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Huang L, Huang H, Zhang Z, Li G. Three-Dimensional DNA Hydrogel Mediated Dual-Mode Sensing Method for Quantification of Epithelial Cell Adhesion Molecule in Biological Fluid Samples. Anal Chem 2024. [PMID: 39007488 DOI: 10.1021/acs.analchem.4c01006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Monitoring changes in the expression of marker proteins in biological fluids is essential for biomarker-based disease diagnosis. Epithelial cell adhesion molecule (EpCAM) has been identified as a broad-spectrum biomarker for various chronic diseases and as a therapeutic target. However, the development of simple and reliable methods for quantifying EpCAM changes in biological fluids faces challenges due to the variability of its expression across different diseases, the presence of soluble forms, and matrix effects. In this paper, a surface-enhanced Raman scattering (SERS)-fluorescence (FL) dual-mode sensing method was established for quantification of trace EpCAM in biological fluids based on bimetallic Au@Ag nanoparticles and nitrogen-doped quantum dots encapsulated DNA hydrogel hybrid with graphene oxide (Au@Ag-NQDs/GO). The DNA hydrogel was constructed based on three-dimensional (3D) structure DNA-mediated strategy using an aptamer DNA (AptDNA) linker. The interaction of the AptDNA with EpCAM triggered the disassembly of the DNA hydrogel. Consequently, the release of Au@Ag nanoparticles induced an "on-off" switch in the SERS signal while the weakened FL quenching effect in Au@Ag-NQDs/GO system achieved "off-on" switch of FL signal, enabling the simultaneous SERS-FL quantification of EpCAM. The established dual-mode method exhibited outstanding sensitivity and stability in quantifying EpCAM in the range of 0.5-60.0 pg/mL, with the limits of detection (LODs) of SERS and FL as 0.17 and 0.35 pg/mL, respectively. When applied for real sample analysis, the method showed satisfactory specificity and recoveries in cancer cells lysate, serum, and urine samples with RSDs of 2.8-6.3%, 4.0-6.3%, and 2.8-5.7%, respectively. The developed SERS-FL sensing method offered a sensitive, reliable, and practical quantification strategy for trace EpCAM in diverse biological fluid samples, which would benefit the early diagnosis of disease and further health management.
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Affiliation(s)
- Lu Huang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Hanbing Huang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhuomin Zhang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
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2
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Duan X, Qin W, Hao J, Yu X. Recent advances in the applications of DNA frameworks in liquid biopsy: A review. Anal Chim Acta 2024; 1308:342578. [PMID: 38740462 DOI: 10.1016/j.aca.2024.342578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 05/16/2024]
Abstract
Cancer is one of the serious threats to public life and health. Early diagnosis, real-time monitoring, and individualized treatment are the keys to improve the survival rate and prolong the survival time of cancer patients. Liquid biopsy is a potential technique for cancer early diagnosis due to its non-invasive and continuous monitoring properties. However, most current liquid biopsy techniques lack the ability to detect cancers at the early stage. Therefore, effective detection of a variety of cancers is expected through the combination of various techniques. Recently, DNA frameworks with tailorable functionality and precise addressability have attracted wide spread attention in biomedical applications, especially in detecting cancer biomarkers such as circulating tumor cells (CTCs), exosomes and circulating tumor nucleic acid (ctNA). Encouragingly, DNA frameworks perform outstanding in detecting these cancer markers, but also face some challenges and opportunities. In this review, we first briefly introduced the development of DNA frameworks and its typical structural characteristics and advantages. Then, we mainly focus on the recent progress of DNA frameworks in detecting commonly used cancer markers in liquid-biopsy. We summarize the advantages and applications of DNA frameworks for detecting CTCs, exosomes and ctNA. Furthermore, we provide an outlook on the possible opportunities and challenges for exploiting the structural advantages of DNA frameworks in the field of cancer diagnosis. Finally, we envision the marriage of DNA frameworks with other emerging materials and technologies to develop the next generation of disease diagnostic biosensors.
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Affiliation(s)
- Xueyuan Duan
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China
| | - Weiwei Qin
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China.
| | - Jicong Hao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China.
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3
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Kapinova A, Mazurakova A, Halasova E, Dankova Z, Büsselberg D, Costigliola V, Golubnitschaja O, Kubatka P. Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine. EPMA J 2023; 14:249-273. [PMID: 37275549 PMCID: PMC10236066 DOI: 10.1007/s13167-023-00323-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.
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Affiliation(s)
- Andrea Kapinova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Alena Mazurakova
- Department of Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Erika Halasova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dietrich Büsselberg
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, 24144 Doha, Qatar
| | | | - Olga Golubnitschaja
- Predictive, Preventive, and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
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4
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Baron F, Zhang M, Archer N, Bellows E, Knight HM, Welham S, Rutland CS, Mongan NP, Hayes CJ, Fray RG, Bodi Z. The importance of m 6A topology in chicken embryo mRNA: a precise mapping of m 6A at the conserved chicken β-actin zipcode. RNA (NEW YORK, N.Y.) 2023; 29:777-789. [PMID: 36810234 PMCID: PMC10187669 DOI: 10.1261/rna.079615.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 05/18/2023]
Abstract
N6-methyladenosine (m6A) in mRNA regulates almost every stage in the mRNA life cycle, and the development of methodologies for the high-throughput detection of methylated sites in mRNA using m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIPSeq) or m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) have revolutionized the m6A research field. Both of these methods are based on immunoprecipitation of fragmented mRNA. However, it is well documented that antibodies often have nonspecific activities, thus verification of identified m6A sites using an antibody-independent method would be highly desirable. We mapped and quantified the m6A site in the chicken β-actin zipcode based on the data from chicken embryo MeRIPSeq results and our RNA-Epimodification Detection and Base-Recognition (RedBaron) antibody-independent assay. We also demonstrated that methylation of this site in the β-actin zipcode enhances ZBP1 binding in vitro, while methylation of a nearby adenosine abolishes binding. This suggests that m6A may play a role in regulating localized translation of β-actin mRNA, and the ability of m6A to enhance or inhibit a reader protein's RNA binding highlights the importance of m6A detection at nucleotide resolution.
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Affiliation(s)
- Francis Baron
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
- School of Chemistry, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Mi Zhang
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Nathan Archer
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Eleanor Bellows
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Helen M Knight
- Faculty of Medicine and Health Sciences, Queen's Medical Center, Nottingham NG7 2UH, United Kingdom
| | - Simon Welham
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Catrin S Rutland
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Christopher J Hayes
- School of Chemistry, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Rupert G Fray
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Zsuzsa Bodi
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
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Circulating Tumor DNA Methylation Biomarkers for Characterization and Determination of the Cancer Origin in Malignant Liver Tumors. Cancers (Basel) 2023; 15:cancers15030859. [PMID: 36765815 PMCID: PMC9913861 DOI: 10.3390/cancers15030859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Malignant liver tumors include primary malignant liver tumors and liver metastases. They are among the most common malignancies worldwide. The disease has a poor prognosis and poor overall survival, especially with liver metastases. Therefore, early detection and differentiation between malignant liver tumors are critical for patient treatment selection. The detection of cancer and the prediction of its origin is possible with a DNA methylation profile of the tumor DNA compared to that of normal cells, which reflects tissue differentiation and malignant transformation. New technologies enable the characterization of the tumor methylome in circulating tumor DNA (ctDNA), providing a variety of new ctDNA methylation biomarkers, which can provide additional information to clinical decision-making. Our review of the literature provides insight into methylation changes in ctDNA from patients with common malignant liver tumors and can serve as a starting point for further research.
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Ramzannezhad A, Hayati A, Bahari A, Najafi-Ashtiani H. Magnetic detection of albuminuria using hematite nanorods synthesized via chemical hydrothermal method. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:962-968. [PMID: 34712427 PMCID: PMC8528259 DOI: 10.22038/ijbms.2021.53918.12120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/03/2021] [Indexed: 11/06/2022]
Abstract
Objectives Albuminuria is a biomarker in the diagnosis of kidney disease which is due to the presence of high albumin in the urine and is one of the complications of diabetes. In recent years, the methods used to identify albuminuria have been expensive and time-consuming. Furthermore, another problem is the lack of accurate measurement of albuminuria. This problem leads to kidney isolation as well as a decrease in erythropoietin levels. Therefore, the main aim of our work is to design a magnetic nanobiosensor with better sensitivity to detect minimal levels of albuminuria. Materials and Methods In the present work, we synthesized Hematite Nano Rods (HNRs) using FeCl3, NaOH and Cetyltrimethylammonium bromide (CTAB) precursors via the hydrothermal method. Then, HNRs were characterized using UV-vis spectroscopy, Fourier Transform Infrared Spectroscopy (FTIR), Transmission Electron Microscopy (TEM) and Vibrating Sample Magnetometer (VSM) techniques. Results The obtained results from clinical performance of the HNR nanobiosensor show that the magnetization changes of HNR in interaction with the albumin biomarker can determine the presence or absence of protein in biological samples. The accuracy and repeatability of the HNR nanobiosensor from the value of the R2 coefficient in the standard equation is 0.9743. Conclusion We obtained the standard curve through interaction of the HNRs with albumin protein. The standard equation is obtained by plotting the magnetization curve of a non-interacting sample to interacting samples in terms of protein concentration. The Bland-Altman statistical graph prove that the HNR nanobiosensor is as reliable as experimental methods.
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Affiliation(s)
- Ali Ramzannezhad
- Department of Science, Faculty of Imam Mohammad Bagher, Mazandaran Branch, Technical and Vocational University, Sari, Iran.,Department of Physics, Faculty of Basic Sciences, University of Mazandaran,Sari, Iran
| | - Amir Hayati
- Department of Science, Faculty of Imam Mohammad Bagher, Mazandaran Branch, Technical and Vocational University, Sari, Iran
| | - Ali Bahari
- Department of Physics, Faculty of Basic Sciences, University of Mazandaran,Sari, Iran
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Emerging noninvasive methylation biomarkers of cancer prognosis and drug response prediction. Semin Cancer Biol 2021; 83:584-595. [PMID: 33757849 DOI: 10.1016/j.semcancer.2021.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/15/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
Cancer is the second leading cause of death worldwide being responsible for 9.6 million deaths in 2018. Epigenetic alterations are key in directing the aberrant expression of tumor-associated genes that drive cellular malignant transformation and cancer progression. Among epigenetic alterations, DNA methylation is the most deeply studied one in relation to environmental exposure. Tissue biopsies have traditionally been the main procedure by which a small sample of body tissue is excised to confirm cancer diagnosis or to indicate the primary site when cancer has spread. In contrast, the analysis of circulating tumor-derived material, or tumor circulome, by means of liquid biopsy of peripheral blood, urine, saliva or sputum is a noninvasive, fast and reproducible alternative to tissue biopsy. Recently, the assessment of epigenetic alterations such as DNA methylation and hydroxymethylation in circulating free DNA has been proved possible. These marks can be associated to prognosis and response to a variety of treatments including chemotherapy, hormonotherapy or immunotherapy. Epigenetic biomarkers may offer some advantages over RNA or genetic biomarkers given their stability in bodily fluids and their high tissue-specificity. While many challenges are still ahead, the unique advantages of these types of biomarkers is urging the scientific community to persevere in their clinical validation and integration into reliable prediction models. This review aims at recapitulating the emerging noninvasive DNA methylated biomarkers of importance for prediction of prognosis and drug response in cancer.
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8
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Non-invasive early detection of cancer four years before conventional diagnosis using a blood test. Nat Commun 2020; 11:3475. [PMID: 32694610 PMCID: PMC7374162 DOI: 10.1038/s41467-020-17316-z] [Citation(s) in RCA: 316] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/24/2020] [Indexed: 02/06/2023] Open
Abstract
Early detection has the potential to reduce cancer mortality, but an effective screening test must demonstrate asymptomatic cancer detection years before conventional diagnosis in a longitudinal study. In the Taizhou Longitudinal Study (TZL), 123,115 healthy subjects provided plasma samples for long-term storage and were then monitored for cancer occurrence. Here we report the preliminary results of PanSeer, a noninvasive blood test based on circulating tumor DNA methylation, on TZL plasma samples from 605 asymptomatic individuals, 191 of whom were later diagnosed with stomach, esophageal, colorectal, lung or liver cancer within four years of blood draw. We also assay plasma samples from an additional 223 cancer patients, plus 200 primary tumor and normal tissues. We show that PanSeer detects five common types of cancer in 88% (95% CI: 80-93%) of post-diagnosis patients with a specificity of 96% (95% CI: 93-98%), We also demonstrate that PanSeer detects cancer in 95% (95% CI: 89-98%) of asymptomatic individuals who were later diagnosed, though future longitudinal studies are required to confirm this result. These results demonstrate that cancer can be non-invasively detected up to four years before current standard of care.
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9
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Li Z, Shu J, Yang B, Zhang Z, Huang J, Chen Y. Emerging non-invasive detection methodologies for lung cancer. Oncol Lett 2020; 19:3389-3399. [PMID: 32269611 PMCID: PMC7115116 DOI: 10.3892/ol.2020.11460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 01/17/2020] [Indexed: 12/24/2022] Open
Abstract
The potential for non-invasive lung cancer (LC) diagnosis based on molecular, cellular and volatile biomarkers has been attracting increasing attention, with the development of advanced techniques and methodologies. It is standard practice to tailor the treatments of LC for certain specific genetic alterations, including the epidermal growth factor receptor, anaplastic lymphoma kinase and BRAF genes. Despite these advances, little is known about the internal mechanisms of different types of biomarkers and the involvement of their related biochemical pathways during the development of LC. The development of faster and more effective techniques is essential for the identification of different biomarkers. The present review summarizes some of the latest methods used for detecting molecular, cellular and volatile biomarkers in LC and their potential use in clinical diagnosis and targeted therapy.
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Affiliation(s)
- Zhen Li
- Beijing Advanced Sciences and Innovation Center, Chinese Academy of Sciences, Beijing 101407, P.R. China.,National Engineering Laboratory for VOCs Pollution Control Material and Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
| | - Jinian Shu
- National Engineering Laboratory for VOCs Pollution Control Material and Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
| | - Bo Yang
- National Engineering Laboratory for VOCs Pollution Control Material and Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
| | - Zuojian Zhang
- National Engineering Laboratory for VOCs Pollution Control Material and Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
| | - Jingyun Huang
- National Engineering Laboratory for VOCs Pollution Control Material and Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
| | - Yang Chen
- Beijing Advanced Sciences and Innovation Center, Chinese Academy of Sciences, Beijing 101407, P.R. China
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10
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Xia S, Ye J, Chen Y, Lizaso A, Huang L, Shi L, Su J, Han-Zhang H, Chuai S, Li L, Chen Y. Parallel serial assessment of somatic mutation and methylation profile from circulating tumor DNA predicts treatment response and impending disease progression in osimertinib-treated lung adenocarcinoma patients. Transl Lung Cancer Res 2019; 8:1016-1028. [PMID: 32010579 DOI: 10.21037/tlcr.2019.12.09] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Circulating tumor DNA (ctDNA) harboring tumor-specific genetic and epigenetic aberrations allows for early detection and real-time monitoring of tumor dynamics. In this study, we aimed to evaluate the potential of parallel serial assessment of somatic mutation and methylation profile in monitoring the response to osimertinib of epidermal growth factor receptor (EGFR) T790M-positive advanced lung adenocarcinoma patients. Methods Parallel somatic mutation and DNA methylation profiling was performed on a total of 85 longitudinal plasma samples obtained from 8 stage IV osimertinib-treated EGFR T790M-positive lung adenocarcinoma patients. Results Our results revealed a significant correlation between the by-patient methylation level with the maximum allele fraction (maxAF, P=0.0002). The methylation levels were significantly higher in the plasma samples of patients with detectable somatic mutations than patients without somatic mutations (P=0.0003) and healthy controls (P=0.0018). Moreover, analysis of both the DNA methylation level and maxAF revealed four trends of treatment response. Collectively, the decrease in methylation level and maxAF reflected treatment efficacy, while the gradual increase reflected impending disease progression (PD). Elevated methylation levels and maxAF were observed in 6 and 5 patients in an average lead-time of 3.0 and 1.9 months, respectively, prior to evaluation of PD using radiological imaging. Conclusions DNA methylation profiling has the potential to predict disease relapse prior to evaluation through radiological modalities, suggesting that serial assessment of methylation level in combination with somatic mutation profiling are reliable methods for treatment monitoring. These methods should thus be incorporated with imaging modalities for a more comprehensive work-up of treatment response, particularly for patients treated with targeted therapies.
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Affiliation(s)
- Shu Xia
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Affiliated Hospital of Qinghai University, Xining 810000, China
| | - Junyi Ye
- Burning Rock Biotech, Guangzhou 510300, China
| | - Yu Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | | | - Le Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lei Shi
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Su
- Burning Rock Biotech, Guangzhou 510300, China
| | | | | | - Lingling Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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11
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Circulating Tumour Cells in Lung Cancer. Recent Results Cancer Res 2019. [PMID: 31605226 DOI: 10.1007/978-3-030-26439-0_6] [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: 08/25/2023]
Abstract
Circulating tumour cells (CTCs) constitute a potential tumour surrogate that could serve as "liquid biopsy" with the advantage to be a minimally invasive approach compared to traditional tissue biopsies. As CTCs are thought to be the source of metastatic lesions, their analysis represents a potential means of tracking cancer cells from the primary tumour en route to distant sites, thus providing valuable insights into the metastatic process. However, several problems, such as their rarity in the peripheral blood, the technical limitations of single-cell downstream analysis and their phenotypic variability, make CTC detection and molecular characterisation very challenging. Nevertheless, in the last decade, there has been an exponential increase of interest in the development of powerful cellular and molecular methodologies applied to CTCs. In this chapter, we focus on the recent advances of functional studies and molecular profiling of CTCs. We will also highlight the clinical relevance of CTC detection and enumeration, and discuss their potential as tumour biomarkers with special focus on lung cancer.
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Dvorská D, Braný D, Nagy B, Grendár M, Poka R, Soltész B, Jagelková M, Zelinová K, Lasabová Z, Zubor P, Danková Z. Aberrant Methylation Status of Tumour Suppressor Genes in Ovarian Cancer Tissue and Paired Plasma Samples. Int J Mol Sci 2019; 20:ijms20174119. [PMID: 31450846 PMCID: PMC6747242 DOI: 10.3390/ijms20174119] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/17/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer is a highly heterogeneous disease and its formation is affected by many epidemiological factors. It has typical lack of early signs and symptoms, and almost 70% of ovarian cancers are diagnosed in advanced stages. Robust, early and non-invasive ovarian cancer diagnosis will certainly be beneficial. Herein we analysed the regulatory sequence methylation profiles of the RASSF1, PTEN, CDH1 and PAX1 tumour suppressor genes by pyrosequencing in healthy, benign and malignant ovarian tissues, and corresponding plasma samples. We recorded statistically significant higher methylation levels (p < 0.05) in the CDH1 and PAX1 genes in malignant tissues than in controls (39.06 ± 18.78 versus 24.22 ± 6.93; 13.55 ± 10.65 versus 5.73 ± 2.19). Higher values in the CDH1 gene were also found in plasma samples (22.25 ± 14.13 versus 46.42 ± 20.91). A similar methylation pattern with positive correlation between plasma and benign lesions was noted in the CDH1 gene (r = 0.886, p = 0.019) and malignant lesions in the PAX1 gene (r = 0.771, p < 0.001). The random forest algorithm combining methylation indices of all four genes and age determined 0.932 AUC (area under the receiver operating characteristic (ROC) curve) prediction power in the model classifying malignant lesions and controls. Our study results indicate the effects of methylation changes in ovarian cancer development and suggest that the CDH1 gene is a potential candidate for non-invasive diagnosis of ovarian cancer.
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Affiliation(s)
- Dana Dvorská
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dušan Braný
- Division of Molecular Medicine, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia.
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Marián Grendár
- Bioinformatic Unit, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Robert Poka
- Institute of Obstetrics and Gynecology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Marianna Jagelková
- Department of Gynaecology and Obstetrics, Martin University Hospital, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Katarína Zelinová
- Department of Gynaecology and Obstetrics, Martin University Hospital, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zora Lasabová
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Pavol Zubor
- Department of Gynaecology and Obstetrics, Martin University Hospital, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Danková
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 036 01 Martin, Slovakia
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Functions of RNA N6-methyladenosine modification in cancer progression. Mol Biol Rep 2019; 46:2567-2575. [PMID: 30911972 DOI: 10.1007/s11033-019-04655-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023]
Abstract
N6-methyladenosine (m6A) serves as a major RNA methylation modification and impacts the initiation and progression of various human cancers through diverse mechanisms. It has been reported that m6A RNA methylation is involved in different physiological and pathological processes, including stem cell differentiation and motility, immune response, cellular stress, tissue renewal and viral infection. In this review, the m6A modification and its regulatory functions in a few major cancers is introduced. The detection approaches for the m6A sites identification are discussed. Additionally, the potential of the RNA m6A modification in clinical application is discussed.
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Functions of RNA N6-methyladenosine modification in cancer progression. Mol Biol Rep 2019; 46:1383-1391. [PMID: 30788764 DOI: 10.1007/s11033-018-4471-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
N6-methyladenosine (m6A) serves as a major RNA methylation modification and impacts the initiation and progression of various human cancers through diverse mechanisms. It has been reported that m6A RNA methylation is involved in different physiological and pathological processes, including stem cell differentiation and motility, immune response, cellular stress, tissue renewal and viral infection. In this review, the m6A modification and its regulatory functions in a few major cancers is introduced. The detection approaches for the m6A sites identification are discussed. Additionally, the potential of the RNA m6A modification in clinical application is discussed.
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15
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Epigenetic Biomarkers in Cell-Free DNA and Applications in Liquid Biopsy. Genes (Basel) 2019; 10:genes10010032. [PMID: 30634483 PMCID: PMC6356936 DOI: 10.3390/genes10010032] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022] Open
Abstract
Cell-free circulating DNA (cfDNA) in plasma has gained global interest as a diagnostic material for noninvasive prenatal testing and cancer diagnosis, or the so-called “liquid biopsy”. Recent studies have discovered a great number of valuable genetic and epigenetic biomarkers for cfDNA-based liquid biopsy. Considering that the genetic biomarkers, e.g., somatic mutations, usually vary from case to case in most cancer patients, epigenetic biomarkers that are generalizable across various samples thus possess certain advantages. In this study, we reviewed the most recent studies and advances on utilizing epigenetic biomarkers for liquid biopsies. We first reviewed more traditional methods of using tissue/cancer-specific DNA methylation biomarkers and digital PCR or sequencing technologies for cancer diagnosis, as well as tumor origin determination. In the second part, we discussed the emerging novel approaches for exploring the biological basis and clinical applications of cfDNA fragmentation patterns. We further provided our comments and points of view on the future directions on epigenetic biomarker development for cfDNA-based liquid biopsies.
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Paving the way for precision medicine v2.0 in intensive care by profiling necroinflammation in biofluids. Cell Death Differ 2018; 26:83-98. [PMID: 30201975 PMCID: PMC6294775 DOI: 10.1038/s41418-018-0196-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/16/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022] Open
Abstract
Current clinical diagnosis is typically based on a combination of approaches including clinical examination of the patient, clinical experience, physiologic and/or genetic parameters, high-tech diagnostic medical imaging, and an extended list of laboratory values mostly determined in biofluids such as blood and urine. One could consider this as precision medicine v1.0. However, recent advances in technology and better understanding of molecular mechanisms underlying disease will allow us to better characterize patients in the future. These improvements will enable us to distinguish patients who have similar clinical presentations but different cellular and molecular responses. Treatments will be able to be chosen more “precisely”, resulting in more appropriate therapy, precision medicine v2.0. In this review, we will reflect on the potential added value of recent advances in technology and a better molecular understanding of necrosis and inflammation for improving diagnosis and treatment of critically ill patients. We give a brief overview on the mutual interplay between necrosis and inflammation, which are two crucial detrimental factors in organ and/or systemic dysfunction. One of the challenges for the future will thus be the cellular and molecular profiling of necroinflammation in biofluids. The huge amount of data generated by profiling biomolecules and single cells through, for example, different omic-approaches is needed for data mining methods to allow patient-clustering and identify novel biomarkers. The real-time monitoring of biomarkers will allow continuous (re)evaluation of treatment strategies using machine learning models. Ultimately, we may be able to offer precision therapies specifically designed to target the molecular set-up of an individual patient, as has begun to be done in cancer therapeutics. Critical care mostly implies life-threatening situations involving systemic infection, inflammation and necrosis. Biofluids are an easily accessible source of liquid biopsies that can be used to monitor the evolution of the patient’s critical illness. The cellular and molecular profiling of necrosis and inflammation in biofluids using cutting-edge technologies such as realtime immunodiagnostics, next-generation sequencing and mass spectrometry will pave the way for precision medicine v2.0 in critical care. This is needed for data mining approaches to allow patientclustering, identify novel biomarkers and develop novel intervention strategies controlling necrosis and inflammation. The real-time monitoring of biomarkers will allow continued (re)evaluation of treatment strategies using machine learning models. ![]()
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Zhang J, Han X, Gao C, Xing Y, Qi Z, Liu R, Wang Y, Zhang X, Yang YG, Li X, Sun B, Tian X. 5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:187-199. [PMID: 30010036 PMCID: PMC6076378 DOI: 10.1016/j.gpb.2018.06.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 02/06/2023]
Abstract
Non-small-cell lung cancer (NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identified six potential biomarkers from 66 patients and 67 healthy controls (mean decrease accuracy >3.2, P < 3.68E−19) using machine-learning-based tumor classifiers with high accuracy. Thus, the unique signature of 5hmC in tumor patient’s cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC.
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Affiliation(s)
- Ji Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China
| | - Xiao Han
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunchun Gao
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yurong Xing
- Physical Examination Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zheng Qi
- Department of Anesthesiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ruijuan Liu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China
| | - Yueqin Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China
| | - Xiaojian Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China
| | - Yun-Gui Yang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangnan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Baofa Sun
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China.
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Wang Y, Lei L, Zheng YW, Zhang L, Li ZH, Shen HY, Jiang GY, Zhang XP, Wang EH, Xu HT. Odd-skipped related 1 inhibits lung cancer proliferation and invasion by reducing Wnt signaling through the suppression of SOX9 and β-catenin. Cancer Sci 2018; 109:1799-1810. [PMID: 29660200 PMCID: PMC5989870 DOI: 10.1111/cas.13614] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/02/2018] [Accepted: 04/11/2018] [Indexed: 12/14/2022] Open
Abstract
The odd‐skipped related 1 (OSR1) gene encodes a zinc‐finger transcription factor. The expression and significance of OSR1 in human tumors remains unclear. We found that OSR1 was downregulated in lung cancers, and its expression was correlated with poor differentiation. Overexpression of OSR1 by OSR1 gene transfection into H1299 cells (H1299‐OSR1) inhibited the proliferation and invasion of lung cancer cells. Knockdown of OSR1 with small interfering (si)RNA against OSR1 in A549 cells (A549‐siOSR1) enhanced the proliferation and invasion of lung cancer cells. Western blot analysis showed that the expression level of GSK3β increased, while that of p‐GSK3β, nuclear β‐catenin, cyclin D1, c‐Myc and matrix metallopeptidase 7 significantly decreased in the H1299‐OSR1 cells, and this pattern was reversed in the A549‐siOSR1 cells compared to that in the control cells. Furthermore, upregulation of sex‐determining region Y‐box 9 (SOX9) by SOX9 gene transfection increased the expression of β‐catenin, which was inhibited by OSR1. The mRNA and protein expression levels of SOX9 and β‐catenin were reduced in H1299‐OSR1 cells and increased in A549‐siOSR1 cells. In conclusion, the expression of OSR1 was more reduced in lung cancer tissues than in normal lung tissues, and was correlated with poor differentiation. OSR1 downregulated the activity of the Wnt signaling pathway by suppressing the expression of SOX9 and β‐catenin.
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Affiliation(s)
- Yuan Wang
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China.,Department of Pathology, Jinzhou Medical University, Jinzhou, China
| | - Lei Lei
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Yi-Wen Zheng
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Li Zhang
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Zhi-Han Li
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Hao-Yue Shen
- 100K80B, Clinical Medicine of Seven-year Programme, China Medical University, Shenyang, China
| | - Gui-Yang Jiang
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Xiu-Peng Zhang
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - En-Hua Wang
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Hong-Tao Xu
- Department of Pathology, First Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
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20
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Ren Y, Zhao S, Jiang D, Feng X, Zhang Y, Wei Z, Wang Z, Zhang W, Zhou QF, Li Y, Hou H, Xu Y, Zhou F. Proteomic biomarkers for lung cancer progression. Biomark Med 2018; 12:205-215. [DOI: 10.2217/bmm-2018-0015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Lung adenocarcinoma (LUAD) and lung squamous-cell carcinoma (LUSC) are two major subtypes of lung cancer and constitute about 70% of all the lung cancer cases. The patient's lifespan and living quality will be significantly improved if they are diagnosed at an early stage and adequately treated. Methods & results: This study comprehensively screened the proteomic dataset of both LUAD and LUSC, and proposed classification models for the progression stages of LUAD and LUSC with accuracies 86.51 and 89.47%, respectively. Discussion & conclusion: A comparative analysis was also carried out on related transcriptomic datasets, which indicates that the proposed biomarkers provide discerning power for accurate stage prediction, and will be improved when larger-scale proteomic quantitative technologies become available.
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Affiliation(s)
- Yanjiao Ren
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Shishun Zhao
- Center for Applied Statistical Research, College of Mathematics, Jilin University, Changchun, Jilin 130012, PR China
| | - Dandan Jiang
- Center for Applied Statistical Research, College of Mathematics, Jilin University, Changchun, Jilin 130012, PR China
| | - Xin Feng
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Yexian Zhang
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Zhipeng Wei
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Zhongyu Wang
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Wenniu Zhang
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Qing F Zhou
- School of Electrical Engineering & Intelligentization, Dongguan University of Technology, Dongguan 523000, PR China
| | - Yong Li
- Department of Electronic Engineering, Tsinghua University, Beijing 100084, PR China
| | - Hanxu Hou
- School of Electrical Engineering & Intelligentization, Dongguan University of Technology, Dongguan 523000, PR China
| | - Ying Xu
- Computational Systems Biology Lab, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
- College of Computer Science & Technology, & College of Public Health, Jilin University, Changchun, Jilin 130012, PR China
| | - Fengfeng Zhou
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
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Leroy S, Benzaquen J, Mazzetta A, Marchand-Adam S, Padovani B, Israel-Biet D, Pison C, Chanez P, Cadranel J, Mazières J, Jounieaux V, Cohen C, Hofman V, Ilie M, Hofman P, Marquette CH. Circulating tumour cells as a potential screening tool for lung cancer (the AIR study): protocol of a prospective multicentre cohort study in France. BMJ Open 2017; 7:e018884. [PMID: 29282271 PMCID: PMC5770962 DOI: 10.1136/bmjopen-2017-018884] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/28/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Lung cancer (LC) is the leading cause of death from cancer. Early diagnosis of LC is of paramount importance in terms of prognosis. The health authorities of most countries do not accept screening programmes based on low-dose chest CT (LDCT), especially in Europe, because they are flawed by a high rate of false-positive results, leading to a large number of invasive diagnostic procedures. These authorities advocated further research, including companion biological tests that could enhance the effectiveness of LC screening. The present project aims to validate early diagnosis of LC by detection and characterisation of circulating tumour cells (CTCs) in a peripheral blood sample taken from a prospective cohort of persons at high-risk of LC. METHODS AND ANALYSIS The AIR Project is a prospective, multicentre, double-blinded, cohort study conducted by a consortium of 21 French university centres. The primary objective is to determine the operational values of CTCs for the early detection of LC in a cohort of asymptomatic participants at high risk for LC, that is, smokers and ex-smokers (≥30 pack-years, quitted ≤15 years), aged ≥55 years, with chronic obstructive pulmonary disease (COPD). The study participants will undergo yearly screening rounds for 3 years plus a 1-year follow-up. Each round will include LDCT plus peripheral blood sampling for CTC detection. Assuming 5% prevalence of LC in the studied population and a 10% dropout rate, a total of at least 600 volunteers will be enrolled. ETHICS AND DISSEMINATION The study sponsor is the University Hospital of Nice. The study was approved for France by the ethical committee CPP Sud-Méditerranée V and the ANSM (Ministry of Health) in July 2015. The findings of the trial will be disseminated through peer-reviewed journals and national and international conference presentations. TRIAL REGISTRATION NUMBER NCT02500693.
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Affiliation(s)
- Sylvie Leroy
- Department of Pulmonary Medicine and Thoracic Oncology, Centre Hospitalier Universitaire de Nice, Nice, France
- CNRS, INSERM, IPMC, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Jonathan Benzaquen
- Department of Pulmonary Medicine and Thoracic Oncology, Centre Hospitalier Universitaire de Nice, Nice, France
- Laboratory of Clinical and Experimental Pathology, Hospital-Related Biobank (BB-0033-00025), IRCAN, FHU OncoAge, Nice, France
| | - Andrea Mazzetta
- Department of Pulmonary Medicine and Thoracic Oncology, Centre Hospitalier Universitaire de Nice, Nice, France
| | | | | | | | - Christophe Pison
- Department of Pulmonary Medicine, CHU de Grenoble, Grenoble, France
| | - Pascal Chanez
- Department of Pulmonary Medicine, CHU de Marseille, Marseille, France
| | | | - Julien Mazières
- Department of Pulmonary Medicine, CHU Toulouse, Toulouse, France
| | | | - Charlotte Cohen
- Department of Thoracic Surgery, CHU de Nice, FHU OncoAge, Nice, France
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Hospital-Related Biobank (BB-0033-00025), IRCAN, FHU OncoAge, Nice, France
| | - Marius Ilie
- Laboratory of Clinical and Experimental Pathology, Hospital-Related Biobank (BB-0033-00025), IRCAN, FHU OncoAge, Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Hospital-Related Biobank (BB-0033-00025), IRCAN, FHU OncoAge, Nice, France
| | - Charles Hugo Marquette
- Department of Pulmonary Medicine and Thoracic Oncology, Centre Hospitalier Universitaire de Nice, Nice, France
- Laboratory of Clinical and Experimental Pathology, Hospital-Related Biobank (BB-0033-00025), IRCAN, FHU OncoAge, Nice, France
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22
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Liquid Biopsy and Therapeutic Targets: Present and Future Issues in Thoracic Oncology. Cancers (Basel) 2017; 9:cancers9110154. [PMID: 29125548 PMCID: PMC5704172 DOI: 10.3390/cancers9110154] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
The practice of liquid biopsy (LB) has revolutionized the care of patients with metastatic lung cancer. Many oncologists now use this approach in daily practice, applying precise procedures for the detection of activating or resistance mutations in EGFR. These tests are performed with plasma DNA and have been approved as companion diagnostic test for patients treated with tyrosine kinase inhibitors. ALK is another important target in lung cancer since it leads to treatment of patients who are positive for a rearrangement in ALK identified with tumor tissue. By analogy with EGFR, LB for detection of genomic alterations in ALK (rearrangements or mutations) has been rapidly adopted in the clinic. However, this promising approach has some limitations and has not yet been disseminated as much as the blood test targeting EGFR. In addition to these two therapeutic targets LB can be used for evaluation of the genomic status of other genes of interest of patients with lung cancer (ROS1, RET, NTRK MET, BRAF, HER2, etc.). LB can be performed to evaluate a specific target or for a more or less complex panel of genes. Considering the number of potential targets for clinical trials, techniques of next-generation sequencing of circulating DNA are on the rise. This review will provide an update on the contribution of LB to care of patients with metastatic lung cancer, including the present limits of this approach, and will consider certain perspectives.
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Bouhlel L, Hofman V, Maschi C, Ilié M, Allégra M, Marquette CH, Audigier-Valette C, Thariat J, Hofman P. The liquid biopsy: a tool for a combined diagnostic and theranostic approach for care of a patient with late-stage lung carcinoma presenting with bilateral ocular metastases. Expert Rev Anticancer Ther 2017; 17:1087-1092. [PMID: 29069959 DOI: 10.1080/14737140.2017.1398089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Liquid biopsies (LB) are used routinely in clinical practice in two situations for late stage non-small-cell lung cancer (NSCLC) patients, (i) at the initial diagnosis when looking for activating mutations in EGFR in the absence of analyzable tissue DNA and, (ii) during tumor progression on a tyrosine kinase inhibitor treatment to look for the resistance mutation T790M in EGFR. LB is not presently recommended in daily practice for the diagnosis of NSCLC. Areas covered: We report the diagnosis of a NSCLC in a patient with bilateral ocular metastases after detection of a deletion in exon 19 of EGFR when using plasma DNA. Without histological analysis, the origin of the primary ocular metastasis was uncertain. In this context, a LB showing an activating mutation in EGFR and circulating tumor cells positive for TTF1 led to the diagnosis of NSCLC and targeted therapy. Expert commentary: When no tumor tissue sample is available a LB can be used to diagnose for metastatic NSCLC, when a mutation in EGFR is identified. While a tissue biopsy is the gold standard approach for the diagnosis of a NSCLC and for identification of activating mutations, LB can exceptionally provide both a diagnosis of the primitive tumor and indicate appropriate therapy based on a molecular analysis.
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Affiliation(s)
- Linda Bouhlel
- a Department of Oncology , Antoine Lacassagne Comprehensive Cancer Centre , Nice , France
| | - Véronique Hofman
- b FHU OncoAge, Laboratory of Clinical and Experimental Pathology , CHU of Nice , Nice , France.,c Hospital-Integrated Biobank (BB-0033-00025) , CHU of Nice , Nice , France
| | - Célia Maschi
- d Department of Ophtalmology , CHU of Nice , Nice , France
| | - Marius Ilié
- b FHU OncoAge, Laboratory of Clinical and Experimental Pathology , CHU of Nice , Nice , France.,c Hospital-Integrated Biobank (BB-0033-00025) , CHU of Nice , Nice , France
| | - Maryline Allégra
- b FHU OncoAge, Laboratory of Clinical and Experimental Pathology , CHU of Nice , Nice , France.,c Hospital-Integrated Biobank (BB-0033-00025) , CHU of Nice , Nice , France
| | | | | | - Juliette Thariat
- g Radiation Oncology Department , Antoine Lacassagne Comprehensive Cancer Center , Nice , France
| | - Paul Hofman
- b FHU OncoAge, Laboratory of Clinical and Experimental Pathology , CHU of Nice , Nice , France.,c Hospital-Integrated Biobank (BB-0033-00025) , CHU of Nice , Nice , France
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24
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Affiliation(s)
- David S Schrump
- Thoracic Epigenetics Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Md.
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