease status, both during active surveillance and in the case of anti-tumor treatment.
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Affiliation(s)
- Vincenzo Marotta
- UOC Clinica Endocrinologica e Diabetologica, AOU San Giovanni di Dio e Ruggi d’Aragona, 84131 Salerno, Italy
- Correspondence: ; Tel.: +39-333-852-1005
| | - Michele Cennamo
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
| | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
| | - Mario Vitale
- Dipartimento di Medicina, Chirurgia e Odontoiatria, Università di Salerno, 84081 Baronissi, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
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Nkosi D, Miller CA, Jajosky AN, Oltvai ZN. Incidental discovery of acute myeloid leukemia during liquid biopsy of a lung cancer patient. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006201. [PMID: 35732498 PMCID: PMC9235846 DOI: 10.1101/mcs.a006201] [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: 02/08/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Liquid biopsy is considered an alternative to standard next-generation sequencing (NGS) of solid tumor samples when biopsy tissue is inadequate for testing or when testing of a peripheral blood sample is preferred. A common assumption of liquid biopsies is that the NGS data obtained on circulating cell-free DNA is a high-fidelity reflection of what would be found by solid tumor testing. Here, we describe a case that challenges this widely held assumption. A patient diagnosed with lung carcinoma showed pathogenic IDH1 and TP53 mutations by liquid biopsy NGS at an outside laboratory. Subsequent in-house NGS of a metastatic lymph node fine-needle aspiration (FNA) sample revealed two pathogenic EGFR mutations. Morphologic and immunophenotypic assessment of the patient's blood sample identified acute myeloid leukemia, with in-house NGS confirming and identifying pathogenic IDH1, TP53, and BCOR mutations, respectively. This case, together with a few similar reports, demonstrates that caution is needed when interpreting liquid biopsy NGS results, especially if they are inconsistent with the presumptive diagnosis. Our case suggests that routine parallel sequencing of peripheral white blood cells would substantially increase the fidelity of the obtained liquid biopsy results.
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Affiliation(s)
- Dingani Nkosi
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Caroline A Miller
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Audrey N Jajosky
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Zoltán N Oltvai
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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11
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Cell-Free DNA Variables including Gene Mutations in CA15-3 Normal Breast Cancer Reflect Prognosis. DISEASE MARKERS 2022; 2022:5470166. [PMID: 35251373 PMCID: PMC8894049 DOI: 10.1155/2022/5470166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/16/2022] [Accepted: 01/31/2022] [Indexed: 11/22/2022]
Abstract
Background Cell-free DNA (cfDNA) has attracted considerable attention in precision medicine. However, few data are available regarding to the prognostic value of cfDNA variables in CA15-3 normal breast cancer (BC) patients. Here, we aimed at investigating the prognostic value of cfDNA variables including gene mutations in CA15-3 normal BC patients. Methods A total of 68 BC patients with normal CA15-3 levels were enrolled. cfDNA concentration and integrity were assessed based on qPCR. cfDNA gene mutations were conducted by using next gene sequencing (NGS). The association between cfDNA variables and the prognosis of patients was analyzed. Results cfDNA concentration was related to tumor stage (P = 0.002), metastases (P = 0.001), and distant metastases (P < 0.001). The elevated copy number variants (CNV) were found in distant metastasis patients compared with patients without distant metastases (P = 0.008). Nineteen mutant genes were validated in enrolled CA15-3 normal BC patients. Thirty-two patients (47.0%) had single nucleotide variants (SNV), and 13 (19.1%) patients had TP53 mutations (TP53mut). SNV (P = 0.033) was related to tumor stage, and TP53mut was related to metastases (P = 0.016) and distant metastases (P = 0.006). In multivariate logistic analysis, cfDNA concentration was associated with metastases (OR = 3.404, 95% CI: 1.074-10.788, P = 0.037) and distant metastases (OR = 13.750, 95% CI: 1.473-128.358, P = 0.021). Cases with high cfDNA levels (>15.6 ng/ml), SNV, and TP53mut showed worse DFS compared with patients with low cfDNA levels (P < 0.001), without SNV (P = 0.002) and with TP53 wildtype (P < 0.001), respectively. In the multivariate Cox proportional hazard model, cfDNA concentration was an independent predictor of poor survival (HR = 5.786, 95% CI: 1.101-30.407, P = 0.038). Conclusions Assessment of cfDNA concentration, CNV, SNV, and TP53mut could be useful in predicting prognosis for CA15-3 normal BC patients. The cfDNA concentration was an independent predictor prognostic factor in CA15-3 normal BC patients.
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Stawski R, Stec-Martyna E, Chmielecki A, Nowak D, Perdas E. Current Trends in Cell-Free DNA Applications. Scoping Review of Clinical Trials. BIOLOGY 2021; 10:biology10090906. [PMID: 34571783 PMCID: PMC8468988 DOI: 10.3390/biology10090906] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023]
Abstract
We aimed to summarize the current knowledge about the trends in cfDNA application based on the analysis of clinical trials registered until April 2021. International Clinical Trials Registry Platform (ICTRP) and Clinicaltrials.gov were searched with the keywords: "cf-DNA"; "Circulating DNA"; "Deoxyribonucleic Acid"; and "Cell-Free Deoxyribonucleic Acid". Of 605 clinical trials, we excluded 237 trials, and 368 remaining ones were subject to further analysis. The subject, number of participants, and study design were analyzed. Our scoping review revealed three main trends: oncology (n = 255), non-invasive prenatal diagnostic (n = 48), and organ transplantation (n = 41), and many (n = 22) less common such as sepsis, sport, or autoimmune diseases in 368 clinical trials. Clinical trials are translating theory into clinical care. However, the diagnostic value of cfDNA remains controversial, and diagnostic accuracy still needs to be evaluated. Thus, further studies are necessary until cfDNA turns into a standard in clinical practice.
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Affiliation(s)
- Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
- Correspondence: (R.S.); (E.P.)
| | - Emilia Stec-Martyna
- Central Scientific Laboratory, Medical University of Lodz, 6/8 Mazowiecka St., 92-215 Lodz, Poland;
| | - Adam Chmielecki
- Sport Centre of the Medical University of Lodz, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Ewelina Perdas
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
- Correspondence: (R.S.); (E.P.)
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Romano C, Martorana F, Pennisi MS, Stella S, Massimino M, Tirrò E, Vitale SR, Di Gregorio S, Puma A, Tomarchio C, Manzella L. Opportunities and Challenges of Liquid Biopsy in Thyroid Cancer. Int J Mol Sci 2021; 22:7707. [PMID: 34299334 PMCID: PMC8303548 DOI: 10.3390/ijms22147707] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
Thyroid cancer is the most common malignancy of the endocrine system, encompassing different entities with distinct histological features and clinical behavior. The diagnostic definition, therapeutic approach, and follow-up of thyroid cancers display some controversial aspects that represent unmet medical needs. Liquid biopsy is a non-invasive approach that detects and analyzes biological samples released from the tumor into the bloodstream. With the use of different technologies, tumor cells, free nucleic acids, and extracellular vesicles can be retrieved in the serum of cancer patients and valuable molecular information can be obtained. Recently, a growing body of evidence is accumulating concerning the use of liquid biopsy in thyroid cancer, as it can be exploited to define a patient's diagnosis, estimate their prognosis, and monitor tumor recurrence or treatment response. Indeed, liquid biopsy can be a valuable tool to overcome the limits of conventional management of thyroid malignancies. In this review, we summarize currently available data about liquid biopsy in differentiated, poorly differentiated/anaplastic, and medullary thyroid cancer, focusing on circulating tumor cells, circulating free nucleic acids, and extracellular vesicles.
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Affiliation(s)
- Chiara Romano
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Federica Martorana
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Maria Stella Pennisi
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Stefania Stella
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Michele Massimino
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Elena Tirrò
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, 90127 Palermo, Italy
| | - Silvia Rita Vitale
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Sandra Di Gregorio
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Adriana Puma
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Cristina Tomarchio
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Livia Manzella
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico—San Marco”, 95123 Catania, Italy; (C.R.); (F.M.); (M.S.P.); (S.S.); (M.M.); (E.T.); (S.R.V.); (S.D.G.); (A.P.); (C.T.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
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Translational Utility of Liquid Biopsies in Thyroid Cancer Management. Cancers (Basel) 2021; 13:cancers13143443. [PMID: 34298656 PMCID: PMC8306718 DOI: 10.3390/cancers13143443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/21/2022] Open
Abstract
Liquid biopsies are a novel technique to assess for either circulating tumor cells (CTC) or circulating tumor DNA (ctDNA and microRNA (miRNA)) in peripheral blood samples of cancer patients. The diagnostic role of liquid biopsy in oncology has expanded in recent years, particularly in lung, colorectal and breast cancer. In thyroid cancer, the role of liquid biopsy in either diagnosis or prognosis is beginning to translate from the lab to the clinic. In this review, we describe the evolution of liquid biopsies in detecting CTC, ctDNA and miRNA in thyroid cancer patients, together with its limitations and future directions in clinical practice.
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Dutta S, Tarafdar S, Mukhopadhyay P, Bhattacharyya NP, Ghosh S. Plasma Cell-Free DNA to Differentiate Malignant from Benign Thyroid Nodules. J Clin Endocrinol Metab 2021; 106:e2262-e2270. [PMID: 33475693 DOI: 10.1210/clinem/dgab030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND Molecular testing is increasingly used to identify malignancy in thyroid nodules (especially indeterminate category). Measurement of cell-free DNA (cfDNA) levels from plasma has been useful in diagnosis of cancers of other organs/tissues; herein we analyze cfDNA levels in patients with thyroid nodules to explore the possibility of establishing a cutoff for identification of malignancy. METHODS Patients underwent ultrasonography (USG) and USG-guided fine needle aspiration as well as surgery, where indicated. Cell-free DNA was extracted from plasma and quantified. In initial analysis (determination of cutoff), cfDNA levels were compared between Bethesda 2 and Bethesda 5 &6 to establish a cutoff value that could differentiate malignant from benign nodules. In the subsequent analysis, the aforementioned cutoff was applied (validation of cutoff) to those with indeterminate nodules to check ability to predict malignancy. RESULTS Fine needle aspiration (n = 119) yielded patients with Bethesda 2 (n = 69) Bethesda 5 & 6 (n = 13) who underwent histopathological confirmation. Cell-free DNA levels in these 2 groups were 22.85 ± 1.27 and 96.20 ± 8.31 (ng/mL) respectively. A cfDNA cutoff of 67.9 ng/mL, with area under the curve of 0.992 (95% CI, 0.97-1.0) with 100% sensitivity and 93% specificity was established to identify malignant lesions. Indeterminate group (Bethesda 3 & 4) underwent surgery (malignant n = 24), (benign n = 13), and using the previously identified cutoff for cfDNA, we were able to identify malignant lesions with a sensitivity of 100% and specificity of 92.3%. There was a very strong agreement between cfDNA-based classification with histopathology-based classification of benign and malignant nodules (Cohen's kappa 0.94; P < 0.001). CONCLUSION Plasma cfDNA estimation could help differentiate malignant from benign thyroid nodules.
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Affiliation(s)
- Susmita Dutta
- Department of Endocrinology and Metabolism, Institute of Post-Graduate Medical Education and Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata, India
| | - Soham Tarafdar
- Department of Endocrinology and Metabolism, Institute of Post-Graduate Medical Education and Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata, India
| | - Pradip Mukhopadhyay
- Department of Endocrinology and Metabolism, Institute of Post-Graduate Medical Education and Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata, India
| | - Nitai P Bhattacharyya
- Department of Endocrinology and Metabolism, Institute of Post-Graduate Medical Education and Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata, India
| | - Sujoy Ghosh
- Department of Endocrinology and Metabolism, Institute of Post-Graduate Medical Education and Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata, India
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16
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Limited Clinical and Diagnostic Utility of Circulating Tumor DNA Detection in Patients with Early-Stage Well-Differentiated Thyroid Cancer: Comparison with Benign Thyroid Nodules and Healthy Individuals. Healthcare (Basel) 2021; 9:healthcare9040386. [PMID: 33915745 PMCID: PMC8065614 DOI: 10.3390/healthcare9040386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 01/10/2023] Open
Abstract
Limited data are available on the diagnostic utility of circulating tumor DNA (ctDNA) in early-stage thyroid cancers for BRAF, KRAS, NRAS, and TERT promoter mutations, which are known detectable markers for thyroid cancers. Here, we analyzed the above driver mutations in ctDNA and matched neoplastic tissues from patients with early-stage thyroid cancers in order to investigate diagnostic utility of circulating markers in distinguishing from other mimicking thyroid lesions and healthy individuals. In total, 73 matched neoplastic tissue and plasma samples [thyroid cancers (n = 62), benign thyroid disorders (n = 8), and parathyroid lesions (n = 3)] and 54 plasma samples from healthy individuals (as controls) were analyzed for BRAF, KRAS, NRAS, and TERT promoter mutations using peptide nucleic acid clamp real-time PCR. Although only one patient with an indeterminate lesion on thyroid cytology showed KRAS mutation (codon 146) in the preoperative plasma, that KRAS mutation was not identified in the stage I papillary thyroid carcinoma tissue. In the remaining 72 plasma samples, no other mutations were identified in BRAF, NRAS, and TERT promoter genes. The concordance rates of mutational results between the plasma and tumor tissue or metastatic lymph node were very low. One (1.9%) of the 54 healthy individuals harbored a KRAS mutation in the plasma samples. The ctDNA results did not represent the mutational profile of primary or metastatic thyroid cancers, warranting a caution for interpretation. The clinical utility of BRAF, KRAS, NRAS, and TERT promoter mutation analysis on ctDNA appears to be limited to early-stage thyroid cancers.
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Zhao Q, Miao C, Lu Q, Wu W, He Y, Wu S, Liu H, Lian C. Clinical Significance of Monitoring Circulating Free DNA and Plasma Heat Shock Protein 90alpha in Patients with Esophageal Squamous Cell Carcinoma. Cancer Manag Res 2021; 13:2223-2234. [PMID: 33707971 PMCID: PMC7943328 DOI: 10.2147/cmar.s295927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/15/2021] [Indexed: 12/24/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is the predominant histological type of esophageal cancer in China and has an extremely poor prognosis. Circulating free DNA (cfDNA) and plasma heat shock protein 90alpha (Hsp90a) are two novel noninvasive biomarkers for diagnosis and prognostic prediction of several types of cancer. However, to the best of our knowledge, the roles of the two biomarkers in ESCC are still unknown. Methods Here, we recruited 93 primary ESCC patients and detected plasma concentrations of the two markers at different time points, including 1-3 days pre-chemotherapy, 1-7 days pre-surgery and 7-14 days post-surgery. Baseline concentrations of the two markers were associated with main characteristics of ESCC patients which were collected at first diagnosis. Correlation between the two markers and traditional serum biomarkers at baseline was also examined. Furthermore, dynamic changes of the cfDNA and Hsp90α concentrations among different time points and the potential clinical significance were assessed. Results Consequently, there was no significant association between baseline concentrations of the two markers and clinical features. Especially, cfDNA demonstrated stronger correlation with other circulating biomarkers than Hsp90α at baseline level. Importantly, both cfDNA and Hsp90α concentrations were significantly increased after surgery. Kaplan-Meier survival analysis showed that a change in concentration of cfDNA (ΔcfDNA) but not Hsp90α (ΔHSP90ɑ) between pre-surgery and post-surgery had significant effect on the overall survival of surgical patients with ESCC. Conclusion Thus, ΔcfDNA evaluation could be a promising prognostic marker for surgical ESCC patients. Our findings may improve the understanding of the function of cfDNA and Hsp90α in ESCC.
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Affiliation(s)
- Qiang Zhao
- Department of Gastrointestinal Surgery, Heping Hospital, Changzhi Medical College, Changzhi, 046000, Shanxi, People's Republic of China
| | - Congxiu Miao
- Department of Science and Technology, Changzhi Medical College, Changzhi, 046000, Shanxi, People's Republic of China
| | - Qingpu Lu
- Department of Gastrointestinal Surgery, Heping Hospital, Changzhi Medical College, Changzhi, 046000, Shanxi, People's Republic of China
| | - Weipeng Wu
- Department of Gastrointestinal Surgery, Heping Hospital, Changzhi Medical College, Changzhi, 046000, Shanxi, People's Republic of China
| | - Yuan He
- Department of Gastrointestinal Surgery, Heping Hospital, Changzhi Medical College, Changzhi, 046000, Shanxi, People's Republic of China
| | - Shouxin Wu
- Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai, 201203, People's Republic of China
| | - Huimin Liu
- Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai, 201203, People's Republic of China
| | - Changhong Lian
- Department of Gastrointestinal Surgery, Heping Hospital, Changzhi Medical College, Changzhi, 046000, Shanxi, People's Republic of China
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Martins I, Ribeiro IP, Jorge J, Gonçalves AC, Sarmento-Ribeiro AB, Melo JB, Carreira IM. Liquid Biopsies: Applications for Cancer Diagnosis and Monitoring. Genes (Basel) 2021; 12:349. [PMID: 33673461 PMCID: PMC7997281 DOI: 10.3390/genes12030349] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The minimally-or non-invasive detection of circulating tumor-derived components in biofluids, such as blood, liquid biopsy is a revolutionary approach with significant potential for the management of cancer. Genomic and transcriptomic alterations can be accurately detected through liquid biopsies, which provide a more comprehensive characterization of the heterogeneous tumor profile than tissue biopsies alone. Liquid biopsies could assist diagnosis, prognosis, and treatment selection, and hold great potential to complement current surveilling strategies to monitor disease evolution and treatment response in real-time. In particular, these are able to detect minimal residual disease, to predict progression, and to identify mechanisms of resistance, allowing to re-orient treatment strategies in a timelier manner. In this review we gathered current knowledge regarding the role and potential of liquid biopsies for the diagnosis and follow-up of cancer patients. The presented findings emphasize the strengths of liquid biopsies, revealing their chance of improving the diagnosis and monitoring of several tumor types in the near future. However, despite growing evidence supporting their value as a management tool in oncology, some limitations still need to be overcome for their implementation in the routine clinical setting.
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Affiliation(s)
- Ivana Martins
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| | - Joana Jorge
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Ana Cristina Gonçalves
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Ana Bela Sarmento-Ribeiro
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Haematology Department, Coimbra University Hospital Centre (CHUC), 3004-531 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
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Yan YY, Guo QR, Wang FH, Adhikari R, Zhu ZY, Zhang HY, Zhou WM, Yu H, Li JQ, Zhang JY. Cell-Free DNA: Hope and Potential Application in Cancer. Front Cell Dev Biol 2021; 9:639233. [PMID: 33693004 PMCID: PMC7938321 DOI: 10.3389/fcell.2021.639233] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Cell-free DNA (cfDNA) is easily accessible in peripheral blood and can be used as biomarkers for cancer diagnostics, prognostics, and therapeutics. The applications of cfDNA in various areas of cancer management are attracting attention. In this review article, we discuss the potential relevance of using cfDNA analysis in clinical oncology, particularly in cancer screening, early diagnosis, therapeutic evaluation, monitoring disease progression; and determining disease prognosis.
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Affiliation(s)
- Yan-Yan Yan
- School of Medicine, Shanxi Datong University, Datong, China.,Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qiao-Ru Guo
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Feng-Hua Wang
- Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Rameshwar Adhikari
- Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur, Nepal
| | - Zhuang-Yan Zhu
- School of Medicine, Shanxi Datong University, Datong, China
| | - Hai-Yan Zhang
- School of Medicine, Shanxi Datong University, Datong, China
| | - Wen-Min Zhou
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hua Yu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, Avenida da Universidade, Taipa, China
| | - Jing-Quan Li
- The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Jian-Ye Zhang
- School of Medicine, Shanxi Datong University, Datong, China.,Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,The First Affiliated Hospital, Hainan Medical University, Haikou, China
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20
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Diagnostic Role of Cell-free DNA Integrity in Thyroid Cancer Particularly for Bethesda IV Cytology. Endocr Pract 2021; 27:673-681. [PMID: 33601025 DOI: 10.1016/j.eprac.2021.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND The cell-free DNA integrity index (cfDI) is promising for the differentiation between malignant and benign tumors, but little data has been reported on thyroid cancer (TC). We explored its diagnostic role in TC, mainly in cases of Bethesda category IV. METHODS cfDI was evaluated by quantitative real-time polymerase chain reaction using 2 primer sets to identify cell-free DNAs (cfDNAs) Alu83 and Alu244. Blood samples were collected from 85 patients with thyroid nodules (18 papillary [PTC], 21 follicular [FTC], 21 medullary, and 25 benign thyroid nodules [BTN]) before fine-needle aspiration cytology and surgical treatment and also from 25 patients with autoimmune thyroid disease (ATD) and 25 healthy subjects (HS). RESULTS cfDNA Alu244 concentration ≥6.95 ng/mL and cfDI ≥0.3 were excellent sensitive and specific tests to discriminate TC particularly cytologically indeterminate thyroid nodules (Bethesda IV) from the control groups (BTN, ATD, and HS). The levels of both cfDNA Alu83 and Alu244 were decreased while cfDI was increased significantly in medullary compared with FTC and PTC, with a nonsignificant difference between the latter subgroups. There was a significantly positive correlation between both cfDNA Alu83 and Alu244 with the T-classification of TNM staging and capsular invasion among PTC and FTC patients and between cfDI with Bethesda categories. Additionally, ATD had significantly higher cfDNA Alu83 and lower cfDI than HS. CONCLUSION cfDI is a useful noninvasive molecular biomarker in TC that correlates with the Bethesda classification and histopathology. Tumor size and capsular invasion were correlated with quantitative cfDNA among PTC and FTC.
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21
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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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22
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Pogliaghi G. Liquid biopsy in thyroid cancer: from circulating biomarkers to a new prospective of tumor monitoring and therapy. Minerva Endocrinol (Torino) 2020; 46:45-61. [PMID: 33213118 DOI: 10.23736/s2724-6507.20.03339-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recently, liquid biopsy has attracted much interest as a tool for early cancer screening, prognosis, monitoring and response to treatment in many different cancer types. Indeed, liquid biopsies can be repeatedly performed in a noninvasive way, at lower cost and without the risks associated to the classic tissue biopsy. The objective of this monography was to describe the main components studied in liquid biopsy (circulating tumor nucleic acids, circulating tumor cells and extracellular vesicles) and how they have been explored in thyroid cancer, through an in-depth scientific literature review. While circulating tumor cells are the most represented component in the literature of liquid biopsy in thyroid cancer, circulating tumor nucleic acids and extracellular vesicles have also been recently explored. One important challenge in this field of research, especially for differentiated thyroid cancer, has been the low quantity of circulating components with respect to other cancer types, requiring more advanced techniques for both isolation and analysis. Despite these limitations, liquid biopsy showed promise as an additional noninvasive tool for diagnosis, prognosis, to predict outcome and therapeutic response in differentiated, medullary and anaplastic thyroid cancer.
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Affiliation(s)
- Gabriele Pogliaghi
- Division of Endocrine and Metabolic Research, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy -
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23
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Cao S, Yu S, Yin Y, Su L, Hong S, Gong Y, Lv W, Li Y, Xiao H. Genetic alterations in cfDNA of benign and malignant thyroid nodules based on amplicon-based next-generation sequencing. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1225. [PMID: 33178757 PMCID: PMC7607131 DOI: 10.21037/atm-20-4544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Circulating cell-free DNA (cfDNA) serves as a biomarker in multiple malignant diseases. However, controversy still surrounds the role of cfDNA detection in the diagnosis and monitoring of papillary thyroid carcinoma (PTC). This study set out to identify the role of cfDNA detection in distinguishing between benign and malignant thyroid nodules. Methods Tissue, blood cell, and plasma samples were collected from 10 patients with benign nodules and 10 patients with malignant nodules. The DNA isolated from these samples was subject to PCR-based amplification using primers designed for 50 proto-oncogenes and tumor suppressor genes. PCR products were sequenced using Illumina technology, and the mutations were detected with varScan among sequencing data for each sample and comparative analysis was carried out. Results Through amplicon sequencing, we found one non-synonymous somatic mutation in the benign nodules and three in the malignant nodules. Among these four mutations, BRAFV600E mutation was detected in the tissue samples of 8 out of the 10 PTC patients, but it was not detected in the benign nodules. However, no BRAFV600E mutation was detected in cfDNA. Further differential analysis of cfDNA indicated that some genes had more mutations in benign patients than in malignant patients, such as MET and IDH, and some genes had more mutations in malignant patients, such as PIK3CA and EZH2. Conclusions We found that BRAFV600E mutation was a credible disease-related mutation in PTC; however, it could not be detected in cfDNA. Moreover, there was a large difference in mutation gene distribution between benign and malignant thyroid nodules.
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Affiliation(s)
- Siting Cao
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuang Yu
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yali Yin
- Department of Endocrinology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Lei Su
- Department of Gerontology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shubin Hong
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yingying Gong
- Department of Gerontology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Weiming Lv
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanbing Li
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haipeng Xiao
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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24
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Evaluation of circulating cell free DNA in plasma as a biomarker of different thyroid diseases. Braz J Otorhinolaryngol 2020; 86:321-326. [PMID: 30826312 PMCID: PMC9422580 DOI: 10.1016/j.bjorl.2018.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/15/2018] [Indexed: 12/14/2022] Open
Abstract
Introduction Many studies have been done on proteomics, genomics, epigenetic, immunogenetics in many body fluids. Among these, circulating cell-free DNA (ccfDNA) entered the literature in 1948, but it has not been studied for many years due to technological deficiencies. Following recent advances, geno-metastasis has been mentioned and new research is needed in this area. ccfDNA is known to be an important biomolecule in this regard. Objective The presence of cell-free DNA in the circulatory system may offer a tremendous opportunity to provide novel biomarkers for thyroid diseases. This experimental study was conducted to determine the amount of ccfDNA in different thyroid diseases, then to evaluate whether the ccfDNA concentration varied between the disease groups and control group. Methods In total, we included 121 individuals in the present study. We collected blood samples and then determined the ccfDNA concentration in plasma of collected blood samples from three groups: thyroiditis (n = 33), benign (n = 37), and malignant (n = 30) and from a control group (n = 21). Results The median values of the ccfDNA groups were found as 1610, 1665, 1685 and 576 ng/mL for the thyroiditis, benign, malign, and control groups, respectively. Findings showed that the ccfDNA of the three groups was significantly higher than the control (p < 0.0001). Each group was compared in terms of ccfDNA and the p-values of benign-thyroiditis, benign-malign, and thyroiditis-malign were 0.09, 0.65, and 0.29, respectively. Conclusions The clear differences between thyroid diseases and controls suggest that ccfDNA is worthy of attention as a biomarker for further evaluation of different thyroid diseases. Likewise, it might indicate a clear tendency that ccfDNA can also be used to distinguish different thyroid diseases.
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25
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Suleiman AA, Habeeb WH, Al-Hitawee HT. Exploration of the Beta-Actin DNA Integrity Index as Early Genetic Marker of Presence of Breast Cancer. ELECTRONIC JOURNAL OF GENERAL MEDICINE 2020. [DOI: 10.29333/ejgm/7618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Chen A, Li J, Wang L, Huang Q, Zhu J, Wen S, Lyu J, Wu W. Comparison of paired cerebrospinal fluid and serum cell-free mitochondrial and nuclear DNA with copy number and fragment length. J Clin Lab Anal 2020; 34:e23238. [PMID: 32052892 PMCID: PMC7307366 DOI: 10.1002/jcla.23238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 01/11/2020] [Accepted: 01/21/2020] [Indexed: 12/22/2022] Open
Abstract
Background Most studies on cell‐free DNA (cfDNA) were only for single body fluids; however, the differences in cfDNA distribution between two body fluids are rarely reported. Hence, in this work, we compared the differences in cfDNA distribution between cerebrospinal fluid (CSF) and serum of patients with brain‐related diseases. Methods The fragment length of cfDNA was determined by using Agilent 2100 Bioanalyzer. The copy numbers of cell‐free mitochondrial DNA (cf‐mtDNA) and cell‐free nuclear DNA (cf‐nDNA) were determined by using real‐time quantitative PCR (qPCR) and droplet digital PCR (ddPCR) with three pairs of mitochondrial ND1 and nuclear GAPDH primers, respectively. Results There were short (~60 bp), medium (~167 bp), and long (>250 bp) cfDNA fragment length distributions totally obtained from CSF and serum using Agilent 2100 Bioanalyzer. The results of both qPCR and ddPCR confirmed the existence of these three cfDNA fragment ranges in CSF and serum. According to qPCR, the copy numbers of long cf‐mtDNA, medium, and long cf‐nDNA in CSF were significantly higher than in paired serum. In CSF, only long cf‐mtDNA's copy numbers were higher than long cf‐nDNA. But in serum, the copy numbers of medium and long cf‐mtDNA were higher than the corresponding cf‐nDNA. Conclusion The cf‐nDNA and cf‐mtDNA with different fragment lengths differentially distributed in the CSF and serum of patients with brain disorders, which might serve as a biomarker of human brain diseases.
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Affiliation(s)
- Aolong Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jun Li
- Department of Clinical Laboratory, Wenzhou People's Hospital, Wenzhou, China
| | - Lei Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qin Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jiajin Zhu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shumeng Wen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Hangzhou Medical College, Hangzhou, China
| | - Wenhe Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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27
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Perdas E, Stawski R, Kaczka K, Nowak D, Zubrzycka M. Altered levels of circulating nuclear and mitochondrial DNA in patients with Papillary Thyroid Cancer. Sci Rep 2019; 9:14438. [PMID: 31594998 PMCID: PMC6783406 DOI: 10.1038/s41598-019-51000-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/20/2019] [Indexed: 12/28/2022] Open
Abstract
Papillary thyroid cancer is the most common thyroid cancer type. However, diagnostics based on fine needle biopsy cannot make a definitive diagnosis in 25% of thyroid nodules. Additionally, approximately 70% to 80% of thyroid lobectomies performed just for diagnostic purposes are benign. Despite this, biopsy still remains the main method of evaluation of thyroid nodules. Cell-free DNA (cf-DNA) measurement could give a new diagnostic opportunities which may reduce the number of unnecessary thyroid procedures. In this study, using a qPCR, we have examined the nuclear cf-DNA and mitochondrial cf-DNA in the plasma of 32 patients. We have found that the level of nuclear cf-DNA is almost 2-fold increased (median 3 089 vs. 1 872, p = 0.022), whereas mitochondrial cf-DNA content was significantly decreased in respect to healthy controls (median 44 992 vs. 92 220, p = 0.010). The ROC curve analysis showed high specificity for nuclear cf-DNA and mitochondrial cf-DNA, which may serve as a useful tool to decrease the number of unneeded surgeries. Our study reports the first epidemiological evidence for lower mitochondrial cf-DNA content in the patient group, what suggests that apart from nuclear cf-DNA also mitochondrial cf-DNA is affected by disease development.
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Affiliation(s)
- Ewelina Perdas
- Department of Cardiovascular Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland.
| | - Robert Stawski
- Department of Clinical Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Krzysztof Kaczka
- Department of General and Oncological Surgery, Medical University of Lodz, Lodz, Poland
| | - Dariusz Nowak
- Department of Clinical Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Maria Zubrzycka
- Department of Cardiovascular Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
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28
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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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Cervena K, Vodicka P, Vymetalkova V. Diagnostic and prognostic impact of cell-free DNA in human cancers: Systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:100-129. [DOI: 10.1016/j.mrrev.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
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30
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Grimm D. Cell and Molecular Biology of Thyroid Disorders. Int J Mol Sci 2019; 20:ijms20122895. [PMID: 31200596 PMCID: PMC6627965 DOI: 10.3390/ijms20122895] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023] Open
Affiliation(s)
- Daniela Grimm
- Department of Biomedicine, Pharmacology, Aarhus University, Wilhelm Meyers Allé 4, 8000 Aarhus C, Denmark.
- University Clinic for Plastic, Aesthetic and Hand Surgery, Otto von Guericke University, Leipziger Str. 44, 39120 Magdeburg, Germany.
- Department of Microgravity and Translational Regenerative Medicine, Faculty of Medicine and Mechanical Engineering, Otto von Guericke University, Leipziger Str. 44, 39120 Magdeburg, Germany.
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31
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Rappa G, Puglisi C, Santos MF, Forte S, Memeo L, Lorico A. Extracellular Vesicles from Thyroid Carcinoma: The New Frontier of Liquid Biopsy. Int J Mol Sci 2019; 20:E1114. [PMID: 30841521 PMCID: PMC6429352 DOI: 10.3390/ijms20051114] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/22/2022] Open
Abstract
The diagnostic approach to thyroid cancer is one of the most challenging issues in oncology of the endocrine system because of its high incidence (3.8% of all new cancer cases in the US) and the difficulty to distinguish benign from malignant non-functional thyroid nodules and establish the cervical lymph node involvement during staging. Routine diagnosis of thyroid nodules usually relies on a fine-needle aspirate biopsy, which is invasive and often inaccurate. Therefore, there is an urgent need to identify novel, accurate, and non-invasive diagnostic procedures. Liquid biopsy, as a non-invasive approach for the detection of diagnostic biomarkers for early tumor diagnosis, prognosis, and disease monitoring, may be of particular benefit in this context. Extracellular vesicles (EVs) are a consistent source of tumor-derived RNA due to their prevalence in circulating bodily fluids, the well-established isolation protocols, and the fact that RNA in phospholipid bilayer-enclosed vesicles is protected from blood-borne RNases. Recent results in other types of cancer, including our recent study on plasma EVs from glioblastoma patients suggest that information derived from analysis of EVs from peripheral blood plasma can be integrated in the routine diagnostic tumor approach. In this review, we will examine the diagnostic and prognostic potential of liquid biopsy to detect tumor-derived nucleic acids in circulating EVs from patients with thyroid carcinoma.
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Affiliation(s)
- Germana Rappa
- College of Medicine, Touro University Nevada, 874 American Pacific Drive, Henderson, NV 89014, USA.
| | - Caterina Puglisi
- Mediterranean Institute of Oncology Foundation, Via Penninazzo 7, 95029 Viagrande, Italy.
| | - Mark F Santos
- College of Medicine, Touro University Nevada, 874 American Pacific Drive, Henderson, NV 89014, USA.
| | - Stefano Forte
- Mediterranean Institute of Oncology Foundation, Via Penninazzo 7, 95029 Viagrande, Italy.
| | - Lorenzo Memeo
- Mediterranean Institute of Oncology Foundation, Via Penninazzo 7, 95029 Viagrande, Italy.
| | - Aurelio Lorico
- College of Medicine, Touro University Nevada, 874 American Pacific Drive, Henderson, NV 89014, USA.
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32
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Su YH, Kim AK, Jain S. Liquid biopsies for hepatocellular carcinoma. Transl Res 2018; 201:84-97. [PMID: 30056068 PMCID: PMC6483086 DOI: 10.1016/j.trsl.2018.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/18/2018] [Accepted: 07/02/2018] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is the world's second leading cause of cancer death; 82.4% of patients die within 5 years. This grim prognosis is the consequence of a lack of effective early detection tools, limited treatment options, and the high frequency of HCC recurrence. Advances in the field of liquid biopsy hold great promise in improving early detection of HCC, advancing patient prognosis, and ultimately increasing the survival rate. In an effort to address the current challenges of HCC screening and management, several studies have identified and evaluated liver-cancer-associated molecular signatures such as genetic alterations, methylation, and noncoding RNA expression in the form of circulating biomarkers in body fluids and circulating tumor cells of HCC patients. In this review, we summarize the recent progress in HCC liquid biopsy, organized by the intended clinical application of the reported study.
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Affiliation(s)
- Ying-Hsiu Su
- The Baruch S. Blumberg Institute, Doylestown, Pennsylvania.
| | - Amy K Kim
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins School of Medicine, Baltimore Maryland.
| | - Surbhi Jain
- JBS Science, Inc., Doylestown, Pennsylvania.
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33
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Fussey JM, Bryant JL, Batis N, Spruce RJ, Hartley A, Good JS, McCabe CJ, Boelaert K, Sharma N, Mehanna H. The Clinical Utility of Cell-Free DNA Measurement in Differentiated Thyroid Cancer: A Systematic Review. Front Oncol 2018; 8:132. [PMID: 29761074 PMCID: PMC5937025 DOI: 10.3389/fonc.2018.00132] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/11/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) can be detected in the circulation of healthy individuals, but is found in higher concentrations in cancer patients. Furthermore, mutations in tumor cells can be identified in circulating DNA fragments. This has been the subject of significant interest in the field of cancer research, but little has been published in thyroid cancer. OBJECTIVES To assess all available evidence on the use of circulating cfDNA in the diagnosis, management and surveillance of patients with differentiated thyroid cancer, and collate it into a systematic review to guide future research. METHODS A comprehensive literature search on the measurement of cfDNA in thyroid cancer was undertaken, and results from relevant studies collated into a systematic review. RESULTS Nine studies were identified, with varying methodologies and findings. Key techniques and findings are summarized. CONCLUSION There is limited but promising evidence that somatic mutations in thyroid cancer can be detected in circulating cfDNA and are associated with more advanced disease. Further research is required to develop a clinically useful tool based on cfDNA to improve the management of thyroid cancers.
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Affiliation(s)
- Jonathan M. Fussey
- School of Cancer Sciences, Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham, United Kingdom
| | - Jennifer L. Bryant
- School of Cancer Sciences, Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham, United Kingdom
| | - Nikolaos Batis
- School of Cancer Sciences, Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham, United Kingdom
| | - Rachael J. Spruce
- School of Cancer Sciences, Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham, United Kingdom
| | - Andrew Hartley
- Hall-Edwards Radiotherapy Research Group, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - James S. Good
- Department of Oncology, University Hospital Birmingham, Birmingham, United Kingdom
| | - Christopher J. McCabe
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Kristien Boelaert
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Neil Sharma
- School of Cancer Sciences, Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham, United Kingdom
| | - Hisham Mehanna
- School of Cancer Sciences, Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham, United Kingdom
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Grimm D. Current Knowledge in Thyroid Cancer-From Bench to Bedside. Int J Mol Sci 2017; 18:ijms18071529. [PMID: 28714875 PMCID: PMC5536017 DOI: 10.3390/ijms18071529] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 02/07/2023] Open
Affiliation(s)
- Daniela Grimm
- Department of Biomedicine, Pharmacology, Aarhus University, Wilhelm Meyers Allé 4, 8000 Aarhus C, Denmark.
- University Clinic for Plastic, Aesthetic and Hand Surgery, Otto von Guericke University, Leipziger Str. 44, 39120 Magdeburg, Germany.
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