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Schwarzenbach H, Carmignac D, Gahan J. In Memoriam Peter B. Gahan 1933-2023. Histochem Cell Biol 2023; 160:369-370. [PMID: 37553538 DOI: 10.1007/s00418-023-02228-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2023] [Indexed: 08/10/2023]
Affiliation(s)
- Heidi Schwarzenbach
- University Medical Center Hamburg-Eppendorf, Martinistrasse, 20246, Hamburg, Germany.
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Lledo B, Morales R, Antonio Ortiz J, Bernabeu A, Bernabeu R. Noninvasive preimplantation genetic testing using the embryo spent culture medium: an update. Curr Opin Obstet Gynecol 2023; 35:294-299. [PMID: 37144571 DOI: 10.1097/gco.0000000000000881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
PURPOSE OF REVIEW The presence of cell-free DNA (cf-DNA) in the embryo spent culture medium allows to develop a noninvasive PGT-A (niPGTA). Noninvasive PGT-A may provide a simpler, safer and less costly approach to preimplantation genetic testing of aneuploidy (PGT-A). Furthermore, niPGTA would provide wider access to embryo genetic analysis and circumvent many legal and ethical considerations. However, the concordance rate between the results obtained by PGT-A and niPGTA varies among studies and, their clinical utility has not been already demonstrated. This review evaluates the niPGTA reliability based on SCM and adds new knowledge about the clinical relevance of SCM for noninvasive PGT-A. RECENT FINDINGS The most recent concordance studies evaluating the accuracy of niPGTA using SCM showed a high variation in the informativity rate of SCM and the diagnostic concordance. Also, sensitivity and specificity showed similar heterogeneous results. Therefore, these results do not support the clinical utility of niPGTA. Regarding clinical outcome, the data are initial and further research, including randomized and nonselection studies are needed. SUMMARY Further research, including randomized and nonselection studies, as well as optimization of embryo culture conditions and medium retrieval, are needed to improve the reliability and clinical utility of niPGTA.
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Affiliation(s)
| | | | | | - Andrea Bernabeu
- Instituto Bernabeu of Fertility and Gynaecology
- Chair of Community Medicine and Reproductive Health, Miguel Hernández University, Alicante, Spain
| | - Rafael Bernabeu
- Instituto Bernabeu of Fertility and Gynaecology
- Chair of Community Medicine and Reproductive Health, Miguel Hernández University, Alicante, Spain
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P P, Keshari JR, Prakash P, Kumar M, Mandal M, Kumari R. Correlation Between Circulating Cell-Free DNA Levels and Breast Cancer Subtypes: A Prospective Observational Study. Cureus 2023; 15:e42247. [PMID: 37605702 PMCID: PMC10440043 DOI: 10.7759/cureus.42247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2023] [Indexed: 08/23/2023] Open
Abstract
INTRODUCTION Breast cancer (BC), a heterogeneous disease, is one of the leading causes of cancer-related deaths among women worldwide. Circulating cell-free DNA (cfDNA) levels have been persistently reported to be elevated in BC patients. In the current study, we evaluated the correlation between the cfDNA levels in patients with BC and its subtypes. METHODS We recruited newly diagnosed, histopathologically confirmed BC patients aged >18 years (N=39), who did not have any previous malignancy, from the Department of Surgical Oncology, Indira Gandhi Institute of Medical Sciences (IGIMS), Patna, Bihar, India. A total of 6 ml of venous blood was collected from each subject; of this, 1 ml was subjected to complete blood count (CBC), and 4 ml was transferred to a clot-activated collection vial for plasma separation and the cfDNA isolation thereof. In addition to the basic demographic history of each patient, the information on the cancer subtype was as also recorded from the medical records of each patient. All the data were analysed by GraphPad Prism Version 8 (Insightful Science, LLC, San Diego, California, United States). One-way ANOVA was used to test the difference between more than two groups. Pearson correlation was also estimated between cfDNA levels and various CBC indices. A two-tailed p-value<0.05 was considered statistically significant. RESULTS The mean age of included patients was 48.6±8.20 years. The mean levels of cfDNA were 2.81±2.39 ng/µL. The mean counts of various blood cell types and other indices of CBC were in the normal range. Compared to BC patients with estrogen receptors (ER+), the cfDNA levels were significantly higher in patients with human epidermal growth factor receptor 2 (HER2+) and triple-negative BC (TNBC) (p<0.05). Conclusion: The elevated levels of cfDNA in patients with BC can be a prognostic marker for the disease subtype. However, more replicative studies are warranted to substantiate our findings.
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Affiliation(s)
- Pushpanjali P
- Biochemistry, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - J R Keshari
- Biochemistry, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Pritam Prakash
- Biochemistry, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Manish Kumar
- Surgical Oncology, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Manish Mandal
- Surgical Gastroenterology, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Rekha Kumari
- Biochemistry, Indira Gandhi Institute of Medical Sciences, Patna, IND
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Hadipour M, Fasihi Harandi M, Mirhendi H, Yousofi Darani H. Diagnosis of echinococcosis by detecting circulating cell-free DNA and miRNA. Expert Rev Mol Diagn 2023; 23:133-142. [PMID: 36756744 DOI: 10.1080/14737159.2023.2178903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
INTRODUCTION Diagnosis of echinococcosis is difficult and usually performed based on clinical findings, imaging, and serological test. However, all of them have limitations, especially in follow-up approaches. AREAS COVERED Detection of cell-free DNA (cfDNA) and micro-RNA (miRNA) is currently a hot topic for diagnosis of echinococcosis diseases. For detecting cell-free DNA in echinococcosis patient's samples such as sera, some techniques are based on next-generation sequencing (NGS), DNA-deep sequencing, some are based on PCR-based methods, and a few works related to the detection of miRNA for the diagnosis of human echinococcosis. EXPERT OPINION In the detection of cell-free DNA in echinococcosis patient' samples, NGS and DNA-deep sequencing have shown high level of sensitivity, but are not suitable for routine clinical examination as they are expensive and inaccessible in the majority of endemic areas. However, PCR-based methods have shown a sensitivity of about 20-25%. To improve the sensitivity of these tests, improving the DNA extraction method, designing appropriate primers for detecting short-length fragments of circulating DNA, using a higher volume of a serum sample, and application of more sensitive PCR methods are recommended. In the field of miRNA detection, further works are recommended.
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Affiliation(s)
- Mahboubeh Hadipour
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
| | - Majid Fasihi Harandi
- Research center for Hydatid disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Mirhendi
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
| | - Hossein Yousofi Darani
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
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Maurya A, Murallidharan JS, Sharma A, Agarwal A. Microfluidics geometries involved in effective blood plasma separation. MICROFLUIDICS AND NANOFLUIDICS 2022; 26:73. [PMID: 36090664 PMCID: PMC9440999 DOI: 10.1007/s10404-022-02578-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
The last two decades witnessed a significant advancement in the field of diluted and whole blood plasma separation. This is one of the common procedures used to diagnose, cure and treat numerous acute and chronic diseases. For this separation purpose, various types of geometries of microfluidic devices, such as T-channel, Y-channel, trifurcation, constriction-expansion, curved/bend/spiral channels, a combination of any of the two geometries, etc., are being exploited, and this is detailed in this review article. The evaluation of the performance of such devices is based on the several parameters such as separation efficiency, flow rate, hematocrits, channel dimensions, etc. Thus, the current extensive review article endeavours to understand how particular geometry influences the separation efficiency for a given hematocrit. Additionally, a comparative analysis of various geometries is presented to demonstrate the less explored geometric configuration for the diluted and whole blood plasma separation. Also, a meta-analysis has been performed to highlight which geometry serves best to give a consistent separation efficiency. This article also presents tabulated data for various geometries with necessary details required from a designer's perspective such as channel dimensions, targeted component, studied range of hematocrit and flow rate, separation efficiency, etc. The maximum separation efficiency that can be achieved for a given hematocrits and geometry has also been plotted. The current review highlights the critical findings relevant to this field, state of the art understanding and the future challenges.
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Affiliation(s)
- Anamika Maurya
- Department of Mechanical Engineering, Indian Institute of Technology Mumbai, Mumbai, 400076 India
| | | | - Atul Sharma
- Department of Mechanical Engineering, Indian Institute of Technology Mumbai, Mumbai, 400076 India
| | - Amit Agarwal
- Department of Mechanical Engineering, Indian Institute of Technology Mumbai, Mumbai, 400076 India
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Ultrahigh sensitive and selective detection of single nucleotide polymorphism using peptide nucleic acid and ribonuclease H assembled DNA amplification (PRADA). Anal Chim Acta 2022; 1233:340423. [DOI: 10.1016/j.aca.2022.340423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/06/2022] [Accepted: 09/19/2022] [Indexed: 11/22/2022]
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Allegra A, Cancemi G, Mirabile G, Tonacci A, Musolino C, Gangemi S. Circulating Tumour Cells, Cell Free DNA and Tumour-Educated Platelets as Reliable Prognostic and Management Biomarkers for the Liquid Biopsy in Multiple Myeloma. Cancers (Basel) 2022; 14:cancers14174136. [PMID: 36077672 PMCID: PMC9454477 DOI: 10.3390/cancers14174136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Even though the presently employed biomarkers in the detection and management of multiple myeloma are demonstrating encouraging results, the mortality percentage of the malignancy is still elevated. Thus, searching for new diagnostic or prognostic markers is pivotal. Liquid biopsy allows the examination of circulating tumour DNA, cell-free DNA, extracellular RNA, and cell free proteins, which are released into the bloodstream due to the breakdown of tumour cells or exosome delivery. Liquid biopsy can now be applied in clinical practice to diagnose, and monitor multiple myeloma, probably allowing a personalized treatment of the disease. Abstract Liquid biopsy is one of the fastest emerging fields in cancer evaluation. Circulating tumour cells and tumour-originated DNA in plasma have become the new targets for their possible employ in tumour diagnosis, and liquid biopsy can define tumour burden without invasive procedures. Multiple Myeloma, one of the most frequent hematologic tumors, has been the target of therapeutic progresses in the last few years. Bone marrow aspirate is the traditional tool for diagnosis, prognosis, and genetic evaluation in multiple myeloma patients. However, this painful procedure presents a relevant drawback for regular disease examination as it requires an invasive practice. Moreover, new data demonstrated that a sole bone marrow aspirate is incapable of expressing the multifaceted multiple myeloma genetic heterogeneity. In this review, we report the emerging usefulness of the assessment of circulating tumour cells, cell-free DNA, extracellular RNA, cell-free proteins, extracellular vesicles, and tumour-educated platelets to evaluate the changing mutational profile of multiple myeloma, as early markers of disease, reliable predictors of prognosis, and as useful tools to perform less invasive monitoring in multiple myeloma.
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Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, 98125 Messina, Italy
- Correspondence:
| | - Gabriella Cancemi
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, 98125 Messina, Italy
| | - Giuseppe Mirabile
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, 98125 Messina, Italy
| | - Alessandro Tonacci
- Clinical Physiology Institute, National Research Council of Italy (IFC-CNR), 56124 Pisa, Italy
| | - Caterina Musolino
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, 98125 Messina, Italy
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
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Li D, Pan J. Diagnostic and Prognostic Value Analysis of miR-206 in Asymptomatic Carotid Artery Stenosis. Br J Biomed Sci 2022; 79:10592. [PMID: 35996513 PMCID: PMC9302550 DOI: 10.3389/bjbs.2022.10592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/13/2022] [Indexed: 12/02/2022]
Abstract
Introduction: To investigate the expression level of miR-206 in serum of patients with asymptomatic carotid artery stenosis (CAS) and estimate the value of miR-206 in the diagnosis and prognosis of asymptomatic CAS. Methods: A total of 206 individuals enrolled in this study, including 105 CAS patients and 101 controls. RT-qPCR technology was applied to measure the relative level of miR-206, and Pearson’s correlation coefficient was performed to analyze the relationship between carotid artery stenosis degree and miR-206 level. An ROC curve was drawn to assess the diagnostic value of miR-206 in asymptomatic CAS. The 5-year prognosis of asymptomatic CAS patients was tested using multivariate Cox regression analysis and Kaplan-Meier survival curve. Results: MiR-206 expression was reduced in asymptomatic CAS patients. The AUC of the ROC curve of miR-206 was 0.939, with a sensitivity of 86.70% and a specificity of 86.14%. The amount of CAS gradually increased with the decrease of miR-206 level. Seven-teen patients in the low miR-206 expression group developed CIEs, and 3 patients in the high miR-206 expression group developed CIEs during the 5-year follow-up. miR-206 and the amount of CAS were independent factors for the occurrence of CIEs within 5 years in asymptomatic CAS patients. Conclusion: Serum miR-206 has high diagnostic accuracy for asymptomatic CAS and has predictive value for the incidence of CIEs in patients within 5 years.
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Affiliation(s)
- Dancen Li
- Department of Neurosurgery, Changzhou No. 2 People’s Hospital, Changzhou, China
| | - Jingjun Pan
- Intensive Care Unit, Changzhou No. 2 People’s Hospital, Changzhou, China
- *Correspondence: Jingjun Pan,
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Tutanov O, Tamkovich S. The Influence of Proteins on Fate and Biological Role of Circulating DNA. Int J Mol Sci 2022; 23:7224. [PMID: 35806228 PMCID: PMC9266439 DOI: 10.3390/ijms23137224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Circulating DNA has already proven itself as a valuable tool in translational medicine. However, one of the overlooked areas of circulating DNA research is its association with different proteins, despite considerable evidence that this association might impact DNA's fate in circulation and its biological role. In this review, we attempt to shed light on current ideas about circulating DNA origins and forms of circulation, known biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.
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Affiliation(s)
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
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Kılınç N, Onbaşılar M, Çayır A. Evaluation of circulating cell-free nucleic acids in health workers occupationally exposed to ionizing radiation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:40543-40549. [PMID: 35083692 DOI: 10.1007/s11356-022-18828-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Radiology workers might constantly be exposed to low-dose ionizing radiation due to their profession. Low doses of radiation in a short exposure time have the potential to alter the genome, which might potentially lead to diseases. The main objective of this study was to determine whether the amount of cell-free nucleic acids in plasma samples of radiation-exposed workers was different from the general public, in other words, non-exposed individuals. In this context, we investigated the association between radiation exposure and cell-free nucleic acids concentration by using radiation exposure parameters. The study consisted of 40 radiology workers and 40 individuals who were not exposed to ionizing radiation. The plasma concentrations of cell-free DNA, RNA, and miRNA were measured fluorometrically. We found that the ccfRNA concentration of the radiation-exposed group was significantly different from that of the non-exposed group (p = 0.0001). However, there are no differences between both groups in terms of ccfDNA and ccfmiRNA concentration. The concentration of ccfDNA is significantly correlated with working time in the fluoroscopy field (p < 0.05). We found that the concentration of ccfmiRNA was significantly correlated with working time in plain radiography (p < 0.01) and computed tomography (p < 0.05) and with total working time (p < 0.01). Similarly, the concentrations of ccfRNA were significantly correlated with working time in computed tomography (p < 0.01) and with the total working time (p < 0.05) of the workers. We found that imaging number in computed tomography significantly altered the level of ccfRNA (p = 0.006) and that working time in the computed tomography field significantly affected the ccfRNA concentration (p = 0.03, R2 = 0.36 for model). Finally, we determined that total working time was significantly associated with total ccfRNA concentration (p < 0.05, R2 = 0.25 for model). In conclusion, total RNA measured in radiation-exposed workers has the potential to predict the radiation exposure risk. Furthermore, total working time and working time in the tomography field significantly alter the level of free nucleic acids.
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Affiliation(s)
- Nihal Kılınç
- Medical Pathology, Faculty of Medicine, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Mehmet Onbaşılar
- School of Graduate Studies, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Akın Çayır
- Vocational School of Health Services, Canakkale Onsekiz Mart University, Canakkale, Turkey.
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Vita GM, De Simone G, De Marinis E, Nervi C, Ascenzi P, di Masi A. Serum albumin and nucleic acids biodistribution: from molecular aspects to biotechnological applications. IUBMB Life 2022; 74:866-879. [PMID: 35580148 DOI: 10.1002/iub.2653] [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: 03/07/2022] [Accepted: 05/06/2022] [Indexed: 11/06/2022]
Abstract
Serum albumin (SA) is the most abundant protein in plasma and represents the main carrier of endogenous and exogenous compounds. Several evidence supports the notion that SA binds single and double stranded deoxy- and ribonucleotides at two sites, with values of the dissociation equilibrium constant (i.e., Kd ) ranging from micromolar to nanomolar values. This can be relevant from a physiological and pathological point of view as in human plasma circulate cell-free nucleic acids (cfNAs), which are single and double stranded NAs released by different tissues via apoptosis, necrosis, and secretions. Albeit SA shows low hydrolytic reactivity toward DNA and RNA, the high plasma concentration of this protein and the occurrence of several SA receptors may be pivotal for sequestering and hydrolyzing cfNAs. Therefore, pathological conditions like cancer, characterized by altered levels of human SA or by altered SA post-translational modifications, may influence cfNAs distribution and metabolism. Besides, the stability, solubility, biocompatibility, and low immunogenicity make SA a golden share for biotechnological applications related to the delivery of therapeutic NAs (TNAs). Indeed, pre-clinical studies report the therapeutic potential of SA:TNAs complexes in precision cancer therapy. Here, the molecular and biotechnological implications of SA:NAs interaction are discussed, highlighting new perspectives into SA plasmatic functions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gian Marco Vita
- Department of Science, Section of Biomedical Sciences and Technologies, Roma Tre University, Roma, Italy
| | - Giovanna De Simone
- Department of Science, Section of Biomedical Sciences and Technologies, Roma Tre University, Roma, Italy
| | - Elisabetta De Marinis
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Latina, Italy
| | - Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Latina, Italy
| | - Paolo Ascenzi
- Department of Science, Section of Biomedical Sciences and Technologies, Roma Tre University, Roma, Italy.,Accademia Nazionale dei Lincei, Roma, Italy
| | - Alessandra di Masi
- Department of Science, Section of Biomedical Sciences and Technologies, Roma Tre University, Roma, Italy
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Li H, Li M, Guo H, Lin G, Huang Q, Qiu M. Integrative Analyses of Circulating mRNA and lncRNA Expression Profile in Plasma of Lung Cancer Patients. Front Oncol 2022; 12:843054. [PMID: 35433477 PMCID: PMC9008738 DOI: 10.3389/fonc.2022.843054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Circulating-free RNAs (cfRNAs) have been regarded as potential biomarkers for “liquid biopsy” in cancers. However, the circulating messenger RNA (mRNA) and long noncoding RNA (lncRNA) profiles of lung cancer have not been fully characterized. In this study, we profiled circulating mRNA and lncRNA profiles of 16 lung cancer patients and 4 patients with benign pulmonary nodules. Compared with benign pulmonary nodules, 806 mRNAs and 1,762 lncRNAs were differentially expressed in plasma of lung adenocarcinoma patients. For lung squamous cell carcinomas, 256 mRNAs and 946 lncRNAs were differentially expressed. A total of 231 mRNAs and 298 lncRNAs were differentially expressed in small cell lung cancer. Eleven mRNAs, 51 lncRNAs, and 207 canonical pathways were differentially expressed in lung cancer in total. Forty-five blood samples were collected to verify our findings via performing qPCR. There are plenty of meaningful mRNAs and lncRNAs that were found. MYC, a transcription regulator associated with the stemness of cancer cells, is overexpressed in lung adenocarcinoma. Transforming growth factor beta (TGFB1), which plays pleiotropic roles in cancer progression, was found to be upregulated in lung squamous carcinoma. MALAT1, a well-known oncogenic lncRNA, was also found to be upregulated in lung squamous carcinoma. Thus, this study provided a systematic resource of mRNA and lncRNA expression profiles in lung cancer plasma.
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Affiliation(s)
- Haoran Li
- Department of Thoracic Surgery, Peking University People’s Hospital, Beijing, China
| | - Mingru Li
- Department of Thoracic Surgery, Aerospace 731 Hospital, Beijing, China
| | - Haifa Guo
- The First Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Guihu Lin
- Department of Thoracic Surgery, Aerospace 731 Hospital, Beijing, China
| | - Qi Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Qi Huang, ; Mantang Qiu,
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People’s Hospital, Beijing, China
- *Correspondence: Qi Huang, ; Mantang Qiu,
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Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands. Int J Mol Sci 2021; 22:ijms222313159. [PMID: 34884964 PMCID: PMC8658440 DOI: 10.3390/ijms222313159] [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: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic DNA methylation is involved in many diseases and is expected to be a specific biomarker for even the pre-symptomatic diagnosis of many diseases. Thus, a rapid and inexpensive detection method is required for disease diagnosis. We have previously reported that cytosine methylation in G-quadruplex (G4)-forming oligonucleotides develops different G4 topologies. In this study, we developed a method for detecting CpG methylation in G4-forming oligonucleotides based on the structural differences between methylated and unmethylated G4 DNAs. The differences in G4 topologies due to CpG methylation can be discriminated by G4 ligands. We performed a binding assay between methylated or unmethylated G4 DNAs and G4 ligands. The binding abilities of fluorescent G4 ligands to BCL-2, HRAS1, HRAS2, VEGF G4-forming sequences were examined by fluorescence-based microtiter plate assay. The differences in fluorescence intensities between methylated and unmethylated G4 DNAs were statistically significant. In addition to fluorescence detection, the binding of G4 ligand to DNA was detected by chemiluminescence. A significant difference was also detected in chemiluminescence intensity between methylated and unmethylated DNA. This is the first study on the detection of CpG methylation in G4 structures, focusing on structural changes using G4 ligands.
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14
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Ying L, Sharma A, Chhoda A, Ruzgar N, Hasan N, Kwak R, Wolfgang CL, Wang TH, Kunstman JW, Salem RR, Wood LD, Iacobuzio-Donahue C, Schneider EB, Farrell JJ, Ahuja N. Methylation-based Cell-free DNA Signature for Early Detection of Pancreatic Cancer. Pancreas 2021; 50:1267-1273. [PMID: 34860810 DOI: 10.1097/mpa.0000000000001919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES The potential of DNA methylation alterations in early pancreatic cancer (PC) detection among pancreatic tissue cell-free DNA seems promising. This study investigates the diagnostic capacity of the 4-gene methylation biomarker panel, which included ADAMTS1, BNC1, LRFN5, and PXDN genes, in a case-control study. METHODS A genome-wide pharmacoepigenetic approach identified ADAMTS1, BNC1, LRFN5, and PXDN genes as putative targets. Tissue samples including stage I-IV PC (n = 44), pancreatic intraepithelial neoplasia (n = 15), intraductal papillary mucinous neoplasms (n = 24), and normal pancreas (n = 8), and cell-free DNA, which was acquired through methylation on beads technology from PC (n = 22) and control patients (n = 10), were included. The 2-∆ct was the outcome of interest and underwent receiver operating characteristic analysis to determine the diagnostic accuracy of the panel. RESULTS Receiver operating characteristic analysis revealed an area under the curve of 0.93 among ADAMTS1, 0.76 among BNC1, 0.75 among PXDN, and 0.69 among LRFN5 gene. The combination gene methylation panel (ADAMTS1, BNC1, LRFN5, and PXDN) had an area under the curve of 0.94, with a sensitivity of 100% and specificity of 90%. CONCLUSIONS This methylation-based biomarker panel had promising accuracy for PC detection and warranted further validation in prospective PC surveillance trials.
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Affiliation(s)
| | | | - Ankit Chhoda
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | | | | | | | | | - Tza Huei Wang
- Department of Biomedical Engineering and Department of Mechanical Engineering and Institute for NanoBioTechnology, Johns Hopkins University
| | | | | | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD
| | - Christine Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - James J Farrell
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
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15
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Patel KB, Cormier N, Fowler J, Partridge A, Theurer J, Black M, Pinto N, Yoo J, Fung K, MacNeil D, Stecho W, Howlett C, Brackstone M, Barrett JW, Nichols A. Detection of Circulating Tumor DNA in Patients with Thyroid Nodules. Int J Endocrinol 2021; 2021:8909224. [PMID: 34475951 PMCID: PMC8407979 DOI: 10.1155/2021/8909224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/17/2021] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE Detection of circulating tumor DNA (ctDNA) in cancer patients can potentially serve as a noninvasive, sensitive test of disease status. The purpose of this study was to determine the ability to detect BRAF (V600E) mutations in the plasma of patients with thyroid nodules, with the goal of distinguishing between benign and malignant nodules. METHODS Consecutive patients with thyroid nodules who consented for surgery were recruited. Plasma samples were obtained preoperatively and one month postoperatively. Quantitative PCR was used to determine the levels of the BRAF (V600E) mutation preoperatively and postoperatively. RESULTS A total of 109 patients were recruited. On final pathology, 38 (32.8%) patients had benign thyroid nodules, 45 (38.8%) had classical papillary thyroid cancer (PTC), 23 (19.8%) had nonclassical PTC, and 3 (2.6%) had follicular thyroid cancer. 15/109 patients had detectable BRAF (V600E) ctDNA in their preoperative samples-all of them having classical PTC. Higher T-stage and extrathyroidal extension in PTC were associated with positive BRAF (V600E) ctDNA (p < 0.05). Eighty-eight pairs of preoperative and postoperative plasma samples were collected and analyzed. Of these eighty-eight paired samples, a total of 13/88 (14.8%) patients had detectable BRAF (V600E) ctDNA in their preoperative samples-all of them having classical PTC. 12 of these 13 patients had no detectable BRAF (V600E) postoperatively, while one remaining patient had a significant decline in his levels (p < 0.05). CONCLUSION BRAF (V600E) circulating thyroid tumor DNA can be detected in plasma and is correlated with a final diagnosis of the classical variant of PTC. Given that a postoperative drop in BRAF (V600E) ctDNA levels was observed in all cases suggests its utility as a tumor marker.
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Affiliation(s)
- Krupal B. Patel
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Nicholas Cormier
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - James Fowler
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Allison Partridge
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Julie Theurer
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Morgan Black
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Nicole Pinto
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - John Yoo
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Kevin Fung
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Danielle MacNeil
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - William Stecho
- Department of Pathology, Western University, London, Ontario, Canada
| | | | | | - John W. Barrett
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Anthony Nichols
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, Ontario, Canada
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16
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The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes. Surgeon 2021; 20:e163-e173. [PMID: 34362650 DOI: 10.1016/j.surge.2021.06.006] [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: 01/06/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Liquid biopsy is gaining increasing clinical utility in the management of cancer patients. The main components of a liquid biopsy are circulating nucleic acids, circulating tumour cells and extracellular vesicles such as exosomes. Circulating nucleic acids including cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) in particular have been the focus of recent attention as they have demonstrated excellent potential in cancer screening, provision of prognostic information and in genomic profiling of a tumour without the need for repeated tissue biopsies. The aim of this review was to explore the current evidence in relation to the use of liquid biopsy in the perioperative setting and identify ways in which liquid biopsy may be applied in the future. METHODS This narrative review is based on a comprehensive literature search up to the 1st of June 2020 for papers relevant to the application of liquid biopsy in surgical oncology, focusing particularly on the perioperative period. RESULTS Recent evidence has demonstrated that perioperative liquid biopsy can accurately stratify patients' risk of recurrence compared to conventional biomarkers. Attention to the perioperative dynamics of liquid biopsy components can potentially provide new understanding of the complex relationship between surgery and cancer outcome. In addition, careful evaluation of liquid biopsy components in the perioperative window may provide important diagnostic and therapeutic information for cancer patients. CONCLUSION The rapidly evolving concept of the liquid biopsy has the potential to become the cornerstone for decision making around surveillance and adjuvant therapies the era of personalised medicine.
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17
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Zhang D, Fang C, Li H, Lu C, Huang J, Pan J, Yang Z, Liang E, Liu Z, Zhou X, Xin Z, Chen Y, Cai Q. Long ncRNA MALAT1 promotes cell proliferation, migration, and invasion in prostate cancer via sponging miR-145. Transl Androl Urol 2021; 10:2307-2319. [PMID: 34295718 PMCID: PMC8261405 DOI: 10.21037/tau-20-1526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/12/2021] [Indexed: 12/17/2022] Open
Abstract
Background The long non-coding (lncRNA) RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is known to promote tumorigenesis, whereas microRNA-145 (miR-145) plays an antitumor role in several cancers. In this study, we aimed to elucidate the role of MALAT1 and miR-145 in prostate cancer cells and investigate the effect of MALAT1 downregulation on prostate cancer (PCa) cells in vitro in vivo. Methods The Cancer Genome Atlas (TCGA) datasets were used to carry out the initial bioinformatics analysis; the findings were then tested in LNCaP and CWR22Rv1 cell lines. Western blot and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to evaluate the levels of MALAT1 and miR-145 along with related biomarkers. Furthermore, wound-healing and Transwell assays were performed to test the migratory and invasive abilities of PCa cells. Luciferase reporter assays were used to validate the relationship between MALAT1 and miR-145; their down-stream target genes were also studied. To further substantiate these findings in an animal model, tumor studies including immunofluorescence staining of tissues were carried in nude mice. Results The expression of MALAT1 was upregulated in both LNCaP cell lines and CWR22Rv1 cell lines (F=2.882, t=13.370, P<0.001; F=2.268, t=15.859, P<0.001). Knockdown of MALAT1 reduced the migratory and invasive capabilities of PCa cells (F=0.017, t=12.212, P<0.001; F=10.723, t=6.016, P=0.002). Using direct binding, MALAT1 suppressed the antitumor function of miR-145, which in turn upregulated transforming growth factor-β1 (TGF-β1)-induced epithelial-mesenchymal transition (EMT) via SMAD3 and TGFBR2 (F=2.097, t=5.389, P=0.006; F=1.306, t=4.155, P=0.014). Conclusions We confirmed that MALAT1 acts as a competing endogenous RNA (ceRNA) of miR-145. The MALAT1 based regulation of MiR-145-5p-SMAD3/TGFBR2 interactions could be an intriguing molecular pathway for the progression of PCa.
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Affiliation(s)
- Dingrong Zhang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Cheng Fang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Haibo Li
- Department of Urology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, China
| | - Chunyuan Lu
- Department of Anesthesia, the Second hospital of Tianjin Medical University, Tianjin, China
| | - Jiaohong Huang
- Department of Geriatric, the Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jiancheng Pan
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhizhao Yang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Enli Liang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhifei Liu
- Department of Urology, Tangshan People's Hospital, Tangshan, China
| | - Xiaodong Zhou
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhongcheng Xin
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.,Andrology Center, Peking University First Hospital, Peking University, Beijing, China
| | - Yegang Chen
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Qiliang Cai
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
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18
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Wang YF, Wang XJ, Lu Z, Liu SR, Jiang Y, Wan XQ, Cheng CC, Shi LH, Wang LH, Ding Y. Overexpression of Stat3 increases circulating cfDNA in breast cancer. Breast Cancer Res Treat 2021; 187:69-80. [PMID: 33630196 DOI: 10.1007/s10549-021-06142-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE Current studies on circulating cell-free DNA (cfDNA) have been focusing on its potential as biomarkers in liquid biopsy by detecting its content or genetic and epigenetic changes for the evaluation of tumor burden and therapeutic efficacy. However, the regulatory mechanism of cfDNA release remains unclear. Stat3 has been documented as an oncogene for the development and metastasis of breast cancer cells. In this study, we investigated whether Stat3 affects the release of cfDNA into blood and its association with the number of circulating tumor cells (CTCs). METHODS The cfDNA level in plasma of patients with breast cancer and healthy volunteers were determined by quantitative real-time PCR. Three mouse breast cancer models with different Stat3 expression were generated and used to established three breast cancer orthotopic animal models to examine the effect of Stat3 on cfDNA release in vivo. Stat3 mediated Epithelial-mesenchymal phenotype transition of CTCs was determined by immunofluorescence assay and Western blot assay. RESULTS The data showed that Stat3 increased circulating cfDNA, which is correlated with the increased volume of primary tumors and number of CTCs, accompanied with the dynamic EMT changes regulated by Snail induction. Furthermore, the high level of total circulating cfDNA and Stat3-cfDNA in patients with breast cancer were detected by quantitative real-time PCR using GAPDH and Stat3 primers. CONCLUSION Our results suggested that Stat3 increases the circulating cfDNA and CTCs in breast cancer.
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Affiliation(s)
- Yi-Fei Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xue-Jian Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Zhong Lu
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Shu-Rong Liu
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Yu Jiang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xiao-Qing Wan
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China
| | - Cong-Cong Cheng
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Li-Hong Shi
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Li-Hua Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Yi Ding
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China. .,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China.
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19
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Brancaccio M, Natale F, Falco G, Angrisano T. Cell-Free DNA Methylation: The New Frontiers of Pancreatic Cancer Biomarkers' Discovery. Genes (Basel) 2019; 11:E14. [PMID: 31877923 PMCID: PMC7017422 DOI: 10.3390/genes11010014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal cancer types world-wide. Its high mortality is related to the difficulty in the diagnosis, which often occurs when the disease is already advanced. As of today, no early diagnostic tests are available, while only a limited number of prognostic tests have reached clinical practice. The main reason is the lack of reliable biomarkers that are able to capture the early development or the progression of the disease. Hence, the discovery of biomarkers for early diagnosis or prognosis of PDAC remains, de facto, an unmet need. An increasing number of studies has shown that cell-free DNA (cfDNA) methylation analysis represents a promising non-invasive approach for the discovery of biomarkers with diagnostic or prognostic potential. In particular, cfDNA methylation could be utilized for the identification of disease-specific signatures in pre-neoplastic lesions or chronic pancreatitis (CP), representing a sensitive and non-invasive method of early diagnosis of PDAC. In this review, we will discuss the advantages and pitfalls of cfDNA methylation studies. Further, we will present the current advances in the discovery of pancreatic cancer biomarkers with early diagnostic or prognostic potential, focusing on pancreas-specific (e.g., CUX2 or REG1A) or abnormal (e.g., ADAMTS1 or BNC1) cfDNA methylation signatures in high risk pre-neoplastic conditions and PDAC.
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Affiliation(s)
- Mariarita Brancaccio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Francesco Natale
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Geppino Falco
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
- Biogem Scarl, Istituto di Ricerche Genetiche “Gaetano Salvatore”, Via Camporeale, 83031 Ariano Irpino, Italy
| | - Tiziana Angrisano
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
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20
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Merugu S, Chen L, Gavens E, Gabra H, Brougham M, Makin G, Ng A, Murphy D, Gabriel AS, Robinson ML, Wright JH, Burchill SA, Humphreys A, Bown N, Jamieson D, Tweddle DA. Detection of Circulating and Disseminated Neuroblastoma Cells Using the ImageStream Flow Cytometer for Use as Predictive and Pharmacodynamic Biomarkers. Clin Cancer Res 2019; 26:122-134. [DOI: 10.1158/1078-0432.ccr-19-0656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 08/13/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022]
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21
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Huang L, Bogale B, Tang Y, Lu S, Xie XS, Racowsky C. Noninvasive preimplantation genetic testing for aneuploidy in spent medium may be more reliable than trophectoderm biopsy. Proc Natl Acad Sci U S A 2019; 116:14105-14112. [PMID: 31235575 PMCID: PMC6628824 DOI: 10.1073/pnas.1907472116] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Preimplantation genetic testing for aneuploidy (PGT-A) with trophectoderm (TE) biopsy is widely applied in in vitro fertilization (IVF) to identify aneuploid embryos. However, potential safety concerns regarding biopsy and restrictions to only those embryos suitable for biopsy pose limitations. In addition, embryo mosaicism gives rise to false positives and false negatives in PGT-A because the inner cell mass (ICM) cells, which give rise to the fetus, are not tested. Here, we report a critical examination of the efficacy of noninvasive preimplantation genetic testing for aneuploidy (niPGT-A) in the spent culture media of human blastocysts by analyzing the cell-free DNA, which reflects ploidy of both the TE and ICM. Fifty-two frozen donated blastocysts with TE biopsy results were thawed; each of their spent culture medium was collected after 24-h culture and analyzed by next-generation sequencing (NGS). niPGT-A and TE-biopsy PGT-A results were compared with the sequencing results of the corresponding embryos, which were taken as true results for aneuploidy reporting. With removal of all corona-cumulus cells, the false-negative rate (FNR) for niPGT-A was found to be zero. By applying an appropriate threshold for mosaicism, both the positive predictive value (PPV) and specificity for niPGT-A were much higher than TE-biopsy PGT-A. Furthermore, the concordance rates for both embryo ploidy and chromosome copy numbers were higher for niPGT-A than TE-biopsy PGT-A. These results suggest that niPGT-A is less prone to errors associated with embryo mosaicism and is more reliable than TE-biopsy PGT-A.
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Affiliation(s)
- Lei Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Berhan Bogale
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Yaqiong Tang
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China
| | - Sijia Lu
- Department of Clinical Research, Yikon Genomics Company, Ltd., Shanghai 201499, China
| | - Xiaoliang Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138;
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China
| | - Catherine Racowsky
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115;
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22
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Chen M, Mithraprabhu S, Ramachandran M, Choi K, Khong T, Spencer A. Utility of Circulating Cell-Free RNA Analysis for the Characterization of Global Transcriptome Profiles of Multiple Myeloma Patients. Cancers (Basel) 2019; 11:cancers11060887. [PMID: 31242667 PMCID: PMC6628062 DOI: 10.3390/cancers11060887] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/12/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
In this study, we evaluated the utility of extracellular RNA (exRNA) derived from the plasma of multiple myeloma (MM) patients for whole transcriptome characterization. exRNA from 10 healthy controls (HC), five newly diagnosed (NDMM), and 12 relapsed and refractory (RRMM) MM patients were analyzed and compared. We showed that ~45% of the exRNA genes were protein-coding genes and ~85% of the identified genes were covered >70%. Compared to HC, we identified 632 differentially expressed genes (DEGs) in MM patients, of which 26 were common to NDMM and RRMM. We further identified 54 and 191 genes specific to NDMM and RRMM, respectively, and these included potential biomarkers such as LINC00863, MIR6754, CHRNE, ITPKA, and RGS18 in NDMM, and LINC00462, PPBP, RPL5, IER3, and MIR425 in RRMM, that were subsequently validated using droplet digital PCR. Moreover, single nucleotide polymorphisms and small indels were identified in the exRNA, including mucin family genes that demonstrated different rates of mutations between NDMM and RRMM. This is the first whole transcriptome study of exRNA in hematological malignancy and has provided the basis for the utilization of exRNA to enhance our understanding of the MM biology and to identify potential biomarkers relevant to the diagnosis and prognosis of MM patients.
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Affiliation(s)
- Maoshan Chen
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Malarmathy Ramachandran
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Kawa Choi
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Tiffany Khong
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Andrew Spencer
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
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23
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Clinical implications of circulating cell-free DNA quantification and metabolic tumor burden in advanced non-small cell lung cancer. Lung Cancer 2019; 134:158-166. [PMID: 31319975 DOI: 10.1016/j.lungcan.2019.06.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/10/2019] [Accepted: 06/12/2019] [Indexed: 01/05/2023]
Abstract
OBJECTIVES This study unravels the significance of cell-free DNA (cfDNA) quantification as a promising measure of the biological behavior/aggressiveness of tumors. Metabolic tumor volume (MTV) and total lesion glycolysis (TLG) measured by positron emission tomography/computed tomography scan enable a precise assessment of metabolic tumor burden. However, their clinical implications in identifying patients who need more aggressive treatment in advanced non-small cell lung cancer (NSCLC) are not fully understood. MATERIALS AND METHODS In the current prospective trial, we analyzed 101 newly diagnosed advanced NSCLC (stage III-IV) patients with measurable baseline MTV, TLG, and cfDNA quantification. The best cut-offs for cfDNA levels, MTV, and TLG to predict progression-free survival and overall survival were determined using X-tile analysis. RESULTS There were significant positive correlations between cfDNA and MTV (r = 0.488, p < 0.001) and between cfDNA and TLG (r = 0.554, p < 0.001). High-cfDNA levels and high-MTV/TLG negatively correlated with overall survival (OS) (all p < 0.001). Patients with high-MTV showed similar median OS irrespective of their cfDNA levels (low-cfDNA vs. high-cfDNA=9.2 vs 6.6 months; p > 0.05). However, patients with low-MTV and low-cfDNA levels showed longer OS than those with low-MTV and high-cfDNA levels (low-cfDNA vs. high-cfDNA=49.3 vs 11.5 months; p < 0.001). The patient group with low-TLG also showed similar trends. The cfDNA level was an independent prognostic factor for OS by Cox-proportional hazard analysis. CONCLUSION Although the patients with high metabolic tumor burden had a poor prognosis, regardless of the biological behavior/aggressiveness of the tumor, patients with low metabolic tumor burden and high cfDNA levels showed a poor prognosis. Taken together, this study indicates a stronger prognostic value of baseline cfDNA levels in identifying patients with advanced NSCLC and personalizing their treatment strategies for better survival.
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24
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Eissa MAL, Lerner L, Abdelfatah E, Shankar N, Canner JK, Hasan NM, Yaghoobi V, Huang B, Kerner Z, Takaesu F, Wolfgang C, Kwak R, Ruiz M, Tam M, Pisanic TR, Iacobuzio-Donahue CA, Hruban RH, He J, Wang TH, Wood LD, Sharma A, Ahuja N. Promoter methylation of ADAMTS1 and BNC1 as potential biomarkers for early detection of pancreatic cancer in blood. Clin Epigenetics 2019; 11:59. [PMID: 30953539 PMCID: PMC6451253 DOI: 10.1186/s13148-019-0650-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Despite improvements in cancer management, most pancreatic cancers are still diagnosed at an advanced stage. We have recently identified promoter DNA methylation of the genes ADAMTS1 and BNC1 as potential blood biomarkers of pancreas cancer. In this study, we validate this biomarker panel in peripheral cell-free tumor DNA of patients with pancreatic cancer. RESULTS Sensitivity and specificity for each gene are as follows: ADAMTS1 87.2% and 95.8% (AUC = 0.91; 95% CI 0.71-0.86) and BNC1 64.1% and 93.7% (AUC = 0.79; 95% CI 0.63-0.78). When using methylation of either gene as a combination panel, sensitivity increases to 97.3% and specificity to 91.6% (AUC = 0.95; 95% CI 0.77-0.90). Adding pre-operative CA 19-9 values to the combined two-gene methylation panel did not improve sensitivity. Methylation of ADAMTS1 was found to be positive in 87.5% (7/8) of stage I, 77.8% (7/9) of stage IIA, and 90% (18/20) of stage IIB disease. Similarly, BNC1 was positive in 62.5% (5/8) of stage I patients, 55.6% (5/9) of stage IIA, and 65% (13/20) of patients with stage IIB disease. The two-gene panel (ADAMTS1 and/or BNC1) was positive in 100% (8/8) of stage I, 88.9% (8/9) of stage IIA, and 100% (20/20) of stage IIB disease. The sensitivity and specificity of the two-gene panel for localized pancreatic cancer (stages I and II), where the cancer is eligible for surgical resection with curative potential, was 94.8% and 91.6% respectively. Additionally, the two-gene panel exhibited an AUC of 0.95 (95% CI 0.90-0.98) compared to 57.1% for CA 19-9 alone. CONCLUSION The methylation status of ADAMTS1 and BNC1 in cfDNA shows promise for detecting pancreatic cancer during the early stages when curative resection of the tumor is still possible. This minimally invasive blood-based biomarker panel could be used as a promising tool for diagnosis and screening in a select subset of high-risk populations.
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Affiliation(s)
- Maryam A L Eissa
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lane Lerner
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eihab Abdelfatah
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nakul Shankar
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph K Canner
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nesrin M Hasan
- Department of Surgery, Yale-New Haven Health, Yale University, School of Medicine, P.O. Box 208062, New Haven, CT, 06520-8062, USA
| | - Vesal Yaghoobi
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Barry Huang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zachary Kerner
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Felipe Takaesu
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher Wolfgang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruby Kwak
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Ruiz
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew Tam
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, MD, USA
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.,The Sol Goldman Pancreatic Cancer Research Center, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Jin He
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, MD, USA
| | - Laura D Wood
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.,The Sol Goldman Pancreatic Cancer Research Center, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Anup Sharma
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Surgery, Yale-New Haven Health, Yale University, School of Medicine, P.O. Box 208062, New Haven, CT, 06520-8062, USA
| | - Nita Ahuja
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,The Sol Goldman Pancreatic Cancer Research Center, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA. .,Department of Surgery, Yale-New Haven Health, Yale University, School of Medicine, P.O. Box 208062, New Haven, CT, 06520-8062, USA.
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25
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Bai H, Xia J, Zhao X, Gong Z, Zhang D, Xiong L. Detection of EGFR mutations using target capture sequencing in plasma of patients with non-small-cell lung cancer. J Clin Pathol 2019; 72:379-385. [PMID: 30787028 DOI: 10.1136/jclinpath-2019-205699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 01/06/2023]
Abstract
PURPOSE : Circulating tumour DNA (ctDNA) is a promising biomarker for detection of non-invasive epidermal growth factor receptor ( EGFR) mutations in patients with non-small-cell lung cancer (NSCLC). However, the existing methods have limitations in sensitivity or in availability. The aim was to evaluate the accuracy of capture target sequencing for detecting EGFR mutations in ctDNA. METHODS : A total of 79 patients with NSCLC and available plasma and matched tissue specimens were enrolled. Through capture target sequencing, mutations were searched in over 20 000 reads obtained from each exon region. Parameters corresponding to the limit of detection and limit of quantification were used as the thresholds for mutation detection. To evaluate the accuracy, detection of EGFR mutations in matched tissue samples was performed by target capture sequencing and the amplification refractory mutation system (ARMS). RESULTS: : EGFR mutations were discovered in 32.9 % (26/79) of the patients with NSCLC, the overall rate of consistency for the 79 paired plasma and tissue samples was 86.1 % (68/79). The sensitivity and specificity of detecting EGFR mutations in the plasma were 72.7 % and 95.7 %. In terms of the EGFR mutations identified by ARMS, the overall consistency was 78.5 % (62/79) in three groups. Of 21 patients with EGFR sensitive mutation defined by next generation sequencing in ctDNA, 20 (95.2%) showed long-term disease control with epidermal growth factor receptor tyrosine kinase inhibitor (EGFR TKI) treatment; the median progression-free survival was 10.8 months (95% CI 9.1 to 16.8). CONCLUSIONS: Target capture sequencing of ctDNA can be used for genotyping of EGFR in patients with NSCLC, which may enable a direct recommendation for EGFR TKI on the basis of positive results with plasma DNA.
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Affiliation(s)
- Hao Bai
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jingjing Xia
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaokai Zhao
- Shanghai Yunying Medical Technology Co, Shanghai, China
| | - Ziying Gong
- Shanghai Yunying Medical Technology Co, Shanghai, China
| | - Daoyun Zhang
- Shanghai Yunying Medical Technology Co, Shanghai, China
| | - Liwen Xiong
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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26
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Rohanizadegan M. Analysis of circulating tumor DNA in breast cancer as a diagnostic and prognostic biomarker. Cancer Genet 2018; 228-229:159-168. [PMID: 29572011 PMCID: PMC6108954 DOI: 10.1016/j.cancergen.2018.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
Despite all the advances in diagnosis and treatment of breast cancer, a large number of patients suffer from late diagnosis or recurrence of their disease. Current available imaging modalities do not reveal micrometastasis and tumor biopsy is an invasive method to detect early stage or recurrent cancer, signifying the need for an inexpensive, non-invasive diagnostic modality. Cell-free tumor DNA (ctDNA) has been tried for early detection and targeted therapy of breast cancer, but its diagnostic and prognostic utility is still under investigation. This review summarizes the existing evidence on the use of ctDNA specifically in breast cancer, including detection methods, diagnostic accuracy, role in genetics and epigenetics evaluation of the tumor, and comparison with other biomarkers. Current evidence suggests that increasing levels of ctDNA in breast cancer can be of significant diagnostic value for early detection of breast cancer although the sensitivity and specificity of the methods is still suboptimal. Additionally, ctDNA allows for characterizing the tumor in a non-invasive way and monitor the response to therapy, although discordance of ctDNA results with direct biopsy (i.e. due to tumor heterogeneity) is still considered a notable limitation.
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Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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27
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Niu Z, Tang W, Liu T, Xu P, Zhu D, Ji M, Huang W, Ren L, Wei Y, Xu J. Cell-free DNA derived from cancer cells facilitates tumor malignancy through Toll-like receptor 9 signaling-triggered interleukin-8 secretion in colorectal cancer. Acta Biochim Biophys Sin (Shanghai) 2018; 50:1007-1017. [PMID: 30239551 DOI: 10.1093/abbs/gmy104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Indexed: 12/20/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) has become a potential diagnostic and prognostic biomarker for colorectal cancer (CRC). In non-cancerous diseases, it has been confirmed that cfDNA can be recognized by Toll-like receptor 9 (TLR9), leading to a significant biological change. Nevertheless, the biological significance of cfDNA and its relationship with TLR9 in tumor malignancy is still unclear. Therefore, the purpose of this study is to explore the biological role of cfDNA in colorectal cancer (CRC). The expression of TLR9 was measured in different CRC cell lines and cancerous samples by RT-PCR or immunohistochemistry, which showed that high expression of TLR9 was significantly correlated with the tumor metastasis, advanced TNM stage and poor prognosis of patients. Then, cfDNA was obtained from fluorouracil (5FU)-induced apoptotic cancer cells in vitro and transfection techniques were used to transfect siRNA and cDNA plasmid for TLR9. Cancer cells were stimulated using isolated cfDNA fragments, and results showed that cfDNA could promote colorectal cancer cell proliferation via TLR9. Meanwhile, we demonstrated that the cfDNA binding to TLR9 could facilitate cell migration and invasion. Finally, we demonstrated that cfDNA initiated downstream TLR9-MyD88 signaling and induced robust release of chemokine interleukin 8 (IL-8), which helped to elucidate the mechanisms underlying these phenomena. Our data suggest that cancer cell-derived cfDNA contributes to cancer progression through activation of TLR9-MyD88 signaling and IL-8 secretion in CRC. These findings provide a novel perspective for understanding of tumor progression and provoke a potential therapeutic target for CRC treatment.
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Affiliation(s)
- Zhengchuan Niu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Wentao Tang
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Tianyu Liu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Pingping Xu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Meiling Ji
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Wenbai Huang
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Li Ren
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Ye Wei
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
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28
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Liu X, Chu KM. Molecular biomarkers for prognosis of gastrointestinal stromal tumor. Clin Transl Oncol 2018; 21:145-151. [PMID: 30003531 DOI: 10.1007/s12094-018-1914-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/25/2018] [Indexed: 12/13/2022]
Abstract
Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract. However, the development of molecular markers, especially circulating biomarkers, remains largely undone for the prognosis of GIST. We discussed the clinical-pathological characteristics of GIST and identified potential biomarkers for guidance of therapy and prognosis of GIST. Around 90% of GISTs contain mutations in KIT or PDGFRA and the remaining 10% of GISTs are wild-type. Recent studies have indicated that various DNAs and miRNAs could serve as potential biomarkers for prognosis of GIST, including KIT, PDGFRA, other DNAs (such as BRAF, SDH, SETD2 and ROR2), and microRNAs (miRNAs). The pressing need and challenges in the development of circulating prognostic biomarkers for GIST are also discussed. Although challenges remain, DNAs and miRNAs are promising circulating biomarkers for surveillance and prognosis of GIST. Advances in clarification of aberrant molecular alterations may open new avenues for exploration of reliable and robust biomarkers to improve the management of GIST.
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Affiliation(s)
- X Liu
- Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong.
| | - K-M Chu
- Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong. .,Department of Surgery, Queen Mary Hospital, Pokfulam, Hong Kong.
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29
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Abstract
Central nervous system (CNS) injuries, such as stroke, traumatic brain injury (TBI) and spinal cord injury (SCI), are important causes of death and long-term disability worldwide. MicroRNA (miRNA), small non-coding RNA molecules that negatively regulate gene expression, can serve as diagnostic biomarkers and are emerging as novel therapeutic targets for CNS injuries. MiRNA-based therapeutics include miRNA mimics and inhibitors (antagomiRs) to respectively decrease and increase the expression of target genes. In this review, we summarize current miRNA-based therapeutic applications in stroke, TBI and SCI. Administration methods, time windows and dosage for effective delivery of miRNA-based drugs into CNS are discussed. The underlying mechanisms of miRNA-based therapeutics are reviewed including oxidative stress, inflammation, apoptosis, blood-brain barrier protection, angiogenesis and neurogenesis. Pharmacological agents that protect against CNS injuries by targeting specific miRNAs are presented along with the challenges and therapeutic potential of miRNA-based therapies.
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Affiliation(s)
- Ping Sun
- Department of Neurology, Pittsburgh Institute of Brain Disorders & Recovery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Da Zhi Liu
- Department of Neurology and the M.I.N.D. Institute, University of California at Davis, Sacramento, CA, USA
| | - Glen C Jickling
- Department of Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Frank R Sharp
- Department of Neurology and the M.I.N.D. Institute, University of California at Davis, Sacramento, CA, USA
| | - Ke-Jie Yin
- Department of Neurology, Pittsburgh Institute of Brain Disorders & Recovery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Ke-Jie Yin, Department of Neurology, Pittsburgh Institute of Brain Disorders & Recovery, University of Pittsburgh School of Medicine, 200 Lothrop Street, BST S514, Pittsburgh, PA 15213, USA. Da Zhi Liu, Department of Neurology, University of California at Davis, Sacramento, CA 95817, USA.
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30
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Faria G, Silva E, Da Fonseca C, Quirico-Santos T. Circulating Cell-Free DNA as a Prognostic and Molecular Marker for Patients with Brain Tumors under Perillyl Alcohol-Based Therapy. Int J Mol Sci 2018; 19:ijms19061610. [PMID: 29848970 PMCID: PMC6032335 DOI: 10.3390/ijms19061610] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 12/28/2022] Open
Abstract
Tumor infiltration into brain tissue usually remains undetected even by high-resolution imaging. Molecular markers are used to increase diagnostic accuracy, but with limited continuous monitoring application. We evaluated the potential of circulating cell-free DNA (cfDNA) as a molecular indicator of the response to therapy by the intranasal administration (ITN) of perillyl alcohol (POH) in brain tumors. The cohort included 130 healthy subjects arranged as control-paired groups and patients at terminal stages with glioblastoma (GBM, n = 122) or brain metastasis (BM, n = 55) from stage IV adenocarcinomas. Serum cfDNA was isolated and quantified by fluorimetry. Compared with the controls (40 ng/mL), patients with brain tumors before ITN-POH treatment had increased (p < 0.0001) cfDNA median levels: GBM (286 ng/mL) and BM (588 ng/mL). ITN-POH treatment was significantly correlated (rho = −0.225; p = 0.024) with survival of >6 months at a concentration of 599 ± 221 ng/mL and of <6 months at 1626 ± 505 ng/mL, but a sharp and abrupt increase of cfDNA and tumor recurrence occurred after ITN-POH discontinuation. Patients under continuous ITN-POH treatment and checked with brain magnetic resonance imaging (MRI) compatible with complete response had cfDNA levels similar to the controls. cfDNA may be used as a noninvasive prognostic and molecular marker for POH-based therapy in brain tumors and as an accurate screening tool for the early detection of tumor progression.
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Affiliation(s)
- Giselle Faria
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro 24020-141, Brazil.
| | - Emanuelle Silva
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro 24020-141, Brazil.
| | - Clovis Da Fonseca
- Department of Specialized Medicine, School of Medicine, Fluminense Federal University, Niteroi, Rio de Janeiro 24020-141, Brazil.
| | - Thereza Quirico-Santos
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro 24020-141, Brazil.
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31
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Tadimety A, Closson A, Li C, Yi S, Shen T, Zhang JXJ. Advances in liquid biopsy on-chip for cancer management: Technologies, biomarkers, and clinical analysis. Crit Rev Clin Lab Sci 2018; 55:140-162. [PMID: 29388456 PMCID: PMC6101655 DOI: 10.1080/10408363.2018.1425976] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Liquid biopsy, as a minimally invasive method of gleaning insight into the dynamics of diseases through a patient fluid sample, has been growing in popularity for cancer diagnosis, prognosis, and monitoring. While many technologies have been developed and validated in research laboratories, there has also been a push to expand these technologies into other clinical settings and as point of care devices. In this article, we discuss and evaluate microchip-based technologies for circulating tumor cell (CTC), exosome, and circulating tumor nucleic acid (ctNA) capture, detection, and analysis. Such integrated systems streamline otherwise multiple-step, manual operations to get a sample-to-answer quantitation. In addition, analysis of disease biomarkers is suited to point of care settings because of ease of use, low consumption of sample and reagents, and high throughput. We also cover the basics of biomarkers and their detection in biological fluid samples suitable for liquid biopsy on-chip. We focus on emerging technologies that process a small patient sample with high spatial-temporal resolution and derive clinically meaningful results through on-chip biomarker sensing and downstream molecular analysis in a simple workflow. This critical review is meant as a resource for those interested in developing technologies for capture, detection, and analysis platforms for liquid biopsy in a variety of settings.
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Affiliation(s)
- Amogha Tadimety
- a Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
| | - Andrew Closson
- a Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
| | - Cathy Li
- a Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
| | - Song Yi
- b Nanolite Systems , Austin , TX , USA
| | - Ting Shen
- b Nanolite Systems , Austin , TX , USA
| | - John X J Zhang
- a Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
- c Dartmouth-Hitchcock Medical Center , Lebanon , NH , USA
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32
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Abstract
Cyclin B2 (CCNB2), a member of the cyclin protein family, has been found to be up-regulated in human cancers. To evaluate the potential use of circulating CCNB2 in serum in cancer surveillance, we examined relative expression levels of serum circulating CCNB2 mRNA in 103 cancer patients, 19 normal controls, and 40 benign disease patients using real-time quantitative reverse transcriptase polymerase chain reaction. We found that the relative expression level of circulating CCNB2 mRNA in cancer patients was significantly higher (p<0.0001) than that in normal controls and benign diseases group. Circulating CCNB2 mRNA level was significantly (p<0.001) correlated with cancer stage and metastasis status. Receiver operating characteristic (ROC) analysis showed an area under the curve (AUC) of 0.87 and 0.83 (p<0.05) in identifying cancer patients' metastasis status in lung and digestive tract cancer, respectively. Moreover, we observed that expression levels of circulating CCNB2 mRNA in cancer patients significantly decreased (p=0.0084) after their therapeutic treatments. These data suggest that detection of serum circulating CCNB2 mRNA may have potential clinical applications in screening and monitoring of metastasis and therapeutic treatments.
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33
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Kim WT, Jeong P, Yan C, Kim YH, Lee IS, Kang HW, Kim YJ, Lee SC, Kim SJ, Kim YT, Moon SK, Choi YH, Kim IY, Yun SJ, Kim WJ. UBE2C cell-free RNA in urine can discriminate between bladder cancer and hematuria. Oncotarget 2018; 7:58193-58202. [PMID: 27528424 PMCID: PMC5295424 DOI: 10.18632/oncotarget.11277] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 08/08/2016] [Indexed: 02/06/2023] Open
Abstract
Background There is growing interest in circulating nucleic acids as cancer detection biomarkers. Therefore, the aim of the present study was to identify a key urinary cell-free RNA marker that may assist in the diagnosis of BC. Results Five cell-free RNAs were selected as candidate cell-free RNAs from tissue microarray data. An area under the curve (AUC) cut-off value of 0.7 in receiver operating characteristic (ROC) curve analysis identified four urinary cell-free RNAs for further analysis (CDC20, ESM1, UBE2C, and CA9; AUC = 0.716, 0.704, 0.721, and 0.702, respectively). Binary logistic regression analysis revealed that high expression of UBE2C was significantly associated with BC (OR, 1.754; CI, 1.147–2.682; p = 0.010). Analysis of UBE2C expression in urine samples from BC patients and hematuria controls yielded an AUC of 0.839, with a sensitivity of 82.5% and a specificity of 76.2%. UBE2C levels was significantly increased in G2 and G3 tumors compared to normal controls (p <0.001, respectively). Materials and Methods Urine samples from 212 BC patients and 106 normal controls (64 healthy individuals and 42 with hematuria) were examined. The candidate cell-free RNAs identified from tissue microarrays derived from BC and normal control tissues was then measured in the urine samples. Conclusions The levels of urinary UBE2C cell-free RNA were significantly higher in BC samples than in normal and hematuria control samples. The higher levels of urinary UBE2C cell-free RNA in BC might reflect high expression in BC tissues. Therefore, urinary UBE2C cell-free RNA may be a valuable diagnostic marker for BC.
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Affiliation(s)
- Won Tae Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Pildu Jeong
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Chunri Yan
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Ye Hwan Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Il-Seok Lee
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Ho-Won Kang
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Yong-June Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Sang-Cheol Lee
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Sang Jin Kim
- Department of Urology, Myongji Hospital, Seonam University College of Medicine, Goyang, South Korea.,Department of Urology, Graduate School of Medicine, Hanyang University, Seoul, South Korea
| | - Yong Tae Kim
- Department of Urology, Graduate School of Medicine, Hanyang University, Seoul, South Korea
| | - Sung-Kwon Moon
- School of Food Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Yung-Hyun Choi
- Department of Biochemistry, Dongeui University College of Oriental Medicine, Busan, South Korea
| | - Isaac Yi Kim
- Section of Urological Oncology, The Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Seok Joong Yun
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
| | - Wun-Jae Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Chungbuk, South Korea
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La Barbera G, Capriotti AL, Cavaliere C, Ferraris F, Laus M, Piovesana S, Sparnacci K, Laganà A. Development of an enrichment method for endogenous phosphopeptide characterization in human serum. Anal Bioanal Chem 2018; 410:1177-1185. [DOI: 10.1007/s00216-017-0822-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/05/2017] [Accepted: 12/08/2017] [Indexed: 12/15/2022]
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35
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Chernikov AV, Gudkov SV, Usacheva AM, Bruskov VI. Exogenous 8-oxo-7,8-dihydro-2′-deoxyguanosine: Biomedical properties, mechanisms of action, and therapeutic potential. BIOCHEMISTRY (MOSCOW) 2018. [DOI: 10.1134/s0006297917130089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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36
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Strotman LN, Millner LM, Valdes R, Linder MW. Liquid Biopsies in Oncology and the Current Regulatory Landscape. Mol Diagn Ther 2017; 20:429-36. [PMID: 27324559 DOI: 10.1007/s40291-016-0220-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is a profound need in oncology to detect cancer earlier, guide individualized therapies, and better monitor progress during treatment. Currently, some of this information can be achieved through solid tissue biopsy and imaging. However, these techniques are limited because of the invasiveness of the procedure and the size of the tumor. A liquid biopsy can overcome these barriers as its non-invasive nature allows samples to be collected over time. Liquid biopsies may also allow earlier detection than traditional imaging. Liquid biopsies include the analysis of circulating tumor cells (CTCs), cell-free nucleic acid (cfNA), or extracellular vesicles obtained from a variety of biofluids, such as peripheral blood. In this review, we discuss different liquid biopsy types and how they fit into the current regulatory landscape.
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Affiliation(s)
- Lindsay N Strotman
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Louisville, 511 South Floyd Street, MDR 221, Louisville, KY, 40202, USA
- PGXL Technologies, 201 E. Floyd St., Suite 306, Louisville, KY, USA
| | - Lori M Millner
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Louisville, 511 South Floyd Street, MDR 221, Louisville, KY, 40202, USA
- PGXL Technologies, 201 E. Floyd St., Suite 306, Louisville, KY, USA
| | - Roland Valdes
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Louisville, 511 South Floyd Street, MDR 221, Louisville, KY, 40202, USA
- PGXL Technologies, 201 E. Floyd St., Suite 306, Louisville, KY, USA
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Louisville, 511 South Floyd Street, MDR 221, Louisville, KY, 40202, USA.
- PGXL Technologies, 201 E. Floyd St., Suite 306, Louisville, KY, USA.
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37
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Massively Parallel Sequencing (MPS) of Cell-Free Fetal DNA (cffDNA)
for Trisomies 21, 18, and 13 in Twin Pregnancies. Twin Res Hum Genet 2017; 20:242-249. [DOI: 10.1017/thg.2017.23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Massively parallel sequencing (MPS) technology has become increasingly available
and has been widely used to screen for trisomies 21, 18, and 13 in singleton
pregnancies. This study assessed the performance of MPS testing of cell-free
fetal DNA (cffDNA) from maternal plasma for trisomies 21, 18, and 13 in twin
pregnancies. Ninety-two women with twin pregnancies were recruited. The results
were identified through karyotypes of amniocentesis or clinical examination and
follow-up of the neonates. Fluorescent in-situ hybridization was used to examine
the placentas postnatally in cases of false-positive results. The fetuses with
autosomal trisomy 21 (n = 2) and trisomy 15 (n
= 1) were successfully detected via MPS testing of cffDNA. There was one
false-positive for trisomy 13 (n = 1), and fluorescence in-situ
hybridization (FISH) identified confined placental mosaicism in this case. For
twin pregnancies undergoing second-trimester screening for trisomy, MPS testing
of cffDNA is feasible and can enhance the diagnostic spectrum of non-invasive
prenatal testing, which could effectively reduce invasive prenatal diagnostic
methods. In addition to screening for trisomy 21, 18, and 13 by cffDNA, MPS can
detect fetal additional autosomal trisomy. False-positive results cannot
completely exclude confined placental mosaicism.
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38
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Lee H, Park YM, We YM, Han DJ, Seo JW, Moon H, Lee YH, Kim YG, Moon JY, Lee SH, Lee JK. Evaluation of Digital PCR as a Technique for Monitoring Acute Rejection in Kidney Transplantation. Genomics Inform 2017; 15:2-10. [PMID: 28416944 PMCID: PMC5389945 DOI: 10.5808/gi.2017.15.1.2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
Early detection and proper management of kidney rejection are crucial for the long-term health of a transplant recipient. Recipients are normally monitored by serum creatinine measurement and sometimes with graft biopsies. Donor-derived cell-free deoxyribonucleic acid (cfDNA) in the recipient's plasma and/or urine may be a better indicator of acute rejection. We evaluated digital PCR (dPCR) as a system for monitoring graft status using single nucleotide polymorphism (SNP)-based detection of donor DNA in plasma or urine. We compared the detection abilities of the QX200, RainDrop, and QuantStudio 3D dPCR systems. The QX200 was the most accurate and sensitive. Plasma and/or urine samples were isolated from 34 kidney recipients at multiple time points after transplantation, and analyzed by dPCR using the QX200. We found that donor DNA was almost undetectable in plasma DNA samples, whereas a high percentage of donor DNA was measured in urine DNA samples, indicating that urine is a good source of cfDNA for patient monitoring. We found that at least 24% of the highly polymorphic SNPs used to identify individuals could also identify donor cfDNA in transplant patient samples. Our results further showed that autosomal, sex-specific, and mitochondrial SNPs were suitable markers for identifying donor cfDNA. Finally, we found that donor-derived cfDNA measurement by dPCR was not sufficient to predict a patient's clinical condition. Our results indicate that donor-derived cfDNA is not an accurate predictor of kidney status in kidney transplant patients.
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Affiliation(s)
- Hyeseon Lee
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Young-Mi Park
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Yu-Mee We
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Duck Jong Han
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Jung-Woo Seo
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Korea
| | - Haena Moon
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Korea
| | - Yu-Ho Lee
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Korea
| | - Yang-Gyun Kim
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Korea
| | - Ju-Young Moon
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Korea
| | - Sang-Ho Lee
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Korea
| | - Jong-Keuk Lee
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul 05505, Korea
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Thierry AR, El Messaoudi S, Gahan PB, Anker P, Stroun M. Origins, structures, and functions of circulating DNA in oncology. Cancer Metastasis Rev 2017; 35:347-76. [PMID: 27392603 PMCID: PMC5035665 DOI: 10.1007/s10555-016-9629-x] [Citation(s) in RCA: 532] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While various clinical applications especially in oncology are now in progress such as diagnosis, prognosis, therapy monitoring, or patient follow-up, the determination of structural characteristics of cell-free circulating DNA (cirDNA) are still being researched. Nevertheless, some specific structures have been identified and cirDNA has been shown to be composed of many “kinds.” This structural description goes hand-in-hand with the mechanisms of its origins such as apoptosis, necrosis, active release, phagocytosis, and exocytose. There are multiple structural forms of cirDNA depending upon the mechanism of release: particulate structures (exosomes, microparticles, apoptotic bodies) or macromolecular structures (nucleosomes, virtosomes/proteolipidonucleic acid complexes, DNA traps, links with serum proteins or to the cell-free membrane parts). In addition, cirDNA concerns both nuclear and/or mitochondrial DNA with both species exhibiting different structural characteristics that potentially reveal different forms of biological stability or diagnostic significance. This review focuses on the origins, structures and functional aspects that are paradoxically less well described in the literature while numerous reviews are directed to the clinical application of cirDNA. Differentiation of the various structures and better knowledge of the fate of cirDNA would considerably expand the diagnostic power of cirDNA analysis especially with regard to the patient follow-up enlarging the scope of personalized medicine. A better understanding of the subsequent fate of cirDNA would also help in deciphering its functional aspects such as their capacity for either genometastasis or their pro-inflammatory and immunological effects.
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Affiliation(s)
- A R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France.
| | - S El Messaoudi
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France
| | - P B Gahan
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France
| | - P Anker
- , 135 route des fruitières, 74160, Beaumont, France
| | - M Stroun
- , 6 Pedro-meylan, 1208, Geneva, Switzerland
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles. Cell Mol Life Sci 2016; 73:4355-4381. [PMID: 27652382 PMCID: PMC11108302 DOI: 10.1007/s00018-016-2370-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/20/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.
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Affiliation(s)
- Janine Aucamp
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
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Konstantinov YM, Dietrich A, Weber-Lotfi F, Ibrahim N, Klimenko ES, Tarasenko VI, Bolotova TA, Koulintchenko MV. DNA import into mitochondria. BIOCHEMISTRY (MOSCOW) 2016; 81:1044-1056. [DOI: 10.1134/s0006297916100035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Staniszewska-Slezak E, Mateuszuk L, Chlopicki S, Baranska M, Malek K. Alterations in plasma biochemical composition in NO deficiency induced by L-NAME in mice analysed by Fourier Transform Infrared Spectroscopy. JOURNAL OF BIOPHOTONICS 2016; 9:1098-1108. [PMID: 27440215 DOI: 10.1002/jbio.201600141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Mouse model of nitric oxide deficiency, induced by prolonged treatment with NG -nitro-L-arginine methyl ester (L-NAME) was used for infrared spectroscopy (FTIR) analysis of plasma. L-NAME leads to increased peripheral resistance and systemic hypertension. Classification of spectral response was by principal component analysis (PCA) and linear discriminant analysis (LDA). PCA allowed to separate each animal group showing that FTIR spectra are sensitive to development of NO-deficiency on contrary to blood pressure values indicating hypertension. Globally, the most pronounced spectral alternations were observed in the second and third week of L-NAME treatment indicating that infrared signature of blood plasma can serve as indicator of early and late stages of the disease. The PLS-DA method provided >95% classification accuracy. Spectral features characteristic for L-NAME treatment were mainly associated with an elevated level of proteins accompanied by a decrease of a tyrosine content and changes in lipids/phospholipid concentration. In our work we discuss these changes for which statistically significant differences (p < 0.05 - 0.005) were observed between spectra collected for each time-point of the L-NAME treatment versus control subjects. We demonstrated for the first time that NO-deficiency and hypertension resulted in changes in biochemical profile of plasma that was detected by FTIR spectroscopy.
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Affiliation(s)
- Emilia Staniszewska-Slezak
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Lukasz Mateuszuk
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348, Krakow, Poland
- Department of Experimental Pharmacology (Chair of Pharmacology), Jagiellonian University, Grzegorzecka 16, Krakow, 31-531, Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Kamilla Malek
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland.
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348, Krakow, Poland.
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Malentacchi F, Pizzamiglio S, Verderio P, Pazzagli M, Orlando C, Ciniselli CM, Günther K, Gelmini S. Influence of storage conditions and extraction methods on the quantity and quality of circulating cell-free DNA (ccfDNA): the SPIDIA-DNAplas External Quality Assessment experience. Clin Chem Lab Med 2016; 53:1935-42. [PMID: 25883202 DOI: 10.1515/cclm-2014-1161] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/19/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Circulating cell-free DNA (ccfDNA) has been confirmed as a useful biomarker in cancer and pre-natal clinical practice. One of the main critical points in using ccfDNA is a lack of standardisation for sample processing methods, storage conditions, procedures for extraction, and quantification that can affect ccfDNA quality and quantity. We report the results obtained from the SPIDIA-DNAplas, one of the EU SPIDIA (Standardisation and improvement of generic pre-analytical tools and procedures for in vitro diagnostics) subprojects based on the implementation of an External Quality Assessment scheme for the evaluation of the influence of the pre-analytical phase on ccfDNA. This is the first reported quality control scheme targeting ccfDNA for pre-analytical phase studies. METHODS Fifty-six laboratories throughout Europe were recruited. The participating laboratories received the same plasma sample and extracted ccfDNA by using their own procedures, at defined plasma storage conditions, and sent the isolated ccfDNA to the SPIDIA facility for analyses. Laboratory performance was evaluated by using specific quality parameters such as ccfDNA integrity (by multiplex PCR) and yield (by qPCR). RESULTS The analysis of the ccfDNA extracted by the laboratories showed that most of them (53 of 56) were able to recover ccfDNA but only 12.5% recovered non-fragmented ccfDNA. Extraction methods specifically designed for ccfDNA preserved the integrity profile. CONCLUSIONS The evidence-based results of the SPIDIA-DNAplas EQA have been proposed as a basis for the development of a Technical Specification by the European Committee for standardisation (CEN).
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Sanosyan A, Rutagwera DG, Molès JP, Bollore K, Peries M, Kankasa C, Mwiya M, Tylleskär T, Nagot N, Van De Perre P, Tuaillon E. Increased Epstein-Barr virus in breast milk occurs with subclinical mastitis and HIV shedding. Medicine (Baltimore) 2016; 95:e4005. [PMID: 27399077 PMCID: PMC5058806 DOI: 10.1097/md.0000000000004005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Epstein-Barr virus (EBV) in breast milk and subclinical mastitis (SCM) are both associated with human immunodeficiency virus (HIV) shedding and possibly with postnatal HIV transmission. The objective of this nested case-control study was to investigate the interplay between SCM and EBV replication in breast milk of HIV-infected mothers.The relationships between EBV deoxyribonucleic acid (DNA) shedding, HIV-1 ribonucleic acid (RNA) level, and SCM were explored in breast milk samples of Zambian mothers participating in the ANRS 12174 trial. Mammary gland inflammation was defined as a breast milk sodium to potassium ratio (Na/K) greater than 0.6 and further subclassified as either "possible SCM" (Na/K ratio 0.6-1.0) or SCM (Na/K ratio ≥ 1.0). Breast milk interleukin 8 (IL-8) was measured as a surrogate marker of mammary gland inflammation.EBV DNA was detected in breast milk samples from 42 out of 83 (51%) participants and was associated with HIV-1 shedding in breast milk (P = 0.006). EBV DNA levels were higher in samples with SCM and "possible SCM" compared to non-SCM breast milk samples (P = 0.06; P = 0.007). An EBV DNA level of >200 copies/mL was independently associated with SCM and "possible SCM" (OR: 2.62; 95%: 1.13-6.10). In patients with SCM, higher EBV replication in the mammary gland was associated with a lower induction of IL-8 (P = 0.013). Resistance to DNase treatment suggests that EBV DNA in lactoserum is encapsidated.SCM and decreased IL-8 responses are associated with an increased EBV shedding in breast milk which may in turn facilitate HIV replication in the mammary gland.
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Affiliation(s)
- Armen Sanosyan
- UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
| | - David G. Rutagwera
- UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
- Centre for International Health, University of Bergen, Bergen, Norway
- Department of Paediatrics and Child health, University Teaching Hospital, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Jean-Pierre Molès
- UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
| | - Karine Bollore
- UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
| | - Marianne Peries
- UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
| | - Chipepo Kankasa
- Department of Paediatrics and Child health, University Teaching Hospital, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Mwiya Mwiya
- Department of Paediatrics and Child health, University Teaching Hospital, School of Medicine, University of Zambia, Lusaka, Zambia
| | | | - Nicolas Nagot
- UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
- CHU Montpellier, Montpellier, France
| | - Philippe Van De Perre
- UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
- CHU Montpellier, Montpellier, France
| | - Edouard Tuaillon
- UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
- CHU Montpellier, Montpellier, France
- Correspondence: Edouard Tuaillon, CHU Montpellier and UMR 1058, INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France (e-mail: )
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Yan C, Kim YH, Kang HW, Seo SP, Jeong P, Lee IS, Kim D, Kim JM, Choi YH, Moon SK, Yun SJ, Kim WJ. Urinary Nucleic Acid TSPAN13-to-S100A9 Ratio as a Diagnostic Marker in Prostate Cancer. J Korean Med Sci 2015; 30:1784-92. [PMID: 26713053 PMCID: PMC4689822 DOI: 10.3346/jkms.2015.30.12.1784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/02/2015] [Indexed: 12/11/2022] Open
Abstract
The potential use of urinary nucleic acids as diagnostic markers in prostate cancer (PCa) was evaluated. Ninety-five urine samples and 234 prostate tissue samples from patients with PCa and benign prostatic hyperplasia (BPH) were analyzed. Micro-array analysis was used to identify candidate genes, which were verified by the two-gene expression ratio and validated in tissue mRNA and urinary nucleic acid cohorts. Real-time quantitative polymerase chain reaction (qPCR) was used to measure urinary nucleic acid levels and tissue mRNA expression. The TSPAN13-to-S100A9 ratio was selected to determine the diagnostic value of urinary nucleic acids in PCa (P = 0.037) and shown to be significantly higher in PCa than in BPH in the mRNA and nucleic acid cohort analyses (P < 0.001 and P = 0.013, respectively). Receiver operating characteristic (ROC) analysis showed that the area under the ROC curve was 0.898 and 0.676 in tissue mRNA cohort and urinary nucleic acid cohort, respectively. The TSPAN13-to-S100A9 ratio showed a strong potential as a diagnostic marker for PCa. The present results suggest that the analysis of urine supernatant can be used as a simple diagnostic method for PCa that can be adapted to the clinical setting in the future.
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Affiliation(s)
- Chunri Yan
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Ye-Hwan Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Ho Won Kang
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Sung Phil Seo
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Pildu Jeong
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | | | - Dongho Kim
- Bio-Medical Science Co. Ltd, Daejeon, Korea
| | - Jung Min Kim
- Nucleic Acid Research Center, Inc., Daejeon Oriental Hospital of Daejeon University, Daejeon, Korea
| | - Yung Hyun Choi
- Department of Biochemistry, Dong-Eui University, Busan, Korea
| | - Sung-Kwon Moon
- Department of Food and Biotechnology, Chung-Ang University, Seoul, Korea
| | - Seok Joong Yun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Wun-Jae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
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Liu X, Kwong A, Sihoe A, Chu KM. Plasma miR-940 may serve as a novel biomarker for gastric cancer. Tumour Biol 2015; 37:3589-97. [PMID: 26456959 DOI: 10.1007/s13277-015-4019-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/19/2015] [Indexed: 02/07/2023] Open
Abstract
It was reported that circulating microRNAs could be applied as non-invasive biomarkers for cancer monitoring. The purpose of this study was to identify plasma miRNA that may serve as a novel biomarker for gastric cancer and to evaluate its clinical application. MicroRNA profiles were generated from plasma samples of 5 patients with gastric cancer (GC) versus 5 healthy controls (HC). MicroRNA-940 (miR-940) was one of the most downregulated miRNAs with fold change of 0.164. It was revealed that the expression of miR-940 was downregulated in both the initial set (N = 30, P < 0.0001) and the validation set (N = 80, P < 0.0001) of plasma samples of patients with gastric cancer. The sensitivity was obviously higher than the current biomarkers CEA and CA19-9 (81.25 % vs. 22.54 % and 15.71 %). MiR-940 was also significantly downregulated in gastric cancer tissue samples (N = 34, P = 0.0015), as well as in cancer cell lines (N = 7). Importantly, miR-940 was significantly highly expressed in stomach tissue samples than in other types of tissue samples including the liver, breast, thyroid, and lung. Moreover, there was a trend of lower expression of miR-940 from early to advanced stage of gastric cancer. Target prediction suggested that miR-940 regulated cell signaling including NF-κB and Wnt/β-catenin, as well as pathways of cell communication and adhesion. These pathways play critical roles in gastric cancer initiation and progression. It is the first report that miR-940 may mainly express in the stomach. Downregulation of plasma miR-940 may serve as a novel biomarker for detection of gastric cancer.
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Affiliation(s)
- Xin Liu
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Ava Kwong
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alan Sihoe
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Kent-Man Chu
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong.
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Yun SJ, Yan C, Jeong P, Kang HW, Kim YH, Kim EA, Lee OJ, Kim WT, Moon SK, Kim IY, Choi YH, Kim WJ. Comparison of mRNA, Protein, and Urinary Nucleic Acid Levels of S100A8 and S100A9 between Prostate Cancer and BPH. Ann Surg Oncol 2014; 22:2439-45. [PMID: 25348783 DOI: 10.1245/s10434-014-4194-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND Infections and inflammation in the prostate play a critical role in carcinogenesis, and S100A8 and S100A9 are key mediators in acute and chronic inflammation. Therefore, we investigated the differences of S100A8/A9 expression between prostate cancer (CaP) and benign prostatic hyperplasia (BPH) tissues, and we evaluated the possibilities of urinary nucleic acids of S100A8/A9 as diagnostic and prognostic markers. METHODS Tissues from 132 CaP patients who underwent prostatectomy or transurethral resection and 90 BPH patients who underwent transurethral prostatectomy were assessed.sd In addition, S100A8 and S100A9 nucleic acid levels were measured in the urine of 283 CaP patients and 363 BPH controls. RESULTS S100A8 and S100A9 mRNA levels were lower in CaP than BPH tissues (P < 0.001). S100A8 and S100A9 expression was increased in cancer tissues with poorer prognosis. In 69 specimens from prostatectomy patients, S100A8/A9 were the independent predictor of biochemical recurrence (hazard ratio 5.22, 95 % confidence interval 1.800-15.155, P = 0.002). Immunohistochemical staining revealed that BPH tissues stained more strongly for both S100A8 and S100A9 than CaP tissues (P < 0.001). S100A8 and S100A9 urinary nucleic acid levels were lower in CaP than in BPH (P = 0.001 and <0.001, respectively). CONCLUSIONS S100A8/A9 levels are lower in CaP than in BPH. Both were more highly expressed in patients with aggressive disease and shorter biochemical recurrence-free time. S100A8/A9 urinary cell-free nucleic acid levels correlated positively with expression levels obtained from tissue staining. Therefore, S100A8/A9 measurement in tissues and urine may have diagnostic and prognostic value in CaP.
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Affiliation(s)
- Seok Joong Yun
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
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Siravegna G, Bardelli A. Genotyping cell-free tumor DNA in the blood to detect residual disease and drug resistance. Genome Biol 2014; 15:449. [PMID: 25222559 PMCID: PMC4281953 DOI: 10.1186/s13059-014-0449-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DNA fragments released from cancer cells into the blood can be used to generate molecular profiles of tumors. Non-invasive 'liquid biopsies' can be used to monitor minimal residual disease and detect the emergence of drug resistance.
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Gao T, He B, Pan Y, Xu Y, Li R, Deng Q, Sun H, Wang S. Long non-coding RNA 91H contributes to the occurrence and progression of esophageal squamous cell carcinoma by inhibiting IGF2 expression. Mol Carcinog 2014; 54:359-67. [PMID: 24706416 DOI: 10.1002/mc.22106] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/14/2013] [Accepted: 10/23/2013] [Indexed: 12/16/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been recently recognized as a major class of regulators in mammalian systems. 91H, a novel long noncoding antisense transcripts located on the position of the H19/IGF2 locus has been suggested to play a potential tumor-suppressor role in tumor development. However, little study has proved the mechanism in esophageal squamous cell carcinoma (ESCC). We carried out this study to explore the role of lncRNA 91H in the regulation of H19 imprinting control regions (ICR) and IGF2 expression and the association between 91H and ESCC progression. The cell line TE-1, Eca-109, and 232 ESCC patients' matched sets of paraffin-embedded adjacent normal and tumor samples were obtained in this study. The results showed that 91H expression was significantly lower in patients with higher depth of invasion, neoplastic grading and TNM which usually leads to the overexpression of IGF2 in tumor progression. The expression of 91H usually decreased in TE-1 and Eca-109 when treated with demethylation agent. Further analysis revealed that, in 91H knockdown cell lines, IGF2 expression was also significantly higher than negative controls. Therefore, the results demonstrated that the lncRNA 91H was associated with H19 ICR methylation and inhibited IGF2 expression of ESCC patients which may optimize the mechanism of IGF2 regulation in tumor development. Patients with higher depth of invasion, neoplastic grading and TNM usually demonstrated lower 91H expression potentially represent a novel clinically relevant event to identify individuals at increased risk for the occurrence, progression and prognosis of ESCC.
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Affiliation(s)
- Tianyi Gao
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
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Kuo YB, Chen JS, Fan CW, Li YS, Chan EC. Comparison of KRAS mutation analysis of primary tumors and matched circulating cell-free DNA in plasmas of patients with colorectal cancer. Clin Chim Acta 2014; 433:284-9. [PMID: 24685572 DOI: 10.1016/j.cca.2014.03.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/24/2014] [Accepted: 03/19/2014] [Indexed: 01/04/2023]
Abstract
Colorectal cancer (CRC) patients with KRAS mutations do not benefit from epidermal growth factor receptor (EGFR) targeted therapy. In clinical practice, identifying patients with KRAS mutations is critical prior to EGFR targeting therapy, and gene testing is generally performed using the DNA extracted from tumor tissue. The aim of this study was to compare the presence of KRAS mutations in circulating cell-free DNA (cfDNA) and primary tumor tissue using a peptide nucleic acid mediated polymerase chain reaction. We extracted and analyzed the DNA from plasmas and corresponding primary tumor samples from 52 patients with CRC. The results demonstrated that the detection rate of KRAS sequence variations was 50% (26 of 52) in plasma samples and 28.8% (15 of 52) in resected primary tumor tissue samples. The majority of KRAS mutations detected in tumors were also found in matched plasma specimens with an agreement rate of 78.8%. Eleven plasma cfDNA were found positive for KRAS mutation but not in their corresponding tissue. In conclusion, our results suggest that circulating cfDNA provides a better representation of the malignant disease as a whole and could be a reliable source of diagnostic DNA to replace the tumor tissue in a diagnostic setting.
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Affiliation(s)
- Yung-Bin Kuo
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Jinn-Shiun Chen
- Colorectal Section, Department of Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Wei Fan
- Department of Colorectal Surgery, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Yi-Shuan Li
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Err-Cheng Chan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.
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