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Chen H, Xu C, Fang Z, Mao S. Cell-Free DNA, MicroRNAs, Proteins, and Peptides as Liquid Biopsy Biomarkers in Prostate Cancer and Bladder Cancer. Methods Mol Biol 2023; 2695:165-179. [PMID: 37450118 DOI: 10.1007/978-1-0716-3346-5_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Liquid biopsy, as a novel noninvasive tool for biomarker discovery, has gained a lot of attention and represents a significant innovation in precision medicine. Due to its minimally invasive nature, liquid biopsy has fewer complications and can be scheduled more frequently to provide individualized snapshots of the disease at successive time points. This is particularly valuable in providing simultaneous measurements of tumor burden during treatment and early detection of tumor recurrence or drug resistance. Blood-based liquid biopsy is an attractive, minimally invasive alternative, which has shown promise in diagnosis, risk stratification, disease monitoring, and more. Urine has gained popularity due to its less invasive sampling, the ability to easily repeat samples, and the ability to track tumor evolution in real time, making it a powerful tool for diagnosis and treatment monitoring, especially in urologic cancers. In this review, we provide a detailed discussion on the potential clinical applications of prostate cancer (PCa) and bladder cancer (BCa), with cell-free DNA (cfDNA), microRNAs (miRNAs), proteins, and peptides as liquid biopsy biomarkers.
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Affiliation(s)
- Haoran Chen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chenyang Xu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zujun Fang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Shanhua Mao
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
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2
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Tadimety A, Zhang Y, Molinski JH, Palinski TJ, Tsongalis GJ, Zhang JXJ. Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing. Methods Mol Biol 2022; 2393:73-87. [PMID: 34837175 DOI: 10.1007/978-1-0716-1803-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This chapter details the use of gold nanorods conjugated with peptide nucleic acid probes for sequence-specific detection of circulating tumor DNA (ctDNA). ctDNA is gaining increased attention as a biomarker for liquid biopsy, the process of detecting molecules in the peripheral blood rather than a tissue sample. It has wide ranging applications as a diagnostic and prognostic biomarker with a similar mutational profile as the tumor. Plasmonic nanoparticles offer a relatively rapid, amplification-free method for detection of ctDNA through the use of sequence-specific peptide nucleic acid (PNA) probes. In this chapter, we discuss methods for probe design, conjugation to plasmonic particles, and ctDNA quantitation with the resulting sensor. This chapter is a resource for those looking to use plasmonic gold particles for sensing in a solution format for a range of applications.
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Affiliation(s)
- Amogha Tadimety
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Yichen Zhang
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - John H Molinski
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Timothy J Palinski
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Gregory J Tsongalis
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - John X J Zhang
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA.
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3
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Tadimety A, Wu Z, Molinski JH, Beckerman R, Jin C, Zhang L, Palinski TJ, Zhang JXJ. Rational design of on-chip gold plasmonic nanoparticles towards ctDNA screening. Sci Rep 2021; 11:14185. [PMID: 34244556 PMCID: PMC8270934 DOI: 10.1038/s41598-021-93207-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/31/2021] [Indexed: 11/23/2022] Open
Abstract
This paper demonstrates the design, synthesis, simulation, and testing of three distinct geometries of plasmonic gold nanoparticles for on-chip DNA screening towards liquid biopsy. By employing a seed-mediated growth method, we have synthesized gold nanospheres, nanorods, and nanobipyramids. In parallel, we developed numerical simulations to understand the effects of nanoparticle geometry on the resonance features and refractive index sensitivity. Both experimental and simulation results were compared through a series of studies including in-solution and on-chip tests. We have thoroughly characterized the impact of nanoparticle geometry on the sensitivity to circulating tumor DNA, with immediate implications for liquid biopsy. The results agree well with theoretical predictions and simulations, including both bulk refractive index sensitivity and thin film sensitivity. Importantly, this work quantitatively establishes the link between nanoparticle geometry and efficacy in detecting rare circulating biomarkers. The nanobipyramids provided the highest sensitivity, approximately doubling the sensitivity compared to nanorods. To the best of our knowledge this is the first report carrying through geometric effects of simulation to clinically relevant biosensing. We put forth here synthesis and testing of three nanoparticle geometries, and a framework for both experimental and theoretical validation of plasmonic sensitivities towards liquid biopsy.
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Affiliation(s)
- Amogha Tadimety
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - Ziqian Wu
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - John H Molinski
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - Russell Beckerman
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - Congran Jin
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA
| | - Lauren Zhang
- The Lawrenceville School, Lawrenceville, 08648, USA
| | | | - John X J Zhang
- Thayer School of Engineering, Dartmouth College, Hanover, 03755, USA.
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4
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Jiang Z, Bahr T, Zhou C, Jin T, Chen H, Song S, Ikeno Y, Tian H, Bai Y. Diagnostic value of circulating cell-free mtDNA in patients with suspected thyroid cancer: ND4/ND1 ratio as a new potential plasma marker. Mitochondrion 2020; 55:145-153. [PMID: 33035689 PMCID: PMC9680688 DOI: 10.1016/j.mito.2020.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/06/2020] [Accepted: 09/23/2020] [Indexed: 01/07/2023]
Abstract
Thyroid cancer is the most common endocrine malignancy, and its incidence continues to rise. For clinicians with cancer patients, choosing and interpreting diagnostic laboratory studies has become increasingly important. Previously, changes in plasma free mitochondrial DNA levels have been found in colorectal, breast, lung, and urinary cancers, and have demonstrated diagnostic value. In this study, we investigated whether the occurrence and development of thyroid cancer might be predicted using mtDNA copy number (ND1), mtDNA integrity (ND4/ND1) and levels of cell-free nDNA (GAPDH). We analyzed ND1, ND4, and GAPDH levels in plasma and blood cells from 75 patients with thyroid cancer, 40 patients with nodular goiter, and 107 normal controls using real-time PCR. Although both the thyroid nodule and thyroid cancer patients had significantly increased ND1 levels, the ND4/ND1 ratio in the thyroid cancer group was higher than the thyroid nodule group (P < 0.05), and significantly higher than the normal control group (P < 0.01). Plasma levels of nuclear DNA (GAPDH) in the thyroid cancer group were also higher compared to normal (P < 0.05). These results indicate that increased intactness of plasma free mtDNA is associated with increased levels of plasma cell-free nDNA, and that the ND4/ND1 ratio has the potential to be a new detection indicator in thyroid cancer. Furthermore, we classified thyroid cancer patients according to clinical data including age, tumor size, and metastasis. We found significantly higher levels of GAPDH in malignant tissues. Because ND4/ND1 correlated with plasma GAPDH in the plasma studies, this also suggests a potential relationship between ND4 intactness and thyroid tumor tissue size. Taken together, our findings suggest a tumor-specific process involving increased release of intact mtDNA, detectable in the plasma, which differentiates normal patients from patients with thyroid cancer.
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Affiliation(s)
- Zhiying Jiang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, China; Department of Clinical Laboratory, Nanjing Jiangbei People's Hospital Affiliated of Nantong University, China
| | - Tyler Bahr
- University of Texas Health San Antonio, United States
| | - Chen Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, China
| | - Tao Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, China
| | - Hao Chen
- The Sixth People's Hospital, Shanghai Jiaotong University, China
| | - Shujie Song
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, China
| | - Yuji Ikeno
- University of Texas Health San Antonio, United States
| | - Hengli Tian
- The Sixth People's Hospital, Shanghai Jiaotong University, China
| | - Yidong Bai
- University of Texas Health San Antonio, United States.
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5
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Castilhos LG, Oliveira JS, Adefegha SA, Manzoni AG, Passos DF, Assmann CE, Silveira LL, Trelles KB, Kronbauer M, Doleski PH, Bremm JM, Braun J, Abdalla FH, Gonçalves JF, Andrade CM, Cruz IBM, Burger ME, Leal DBR. Uncaria tomentosa improves cognition, memory and learning in middle-aged rats. Exp Gerontol 2020; 138:111016. [PMID: 32628974 DOI: 10.1016/j.exger.2020.111016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 10/23/2022]
Abstract
Aging accelerates neurodegeneration, while natural and safe neuroprotective agents, such as Uncaria tomentosa, may help to overcome this problem. This study assessed the effects of U. tomentosa extract treatment on the aging process in the brain of Wistar rats. The spatial memory and learning, acetylcholinesterase (AChE) activity, and DNA damage were assessed. Animals of 14 months were tested with different doses of U. tomentosa (5 mg/kg, 15 mg/kg, and 30 mg/kg) and with different durations of treatment (one month and one year). In the Morris Water Maze (MWM), the escape latency was significantly (p < 0.0001) shorter in rats that received 5 mg/kg, 15 mg/kg, and 30 mg/kg of U. tomentosa for both one month and one year of treatment. There was a significant difference in time spent at the platform zone (p < 0.05) of the middle-aged rats treated with U. tomentosa extract for one year when compared to the control rats. The cortex and hippocampus of rats treated with U. tomentosa for one year showed significant (p > 0.05) reduction in AChE activity. DNA damage index on cortex was significantly lower (p < 0.05) in animals treated with 30 mg/kg of U. tomentosa for one month while all the tested doses demonstrated significant (p < 0.001) reductions in DNA damage index in animals treated for one year. In conclusion, U. tomentosa may represent a source of phytochemicals that could enhance memory activity, repair DNA damage, and alter AChE activity, thereby providing neuroprotection during the aging process.
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Affiliation(s)
- Lívia G Castilhos
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil; Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Juliana S Oliveira
- Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Stephen A Adefegha
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil; Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil; Department of Biochemistry, Federal University of Technology, P. M. B. 704, Akure, Nigeria
| | - Alessandra G Manzoni
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Daniela F Passos
- Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Charles E Assmann
- Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Leonardo L Silveira
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Kelly B Trelles
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil; Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Maikel Kronbauer
- Programa de Pós-Graduação em Farmacologia, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Pedro H Doleski
- Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - João M Bremm
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Josiane Braun
- Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Fatima H Abdalla
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil; Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Jamile F Gonçalves
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Cinthia M Andrade
- Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Ivana B M Cruz
- Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil
| | - Marilise E Burger
- Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil; Programa de Pós-Graduação em Farmacologia, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Daniela B R Leal
- Departamento de Microbiologia e Parasitologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil; Programa de Pós-Graduação em Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Av. Roraima, 97105-900 Santa Maria, RS, Brazil.
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6
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Hufnagl C, Leisch M, Weiss L, Melchardt T, Moik M, Asslaber D, Roland G, Steininger P, Meissnitzer T, Neureiter D, Greil R, Egle A. Evaluation of circulating cell-free DNA as a molecular monitoring tool in patients with metastatic cancer. Oncol Lett 2019; 19:1551-1558. [PMID: 31966080 DOI: 10.3892/ol.2019.11192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/06/2019] [Indexed: 01/16/2023] Open
Abstract
The clinical decisions made when treating patients with metastatic cancer require knowledge of the current tumor extent and response to therapy. For the majority of solid tumors, a response assessment, which is based on imaging, is used to guide these decisions. However, measuring serum protein biomarkers (i.e. tumor markers) may be of additional use. Furthermore, tumor markers exhibit variable specificity and sensitivity and cannot therefore be solely relied upon when making decisions regarding cancer treatment. Therefore, there is a clinical requirement for the identification of specific, sensitive and quantitative biomarkers. In recent years, circulating cell-free DNA (cfDNA) and mutation-specific circulating cell-free tumor DNA (cftDNA) have been identified as novel potential biomarkers. In the current study, cfDNA and cftDNA were compared using imaging-based staging and current tumor markers in 15 patients with metastatic colorectal, pancreatic or breast cancer. These patients were treated at the Third Medical Department of Paracelsus Medical University Salzburg (Austria). The results of the current study demonstrated a statistically significant correlation between the concentration changes of cfDNA and cftDNA and response to treatment, which was assessed by imaging. A correlation was not indicated with current clinically used tumor markers, including carcinoembryonic antigen, carcinoma antigen 15-3 and carcinoma antigen 19-9. The present study also indicated a correlation between cfDNA and cftDNA and the tumor volume of metastatic lesions, which was not observed with the current clinically used tumor markers. In conclusion, cfDNA and cftDNA exhibit the potential to become novel biomarkers for the response assessment following cancer treatment, and may serve as a tool for the estimation of tumor volume. The current study further supports the increasingly important role of cfDNA and cftDNA as new monitoring tools for use during cancer therapy.
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Affiliation(s)
- Clemens Hufnagl
- Institute of Pathology, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria
| | - Michael Leisch
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Lukas Weiss
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Thomas Melchardt
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Martin Moik
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Daniela Asslaber
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Geisberger Roland
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Philipp Steininger
- Institute for Research and Development on Advanced Radiation Technologies, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria
| | - Thomas Meissnitzer
- Institute of Radiology, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria
| | - Richard Greil
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Alexander Egle
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
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Zhao Y, Zhao S, Chen Y, Dong X, Peng C, Sun Q, Shan L, Wang Z, Zhao X. Isolation of circulating tumor cells in patients undergoing surgery for esophageal cancer and a specific confirmation method. Oncol Lett 2019; 17:3817-3825. [PMID: 30881502 PMCID: PMC6403499 DOI: 10.3892/ol.2019.10017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 12/06/2018] [Indexed: 01/13/2023] Open
Abstract
The clinical significance of circulating tumor cells (CTCs) in patients with esophageal squamous cell carcinoma (ESCC) who have undergone radical surgery was investigated. A novel confirmation method for identifying CTCs or circulating tumor microemboli (CTM) in ESCC was also investigated. Blood samples from 55 patients with ESCC were collected 1–3 days prior to surgery and 7 days post-surgery. All patients underwent curative thoracic esophagectomy and lymphadenectomy. Blood samples from 20 healthy volunteers were obtained as controls. Isolation by size of epithelial tumor cells (ISET) was performed also. The overall CTC detection rate was 52.7% preoperatively and 49.1% postoperatively. The presence of CTCs correlated with the Tumor-Node-Metastasis stage and the Log odds of positive lymph nodes. No significant difference in perioperative CTC transformation was discovered between the thoracoscopic and laparoscopic approach, and the open approach. The P40+/cluster of differentiation (CD)45− phenotype was confirmed in the CTCs and CTM. ISET appeared to have high sensitivity for detecting CTCs within ESCC patients. Immunofluorescence staining for CD45 and P40 was a specific, accurate and convenient method for confirming the presence of CTCs or CTM in patients with ESCC, and is strongly recommended as a supplement to morphological analysis.
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Affiliation(s)
- Yunpeng Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Shukang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yingjie Chen
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Xiaopeng Dong
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Chuanliang Peng
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Qifeng Sun
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Lei Shan
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Zhendan Wang
- Department of Thoracic Surgery, Shandong Cancer Hospital and Institute (HL), Jinan, Shandong 250177, P.R. China
| | - Xiaogang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
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8
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Takeshita T, Yamamoto Y, Yamamoto-Ibusuki M, Tomiguchi M, Sueta A, Iwase H. ESR1 and PIK3CA mutational status in serum and plasma from metastatic breast cancer patients: A comparative study. Cancer Biomark 2018; 22:345-350. [PMID: 29689710 DOI: 10.3233/cbm-171161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
PURPOSE Plasma and serum cell-free DNA (cfDNA) are useful sources of tumor DNA, but comparative investigations of the tumor mutational status between them are rare. METHODS we performed droplet digital PCR assay for representative hotspot mutations in metastatic breast cancer (MBC) (ESR1 and PIK3CA) in serum and plasma cfDNA concurrently extracted from the blood of 33 estrogen receptor-positive MBC patients. RESULTS ESR1 mutations in plasma cfDNA were found in 7 of the 33 patients; ESR1 mutations in serum cfDNA were detected in only one out of 7 patients with ESR1 mutations in plasma cfDNA. PIK3CA exon 9 and exon 20 mutations in plasma cfDNA were found in 3 and 7 out of the 33 patients, respectively; PIK3CA exon 9 mutations in serum cfDNA were detected in 2 out of 3 patients with PIK3CA exon 9 mutations in plasma cfDNA; PIK3CA exon 20 mutations in serum cfDNA were detected in 2 out of 7 patients with PIK3CA exon 20 mutations in plasma cfDNA. CONCLUSIONS Here we show the higher frequency of ESR1 and PIK3CA mutations in the plasma than in the serum in 33 MBC patients; therefore, serum samples should not be considered the preferred source of cfDNA.
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Affiliation(s)
- Takashi Takeshita
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yutaka Yamamoto
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto 860-8556, Japan
| | - Mutsuko Yamamoto-Ibusuki
- Department of Molecular-Targeting Therapy for Breast Cancer, Kumamoto University Hospital, Kumamoto 860-8556, Japan
| | - Mai Tomiguchi
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto 860-8556, Japan
| | - Aiko Sueta
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hirotaka Iwase
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto 860-8556, Japan
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9
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Lima-Oliveira G, Monneret D, Guerber F, Guidi GC. Sample management for clinical biochemistry assays: Are serum and plasma interchangeable specimens? Crit Rev Clin Lab Sci 2018; 55:480-500. [PMID: 30309270 DOI: 10.1080/10408363.2018.1499708] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The constrained economic context leads laboratories to centralize their routine analyses on high-throughput platforms, to which blood collection tubes are sent from peripheral sampling sites that are sometimes distantly located. Providing biochemistry results as quickly as possible implies to consolidate the maximum number of tests on a minimum number of blood collection tubes, mainly serum tubes and/or tubes with anticoagulants. However, depending on the parameters and their pre-analytical conditions, the type of matrix - serum or plasma - may have a significant impact on results, which is often unknown or underestimated in clinical practice. Importantly, the matrix-related effects may be a limit to the consolidation of analyses on a single tube, and thus must be known by laboratory professionals. The purpose of the present critical review is to put forward the main differences between using serum and plasma samples on clinical biochemistry analyses, in order to sensitize laboratory managers to the need for standardization. To enrich the debate, we also provide an additional comparison of serum and plasma concentrations for approximately 30 biochemistry parameters. Properties, advantages, and disadvantages of serum and plasma are discussed from a pre-analytical standpoint - before, during, and after centrifugation - with an emphasis on the importance of temperature, delay, and transport conditions. Then, differences in results between these matrices are addressed for many classes of biochemistry markers, particularly proteins, enzymes, electrolytes, lipids, circulating nucleic acids, metabolomics markers, and therapeutic drugs. Finally, important key-points are proposed to help others choose the best sample matrix and guarantee quality of clinical biochemistry assays. Moreover, awareness of the implications of using serum and plasma samples on various parameters assayed in the laboratory is an important requirement to ensure reliable results and improve patient care.
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Affiliation(s)
- Gabriel Lima-Oliveira
- a Section of Clinical Biochemistry, Department of Neurosciences , Biomedicine and Movement Sciences, University of Verona , Verona , Italy.,b Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM) of the Latin America Confederation of Clinical Biochemistry (COLABIOCLI) , Montevideo , Uruguay
| | - Denis Monneret
- c Department of Biochemistry and Molecular Biology , Lyon Sud Hospital Group, Hospices Civils de Lyon , Pierre Bénite , France
| | | | - Gian Cesare Guidi
- a Section of Clinical Biochemistry, Department of Neurosciences , Biomedicine and Movement Sciences, University of Verona , Verona , Italy.,b Latin American Working Group for Preanalytical Phase (WG-PRE-LATAM) of the Latin America Confederation of Clinical Biochemistry (COLABIOCLI) , Montevideo , Uruguay
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10
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Sharma B, Kanwar SS. Phosphatidylserine: A cancer cell targeting biomarker. Semin Cancer Biol 2018; 52:17-25. [DOI: 10.1016/j.semcancer.2017.08.012] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/12/2017] [Accepted: 08/30/2017] [Indexed: 12/11/2022]
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11
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Abstract
Darwin's gemmules were supposed to be "thrown off" by cells and were "inconceivably minute and numerous as the stars in heaven." They were capable of self-propagation and diffusion from cell to cell, and circulation through the system. The word "gene" coined by Wilhelm Johannsen, was derived from de Vries's term "pangen," itself a substitute for "gemmule" in Darwin's Pangenesis. Johannsen resisted the "morphological" conception of genes as particles with a certain structure. Morgan's genes were considered to be stable entities arranged in an orderly linear pattern on chromosomes, like beads on a string. In the late 1940s, McClintock challenged the concept of the stability of the gene when she discovered that some genes could move within a chromosome and between chromosomes. In 1948, Mandel and Metais reported the presence of cell-free nucleic acids in human blood for the first time. Over the past several decades, it has been universally accepted that almost all types of cells not only shed molecules such as cell-free DNA (including genomic DNA, tumor DNA and fetal DNA), RNAs (including mRNA and small RNAs) and prions, but also release into the extracellular environment diverse types of membrane vesicles (known as extracellular vesicles) containing DNA, RNA and proteins. Thus Darwin's speculative gemmules of the 19th century have become the experimentally demonstrated circulating cell-free DNA, mobile RNAs, prions and extracellular vesicles.
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Affiliation(s)
- Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China; Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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12
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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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13
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Trevisiol C, Di Fabio F, Nascimbeni R, Peloso L, Salbe C, Ferruzzi E, Salerni B, Gion M. Prognostic Value of Circulating KRAS2 Gene Mutations in Colorectal Cancer with Distant Metastases. Int J Biol Markers 2018. [DOI: 10.1177/172460080602100405] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While tissue KRAS2 mutations have been extensively investigated, the role of circulating mutant KRAS2 gene in patients with colorectal carcinoma remains obscure. The aim of the present study was to explore the prognostic significance of circulating KRAS2 gene mutational status in subjects undergoing primary treatment for colorectal cancer. Codon 12 KRAS2 mutations were examined in DNA samples extracted from the serum of 86 patients with colorectal cancer and were compared with the KRAS2 status of their primary tumors. Tissue and serum KRAS2 status was compared with other clinicopathological variables (including CEA and CA 19-9 levels) and with cancer-related survival. KRAS2 mutations were found in tissue samples of 28 patients (33%); serum KRAS2 mutations were detected in 10 of them (36%). Serum KRAS2 status was significantly associated with Dukes' stage D (p=0.001) and with preoperative CA 19-9 levels (p=0.01). At multivariate analysis, cancer-related survival was associated with Dukes' stage (p<0.0001), CEA level (p=0.02), and mutant circulating KRAS2 (p=0.01). All 7 stage D patients with serum KRAS2 mutations died of the disease within 24 months of primary treatment; cancer-related survival was significantly better in 9 stage D patients without serum KRAS2 mutations, with 5 patients (56%) alive after 24 months and 1 patient (13%) alive after 44 months. Residual disease after surgery was evident in all 7 stage D patients with mutant circulating KRAS2, and in 5 out of 9 stage D patients without serum mutations. Serum KRAS2 status may impact substantially on the management of stage D colorectal carcinoma, since it appears to correlate with prognosis in this patient subgroup.
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Affiliation(s)
- C. Trevisiol
- ABO Association, c/o Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice
| | - F. Di Fabio
- Department General Surgery, University of Brescia, Brescia
| | - R. Nascimbeni
- Department General Surgery, University of Brescia, Brescia
| | - L. Peloso
- ABO Association, c/o Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice
| | - C. Salbe
- ABO Association, c/o Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice
| | - E. Ferruzzi
- ABO Association, c/o Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice
| | - B. Salerni
- Department General Surgery, University of Brescia, Brescia
| | - M. Gion
- Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice - Italy
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14
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Seefeld M, El Tarhouny S, Fan A, Hahn S, Holzgreve W, Zhong X. Parallel Assessment of Circulatory Cell-Free DNA by PCR and Nucleosomes by ELISA in Breast Tumors. Int J Biol Markers 2018; 23:69-73. [DOI: 10.1177/172460080802300202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objectives In order to assess the potential biomolecules for breast cancer, we analyzed in parallel the levels of cell-free glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and cell-free nucleosomes in serum samples from patients with benign and malignant breast tumors. The levels of cell-free DNA obtained by quantitative PCR were compared with those obtained by enzyme-linked immunosorbent assay (ELISA). Methods Twenty-three patients with benign breast tumors, 27 patients with breast cancer, and 32 age-matched healthy women were recruited. The amounts of serum nucleosomes were analyzed by ELISA and the levels of cell-free GAPDH were measured by real-time quantitative PCR. The correlation between nucleosome and cell-free GAPDH levels was examined using the Spearman rank test. Results The levels of cell-free GAPDH were significantly higher in the serum samples of patients with benign and malignant breast tumors than in those of the control group (median 37,966 GE/mL, range 3,802–130,104 versus 11,770 GE/mL, range 2,198–73,522, p=0.035 and median 40,698 GE/mL, range 3,644–192,482 versus 11,770 GE/mL range 2,198–73,522, p=0.001). The concentration of cell-free GAPDH correlated significantly with the quantities of nucleosomes in serum samples (r=0.451, p=0.000). There was, however, no significant difference between healthy individuals and women with benign breast tumors or breast cancer in terms of nucleosomes determined by ELISA. Conclusion Our data suggest that the cell-free serum GAPDH DNA assayed by quantitative PCR is a better biomarker than nucleosomes assayed by ELISA in patients with breast tumors.
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Affiliation(s)
- M. Seefeld
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
- The first two authors contributed
equally to this work
| | - S. El Tarhouny
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
- Department of Medical Biochemistry,
Faculty of Medicine, Zagazig University, Zagazig - Egypt
- The first two authors contributed
equally to this work
| | - A.X.C. Fan
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
| | - S. Hahn
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
| | - W. Holzgreve
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
| | - X.Y. Zhong
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
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15
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Patel K, Nagel M, Wesolowski M, Dees S, Rivera-Milla E, Geldmacher C, Dheda K, Hoelscher M, Labugger I. Evaluation of a Urine-Based Rapid Molecular Diagnostic Test with Potential to Be Used at Point-of-Care for Pulmonary Tuberculosis: Cape Town Cohort. J Mol Diagn 2017; 20:215-224. [PMID: 29269279 DOI: 10.1016/j.jmoldx.2017.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 10/02/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022] Open
Abstract
Tuberculosis (TB) diagnosis among sputum-scarce patients is time consuming. Thus, a nonsputum diagnostic alternative is urgently needed. The Mycobacterium tuberculosis-specific transrenal (Tr) DNA from urine is a potential target for TB diagnostics. In this study, a new urine-based Tr-DNA molecular assay was evaluated for diagnosis of pulmonary tuberculosis among 428 adults suspected of having pulmonary TB (164 HIV positive, 263 HIV negative) from Cape Town, South Africa. Tr-DNA was isolated from 4 mL of EDTA urine, and a rapid, double-stranded, primer-based PCR method was performed targeting the Mycobacterium tuberculosis-specific direct repeat region. Each Tr-DNA eluate was tested in triplicate using an automated molecular analyzer with controls included in each test. With liquid culture used as the gold standard, the Tr-DNA assay showed sensitivity of 42.9% (n = 75/175; 95% CI, 35.4%-50.5%) and specificity of 88.6% (n = 210/237; 95% CI, 83.9%-92.4%). Among HIV-infected patients with TB, sensitivity and specificity were 45.2% and 89.0%, respectively. The combination of smear microscopy and Tr-DNA increased the sensitivity to 83.8% (smear microscopy alone, 75.1%), with 96.6% specificity. This study indicates that Tr-DNA has a moderate specificity with low sensitivity for diagnosis of pulmonary TB. Despite low sensitivity, this diagnostic test may have potential in combination with smear microscopy to support TB diagnosis in HIV-endemic regions, where sputum-scarce patients are common.
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Affiliation(s)
- Krutarth Patel
- Alere Technologies GmbH, Jena, Germany; Center for International Health, University of Munich, Munich, Germany.
| | | | | | | | | | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology & Clinical Immunology, Department of Medicine and UCT Lung Institute, University of Cape Town, Cape Town, South Africa
| | - Michael Hoelscher
- Center for International Health, University of Munich, Munich, Germany; Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
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16
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Abstract
The accuracy and efficiency of tumor treatment depends mainly on early and precise diagnosis. Although histopathology is always the gold standard for cancer diagnosis, noninvasive biomarkers represent an opportunity for early detection and molecular staging of cancer. Besides the classical tumor markers, noncoding RNAs (ncRNAs) emerge to be a novel category of biomarker for cancer diagnosis since the dysregulation of ncRNAs is closely associated with the development and progression of human cancers such as liver, lung, breast, gastric, and other kinds of cancers. In this chapter, we will summarize the different types of ncRNAs in the diagnosis of major human cancers. In addition, we will introduce the recent advances in the detection and applications of circulating serum or plasma ncRNAs and non-blood fluid ncRNAs because the noninvasive body fluid-based assays are easy to examine for cancer diagnosis and monitoring.
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17
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Rykova E, Sizikov A, Roggenbuck D, Antonenko O, Bryzgalov L, Morozkin E, Skvortsova K, Vlassov V, Laktionov P, Kozlov V. Circulating DNA in rheumatoid arthritis: pathological changes and association with clinically used serological markers. Arthritis Res Ther 2017; 19:85. [PMID: 28464939 PMCID: PMC5414163 DOI: 10.1186/s13075-017-1295-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/07/2017] [Indexed: 12/15/2022] Open
Abstract
Background Early diagnosis of rheumatoid arthritis (RA) is crucial to providing effective therapy and often hampered by unspecific clinical manifestations. Elevated levels of extracellular circulating DNA (cirDNA) in patients with autoimmune disease were found to be associated with etiopathogenesis. To our knowledge, this is the first study to investigate the putative diagnostic use of cirDNA in RA and its association with disease activity. Methods Blood samples were taken from 63 healthy subjects (HS) and 74 patients with RA. cirDNA was extracted from plasma and cell surface-bound cirDNA fractions (csbDNA). cirDNA concentration was measured by quantitative real-time polymerase chain reaction. Rheumatoid factor was analyzed by immunonephelometry, whereas C-reactive protein and anticitrullinated protein/peptide antibodies (ACPA) were detected by enzyme-linked immunosorbent assay. Results Plasma cirDNA was significantly elevated in patients with RA compared with HS (12.0 versus 8.4 ng/ml, p < 0.01). In contrast, nuclear csbDNA (n-csbDNA) was significantly decreased (24.0 versus 50.8 ng/ml, p < 0.01), whereas mitochondrial csbDNA (m-csbDNA) was elevated (1.44 × 106 copies/ml versus 0.58 × 106 copies/ml, p < 0.05) in RA. The combination of csbDNA (mitochondrial + nuclear) with ACPA reveals the best positive/negative likelihood ratios (LRs) for the discrimination RA from HS (LR+ 61.00, LR− 0.03) in contrast to ACPA (LR+ 9.00, LR− 0.19) or csbDNA (LR+ 8.00, LR− 0.18) alone. Conclusions Nuclear and mitochondrial cirDNA levels in plasma and on the surface of blood cells are modulated in RA. Combination of cirDNA values with ACPA can improve the serological diagnosis of RA. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1295-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Rykova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Novosibirsk State Technical University, Novosibirsk, Russia
| | - Aleksey Sizikov
- Federal State Budgetary Scientific Institution "Research Institute of Fundamental and Clinical Immunology", Novosibirsk, Russia
| | - Dirk Roggenbuck
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Oksana Antonenko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.
| | | | - Evgeniy Morozkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Academician E. N. Meshalkin, Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
| | - Kseniya Skvortsova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Academician E. N. Meshalkin, Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
| | - Vladimir Kozlov
- Federal State Budgetary Scientific Institution "Research Institute of Fundamental and Clinical Immunology", Novosibirsk, Russia
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18
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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19
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Abstract
Saliva, like other bodily fluids, has been used to monitor human health and disease. This study tests the hypothesis that informative human mRNA exists in cell-free saliva. If present, salivary mRNA may provide potential biomarkers to identify populations and patients at high risk for oral and systemic diseases. Unstimulated saliva was collected from ten normal subjects. RNA was isolated from the cell-free saliva supernatant and linearly amplified. High-density oligonucleotide microarrays were used to profile salivary mRNA. The results demonstrated that there are thousands of human mRNAs in cell-free saliva. Quantitative PCR (Q-PCR) analysis confirmed the present of mRNA identified by our microarray study. A reference database was generated based on the mRNA profiles in normal saliva. Our finding proposes a novel clinical approach to salivary diagnostics, Salivary Transcriptome Diagnostics (STD), for potential applications in disease diagnostics as well as normal health surveillance.
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Affiliation(s)
- Y Li
- School of Dentistry and Dental Research Institute, University of California-Los Angeles, 10833 Le Conte Avenue, Rm. 73-017 CHS, Los Angeles, CA 90095, USA
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20
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Cai H, Stott MA, Ozcelik D, Parks JW, Hawkins AR, Schmidt H. On-chip wavelength multiplexed detection of cancer DNA biomarkers in blood. BIOMICROFLUIDICS 2016; 10:064116. [PMID: 28058082 PMCID: PMC5176344 DOI: 10.1063/1.4968033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/06/2016] [Indexed: 05/03/2023]
Abstract
We have developed an optofluidic analysis system that processes biomolecular samples starting from whole blood and then analyzes and identifies multiple targets on a silicon-based molecular detection platform. We demonstrate blood filtration, sample extraction, target enrichment, and fluorescent labeling using programmable microfluidic circuits. We detect and identify multiple targets using a spectral multiplexing technique based on wavelength-dependent multi-spot excitation on an antiresonant reflecting optical waveguide chip. Specifically, we extract two types of melanoma biomarkers, mutated cell-free nucleic acids -BRAFV600E and NRAS, from whole blood. We detect and identify these two targets simultaneously using the spectral multiplexing approach with up to a 96% success rate. These results point the way toward a full front-to-back chip-based optofluidic compact system for high-performance analysis of complex biological samples.
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Affiliation(s)
- H Cai
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - M A Stott
- Department of Electrical and Computer Engineering, Brigham Young University , 459 Clyde Building, Provo, Utah 84602, USA
| | - D Ozcelik
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - J W Parks
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - A R Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University , 459 Clyde Building, Provo, Utah 84602, USA
| | - H Schmidt
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
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21
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Li J, Macdonald J. Multiplexed lateral flow biosensors: Technological advances for radically improving point-of-care diagnoses. Biosens Bioelectron 2016; 83:177-92. [DOI: 10.1016/j.bios.2016.04.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/22/2022]
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22
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Bozhenko VK, Kharchenko NV, Vaskevich EF, Kudinova EA, Oorzhak AV, Rozhkova NI, Trotsenko ID. [Mammaglobin in peripheral blood and tumor in breast cancer patients]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 62:453-7. [PMID: 27563000 DOI: 10.18097/pbmc20166204453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Currently, no molecular biological markers do exist for early diagnosis of breast cancer. One of the possible candidates for the marker of early breast cancer is mammaglobin (MGB1) or SCGB2A2 (secretoglobin, family 2A, member 2), characterized by the maximal expression level in early breast cancer. Using the RT-PCR method MGB1 mRNA expression was examined in 57 tumor tissue samples and 57 samples of morphologically non-malignant tissue (MNT) of breast cancer (BC) patients. Specificity and sensitivity of the MGB1 mRNA assay in peripheral blood of BC patients was evaluated by nested PCR. 169 blood samples (from 95 BC patients, 22 from patients with benign breast tumors, 28 from patients with tumors of other localizations, and 24 samples from healthy donors) have been analyzed. MGB1 expression was significantly higher in BC tissue samples compared to MNT (p=0.0019). The maximal expression level was in the samples T1 (p=0.013), stage I BC (p=0.037), GI (p=0.0019). The MGB1 expression positively correlated with expression of estrogen (p = 0,034) and progesterone (p=0.0004) receptors. Sensitivity and specificity of the MGB1 mRNA assay in peripheral blood were 60.6% and 92.3%, respectively. Expression of MGB1 was higher in BC than MNT and it decreased during BC progression. The sensitivity and specificity of the MGB1 mRNA assay may be used as an additional diagnostic method.
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Affiliation(s)
- V K Bozhenko
- Russian Scientific Center of Roentgenoradiology, Moscow, Russia
| | | | | | - E A Kudinova
- Russian Scientific Center of Roentgenoradiology, Moscow, Russia
| | - A V Oorzhak
- Russian Scientific Center of Roentgenoradiology, Moscow, Russia
| | - N I Rozhkova
- National center of Oncology of the reproductive organs, Moscow, Russia
| | - I D Trotsenko
- People Friendship University of Russia, Moscow, Russia
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23
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Larrea E, Sole C, Manterola L, Goicoechea I, Armesto M, Arestin M, Caffarel MM, Araujo AM, Araiz M, Fernandez-Mercado M, Lawrie CH. New Concepts in Cancer Biomarkers: Circulating miRNAs in Liquid Biopsies. Int J Mol Sci 2016; 17:ijms17050627. [PMID: 27128908 PMCID: PMC4881453 DOI: 10.3390/ijms17050627] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 12/19/2022] Open
Abstract
The effective and efficient management of cancer patients relies upon early diagnosis and/or the monitoring of treatment, something that is often difficult to achieve using standard tissue biopsy techniques. Biological fluids such as blood hold great possibilities as a source of non-invasive cancer biomarkers that can act as surrogate markers to biopsy-based sampling. The non-invasive nature of these “liquid biopsies” ultimately means that cancer detection may be earlier and that the ability to monitor disease progression and/or treatment response represents a paradigm shift in the treatment of cancer patients. Below, we review one of the most promising classes of circulating cancer biomarkers: microRNAs (miRNAs). In particular, we will consider their history, the controversy surrounding their origin and biology, and, most importantly, the hurdles that remain to be overcome if they are really to become part of future clinical practice.
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Affiliation(s)
- Erika Larrea
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - Carla Sole
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - Lorea Manterola
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - Ibai Goicoechea
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - María Armesto
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - María Arestin
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - María M Caffarel
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
| | - Angela M Araujo
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - María Araiz
- Hematology Department, Donostia Hospital, 20014 San Sebastián, Spain.
| | | | - Charles H Lawrie
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, UK.
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Fernandez-Mercado M, Manterola L, Lawrie CH. MicroRNAs in Lymphoma: Regulatory Role and Biomarker Potential. Curr Genomics 2016; 16:349-58. [PMID: 27047255 PMCID: PMC4763973 DOI: 10.2174/1389202916666150707160147] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 12/19/2022] Open
Abstract
Although it is now evident that microRNAs (miRNAs) play a critical regulatory role in many, if not all, pathological and physiological processes, remarkably they have only formally been recognized for less than fifteen years. These endogenously produced short non-coding RNAs have created a new paradigm of gene control and have utility as both novel biomarkers of cancer and as potential therapeutics. In this review we consider the role of miRNAs in lymphoid biology both under physiological (i.e. lymphopoiesis) and malignant (i.e. lymphomagenesis) conditions. In addition to the functional significance of aberrant miRNA expression in lymphomas we discuss their use as novel biomarkers, both as a in situ tumour biomarker and as a non-invasive surrogate for the tumour by testing miRNAs in the blood of patients. Finally we consider the use of these molecules as potential therapeutic agents for lymphoma (and other cancer) patients and discuss some of the hurdles yet to be overcome in order to translate this potential into clinical practice
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Affiliation(s)
| | - Lorea Manterola
- Oncology area, Biodonostia Research Institute, San Sebastián, Spain
| | - Charles H Lawrie
- Oncology area, Biodonostia Research Institute, San Sebastián, Spain; ; Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK;; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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John K, Rösner I, Keilholz U, Gauler T, Bantel H, Grünwald V. Baseline caspase activity predicts progression free survival of temsirolimus-treated head neck cancer patients. Eur J Cancer 2015; 51:1596-602. [DOI: 10.1016/j.ejca.2015.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 05/09/2015] [Indexed: 10/23/2022]
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El Bali L, Diman A, Bernard A, Roosens NHC, De Keersmaecker SCJ. Comparative study of seven commercial kits for human DNA extraction from urine samples suitable for DNA biomarker-based public health studies. J Biomol Tech 2015; 25:96-110. [PMID: 25365790 DOI: 10.7171/jbt.14-2504-002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at -20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies.
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Affiliation(s)
- Latifa El Bali
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and ; Louvain Center for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, Brussels, Belgium
| | - Aurélie Diman
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Center for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, Brussels, Belgium
| | - Nancy H C Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and
| | - Sigrid C J De Keersmaecker
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and
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Fernandez-Mercado M, Manterola L, Larrea E, Goicoechea I, Arestin M, Armesto M, Otaegui D, Lawrie CH. The circulating transcriptome as a source of non-invasive cancer biomarkers: concepts and controversies of non-coding and coding RNA in body fluids. J Cell Mol Med 2015; 19:2307-23. [PMID: 26119132 PMCID: PMC4594673 DOI: 10.1111/jcmm.12625] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/07/2015] [Indexed: 12/12/2022] Open
Abstract
The gold standard for cancer diagnosis remains the histological examination of affected tissue, obtained either by surgical excision, or radiologically guided biopsy. Such procedures however are expensive, not without risk to the patient, and require consistent evaluation by expert pathologists. Consequently, the search for non-invasive tools for the diagnosis and management of cancer has led to great interest in the field of circulating nucleic acids in plasma and serum. An additional benefit of blood-based testing is the ability to carry out screening and repeat sampling on patients undergoing therapy, or monitoring disease progression allowing for the development of a personalized approach to cancer patient management. Despite having been discovered over 60 years ago, the clear clinical potential of circulating nucleic acids, with the notable exception of prenatal diagnostic testing, has yet to translate into the clinic. The recent discovery of non-coding (nc) RNA (in particular micro(mi)RNAs) in the blood has provided fresh impetuous for the field. In this review, we discuss the potential of the circulating transcriptome (coding and ncRNA), as novel cancer biomarkers, the controversy surrounding their origin and biology, and most importantly the hurdles that remain to be overcome if they are really to become part of future clinical practice.
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Affiliation(s)
| | - Lorea Manterola
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - Erika Larrea
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - Ibai Goicoechea
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - María Arestin
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - María Armesto
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - David Otaegui
- Multiple Sclerosis Group, Biodonostia Research Institute, San Sebastian, Spain
| | - Charles H Lawrie
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain.,Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, UK.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Buehning LJ, Hedayat KM, Sachdeva A, Golshan S, Lapraz JC. A novel use of biomarkers in the modeling of cancer activity based on the theory of endobiogeny. Glob Adv Health Med 2014; 3:55-60. [PMID: 25105079 PMCID: PMC4104563 DOI: 10.7453/gahmj.2013.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Introduction: Cancer is a complex disorder whose detection and monitoring remains challenging. A biological
modeling system, the biology of functions (BoF), claims to be able to evaluate physiologic elements
related to carcinogenic activity. A pilot study was undertaken to evaluate the accuracy of the BoF
in detecting differences between cancer cases and matched controls. Materials and Methods: A retrospective case control study was performed using the BoF analyses of 46 patients with all
types of solid and hematgenous cancers, active and inactive (total cases), and 46 controls from a
private practice. The standard BoF panel of 17 biomarkers was evaluated. Sixty-two of 150 BoF
indices derived from these biomarkers were pre-selected for analysis based on their relationship to
cancer physiology. The data was analyzed with the Wilcoxon Signed Ranks Test using SPSS
software. Results: Of the 62 indices, 7 were found to be statistically significant in comparing total cancer cases
to controls: βMSH/αMSH, Estrogen Fraction #5, Comparative Genital Androgeny, Thyroid,
Genito-thyroid, Catabolism/Anabolism and Pro-inflammatory. Conclusions: In a small retrospective case control study, statistically significant differences were found
between cancer cases and controls in 7 BoF indices. These indices are indicators of physiological
conditions consistent with cancer growth. These results warrant further study of this biological
modeling system in cancer patients.
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Affiliation(s)
- Laura J Buehning
- Samueli Institute, San Diego, University of California at San Diego/ San Diego State University Preventive Medicine Program, California (Dr Buehning), United States
| | - Kamyar M Hedayat
- American Society of Endobiogenic Medicine and Integrative Physiology (ASEMIP), San Diego (Dr Hedayat), United States
| | | | - Shahrokh Golshan
- University of California at San Diego Department of Psychiatry, La Jolla, California (Dr Golshan), United States
| | - Jean Claude Lapraz
- Société internationale de médecine endobiogénique et de physiologie intégrative (SIMEPI), Paris, France (Dr Lapraz)
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Wang S, Chen Y, Wu Z. Advances in the medical research and clinical applications on the plasma DNA. Transl Pediatr 2014; 3:140-8. [PMID: 26835332 PMCID: PMC4729110 DOI: 10.3978/j.issn.2224-4336.2014.03.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Plasma DNA has had a strong impact and influence on basic medical research and clinical practice since the discovery of low levels of plasma DNA in healthy individuals under different physiological conditions. Although the source of circulating DNA still requires further investigation, a wide range of research has also proven the value of qualitative and quantitative measurements of plasma DNA in many disease conditions. The use of plasma DNA has a biomarker is advantageous due to accessibility, reliability, reproducibility, sensitivity, specific and relatively low cost. Recently, the detection of circulating (plasma) DNA quantitative changes have been using in the studies on the tumor gene mutations and to monitor disease progressing and to predict the disease prognosis. Such technique also has been using other many different fields, particularly in prenatal diagnosis, for which plasma DNA testing is preferable due to non-invasiveness. This article reviews the research progression and clinical applications of plasma DNA in the last several years.
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Affiliation(s)
- Shuye Wang
- 1 Department of Hematology, The first Affiliated Hospital of Harbin Medical University, Harbin 150001, China ; 2 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Yuanyuan Chen
- 1 Department of Hematology, The first Affiliated Hospital of Harbin Medical University, Harbin 150001, China ; 2 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Zhanhe Wu
- 1 Department of Hematology, The first Affiliated Hospital of Harbin Medical University, Harbin 150001, China ; 2 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
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Ng RHW, Ngan R, Wei WI, Gullane PJ, Phillips J. Trans-Oral Brush Biopsies and Quantitative PCR for EBV DNA Detection and Screening of Nasopharyngeal Carcinoma. Otolaryngol Head Neck Surg 2014; 150:602-9. [DOI: 10.1177/0194599813520136] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Objectives To evaluate a newly developed noninvasive ambulatory, quantitative polymerase chain reaction (Q-PCR) Epstein-Barr virus (EBV) DNA detection and screening system (NP Screen™) for nasopharyngeal carcinoma (NPC). Study Design Correlation of the nasopharyngeal epithelial EBV-DNA levels and clinical findings by nasopharyngoscopy and final pathologic diagnosis of NPC with biopsy. Setting Multicenter ENT/Oncology clinics in Hong Kong (Radiation Oncology Clinic at the Queen Elizabeth Hospital and Radiation Oncology Clinic and Head and Neck Clinic, Queen Mary Hospital, University of Hong Kong) and in Toronto, Canada (the Otolaryngology-Head and Neck Clinic at the Rouge Valley Health System and 2 large ENT practices in Toronto). Methods A single-use trans-oral brush was used for rapid, nontraumatic nasopharyngeal (NP) epithelial cells DNA harvest in 600 Chinese patients, combined with a preservation and shipping kit for remote, real-time Q-PCR EBV DNA determinations. Results All 600 patients had NP brushings using NP Screen in an ambulatory environment, and no adverse events or complications were recorded. A final 578 patients were included with sufficient amount of DNA for completion of the Q-PCR assay. Of these 578 patients, 94 were confirmed positive for NPC histologically. The study yielded a sensitivity of 98.9%, specificity of 99.3%, positive predictive value (PPV) of 96.9%, and negative predictive value (NPP) of 99.7% for NP Screen in detecting NPC. Endoscopy had a sensitivity of 94%, specificity 97.1%, PPV 85%, and NPP 98.9%. Conclusions The trans-oral brushing system fulfills the characteristics of a noninvasive, sensitive, specific detection method suitable for routine, large-scale ambulatory NPC risk assessment for high-risk NPC populations.
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Affiliation(s)
- Raymond H. W. Ng
- Departments of Otolaryngology-Head and Neck Surgery, Centenary Site, Rouge Valley Health System, Scarborough, Ontario, Canada
| | - Roger Ngan
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | | | - Patrick J. Gullane
- Department of Otolaryngology-Head and Neck Surgery, The Toronto Hospital, University of Toronto, Toronto, Ontario, Canada
| | - John Phillips
- The Hospital for Sick Children, The University of Toronto, Toronto, Ontario, Canada
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MAO X, GURUNG A, XU H, BALODA M, HE Y, LIU G. Simultaneous Detection of Nucleic Acid and Protein Using Gold Nanoparticles and Lateral Flow Device. ANAL SCI 2014; 30:637-42. [DOI: 10.2116/analsci.30.637] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Xun MAO
- Department of Chemistry and Biochemistry, North Dakota State University
| | - Anant GURUNG
- Department of Chemistry and Biochemistry, North Dakota State University
| | - Hui XU
- Department of Chemistry and Biochemistry, North Dakota State University
| | - Meenu BALODA
- Department of Chemistry and Biochemistry, North Dakota State University
| | - Yuqing HE
- Institute of Medical Systems Biology, Guangdong Medical College
| | - Guodong LIU
- Department of Chemistry and Biochemistry, North Dakota State University
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Fojtu M, Gumulec J, Balvan J, Raudenska M, Sztalmachova M, Polanska H, Smerkova K, Adam V, Kizek R, Masarik M. Utilization of paramagnetic microparticles for automated isolation of free circulating mRNA as a new tool in prostate cancer diagnostics. Electrophoresis 2013; 35:306-15. [PMID: 23857647 DOI: 10.1002/elps.201300190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/15/2013] [Accepted: 05/16/2013] [Indexed: 11/10/2022]
Abstract
Determination of serum mRNA gained a lot of attention in recent years, particularly from the perspective of disease markers. Streptavidin-modified paramagnetic particles (SMPs) seem an interesting technique, mainly due to possible automated isolation and high efficiency. The aim of this study was to optimize serum isolation protocol to reduce the consumption of chemicals and sample volume. The following factors were optimized: amounts of (i) paramagnetic particles, (ii) oligo(dT)20 probe, (iii) serum, and (iv) the binding sequence (SMPs, oligo(dT)20 , serum vs. oligo(dT)20 , serum and SMPs). RNA content was measured, and the expression of metallothionein-2A as possible prostate cancer marker was analyzed to demonstrate measurable RNA content with ability for RT-PCR detection. Isolation is possible on serum volume range (10-200 μL) without altering of efficiency or purity. Amount of SMPs can be reduced up to 5 μL, with optimal results within 10-30 μL SMPs. Volume of oligo(dT)20 does not affect efficiency, when used within 0.1-0.4 μL. This optimized protocol was also modified to fit needs of automated one-step single-tube analysis with identical efficiency compared to conventional setup. One-step analysis protocol is considered a promising simplification, making RNA isolation suitable for automatable process.
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Affiliation(s)
- Michaela Fojtu
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Norton SE, Luna KK, Lechner JM, Qin J, Fernando MR. A new blood collection device minimizes cellular DNA release during sample storage and shipping when compared to a standard device. J Clin Lab Anal 2013; 27:305-11. [PMID: 23852790 PMCID: PMC3748785 DOI: 10.1002/jcla.21603] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 02/06/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) circulating in blood is currently used for noninvasive diagnostic and prognostic tests. Minimizing background DNA is vital for detection of low abundance cfDNA. We investigated whether a new blood collection device could reduce background levels of genomic DNA (gDNA) in plasma compared to K(3) EDTA tubes, when subjected to conditions that may occur during sample storage and shipping. METHODS Blood samples were drawn from healthy donors into K(3) EDTA and Cell-Free DNA™ BCT (BCT). To simulate shipping, samples were shaken or left unshaken. In a shipping study, samples were shipped or not shipped. To assess temperature variations, samples were incubated at 6°C, 22°C, and 37°C. In all cases, plasma was harvested by centrifugation and total plasma DNA (pDNA) assayed by quantitative real-time polymerase chain reaction (qPCR). RESULTS Shaking and shipping blood in K(3) EDTA tubes showed significant increases in pDNA, whereas no change was seen in BCTs. Blood in K(3) EDTA tubes incubated at 6°C, 22°C, and 37°C showed increases in pDNA while pDNA from BCTs remained stable. CONCLUSIONS BCTs prevent increases in gDNA levels that can occur during sample storage and shipping. This new device permits low abundance DNA target detection and allows accurate cfDNA concentrations.
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de Carvalho FM, de Almeida Pereira T, Gonçalves PL, Jarske RD, Pereira FEL, Louro ID. Hepatocellular carcinoma and liver cirrhosis TP53 mutation analysis reflects a moderate dietary exposure to aflatoxins in Espírito Santo State, Brazil. Mol Biol Rep 2013; 40:4883-7. [PMID: 23649769 DOI: 10.1007/s11033-013-2587-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 04/29/2013] [Indexed: 01/27/2023]
Abstract
The close relationship between aflatoxins and 249ser TP53 gene mutation (AGG to AGT, Arg to Ser) in hepatocellular carcinoma (HCC) makes this mutation an indirect indicator of dietary contamination with this toxin. We have examined the prevalence of codon 249 TP53 mutation in 41 HCC and 74 liver cirrhosis (without HCC) cases diagnosed at the HUCAM University Hospital in Vitoria, Espírito Santo State, Brazil. DNA was extracted from paraffin sections and from plasma. The mutation was detected by DNA amplification, followed by restriction endonuclease digestion and confirmed by direct sequencing. DNA restriction showed 249ser mutation in 16 HCC and 13 liver cirrhosis, but sequencing confirmed mutations in only 6 HCC and 1 liver cirrhosis. In addition, sequencing revealed 4 patients with mutations at codon 250 (250ser and 250leu) in HCC cases. The prevalence of TP53 mutation was 10/41 (24.3%) in HCC and 1/74 (1.4%) in liver cirrhosis. No relationship between the presence of mutations and the etiology of HCC was observed. TP53 exon 7 mutations, which are related to aflatoxins exposure, were found at 14.6% (249ser), 7.3% (250leu) and 2.4% (250ser) in 41 cases of HCC and 1.4% in 74 liver cirrhosis (without HCC) cases, suggesting a moderate dietary exposure to aflatoxins in the Espírito Santo State, Brazil.
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Affiliation(s)
- Fernanda Magri de Carvalho
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo, Av. Marechal Campos 1468, Campus de Maruípe, Vitória, Espírito Santo, CEP 29040-090, Brazil
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Le QT, Zhang Q, Cao H, Cheng AJ, Pinsky BA, Hong RL, Chang JT, Wang CW, Tsao KC, Lo YD, Lee N, Ang KK, Chan ATC, Chan KCA. An international collaboration to harmonize the quantitative plasma Epstein-Barr virus DNA assay for future biomarker-guided trials in nasopharyngeal carcinoma. Clin Cancer Res 2013; 19:2208-15. [PMID: 23459720 DOI: 10.1158/1078-0432.ccr-12-3702] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Persistently elevated posttreatment plasma EBV DNA is a robust predictor of relapse in nasopharyngeal carcinoma (NPC). However, assay standardization is necessary for use in biomarker-driven trials. We conducted a study to harmonize the method between four centers with expertise in EBV DNA quantitation. EXPERIMENTAL DESIGN Plasma samples of 40 patients with NPC were distributed to four centers. DNA was extracted and EBV DNA copy number was determined by real-time quantitative PCR (BamHI-W primer/probe). Centers used the same protocol but generated their own calibrators. A harmonization study was then conducted using the same calibrators and PCR master mix and validated with ten pooled samples. RESULTS The initial intraclass correlations (ICC) for the first 40 samples between each center and the index center were 0.62 [95% confidence interval (CI): 0.39-0.78], 0.70 (0.50-0.83), and 0.59 (0.35-0.76). The largest variability was the use of different PCR master mixes and calibrators. Standardization improved ICC to 0.83 (0.5-0.95), 0.95 (0.83-0.99) and 0.96 (0.86-0.99), respectively, for ten archival frozen samples. For fresh plasma with spiked-in EBV DNA, correlations were more than 0.99 between the centers. At 5 EBV DNA copies per reaction or above, the coefficient of variance (CV) was less than 10% for the cycle threshold (Ct) among all centers, suggesting this concentration can be reliably used as a cutoff for defining the presence of detectable EBV DNA. CONCLUSIONS Quantitative PCR assays, even when conducted in experienced clinical labs, can yield large variability in plasma EBV DNA copy numbers without harmonization. The use of common calibrators and PCR master mix can help to reduce variability.
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Affiliation(s)
- Quynh-Thu Le
- Department of Radiation Oncology, Stanford University, 875 Blake Wilbur Dr., MC 5847, Stanford, CA 94305, USA.
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Chimonidou M, Tzitzira A, Strati A, Sotiropoulou G, Sfikas C, Malamos N, Georgoulias V, Lianidou E. CST6 promoter methylation in circulating cell-free DNA of breast cancer patients. Clin Biochem 2013; 46:235-40. [DOI: 10.1016/j.clinbiochem.2012.09.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 02/06/2023]
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Fernando DS, Lechner JM, Norton SE, Qin J, Fernando MR. WITHDRAWN: Compatibility of a blood collection tube that stabilizes cell-free DNA with a rapid fluorescence assay. Clin Biochem 2012:S0009-9120(12)00605-4. [PMID: 23107984 DOI: 10.1016/j.clinbiochem.2012.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/11/2012] [Accepted: 10/19/2012] [Indexed: 10/27/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Butt A, Ahmad MS, Powrie J, Swaminathan R. Assessment of diabetic retinopathy by measuring retina-specific mRNA in blood. Expert Opin Biol Ther 2012; 12 Suppl 1:S79-84. [DOI: 10.1517/14712598.2012.688947] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Rykova EY, Morozkin ES, Ponomaryova AA, Loseva EM, Zaporozhchenko IA, Cherdyntseva NV, Vlassov VV, Laktionov PP. Cell-free and cell-bound circulating nucleic acid complexes: mechanisms of generation, concentration and content. Expert Opin Biol Ther 2012; 12 Suppl 1:S141-53. [PMID: 22500614 DOI: 10.1517/14712598.2012.673577] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Extracellular nucleic acids are found in human blood and cell culture medium as cell-free or being adsorbed at cell surface. In the last years, the circulating extracellular nucleic acids in blood were shown to be associated with certain diseases. Attempts are made to develop non-invasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA. AREAS COVERED This article reviews accumulating data regarding cell-free and cell-surface-bound extracellular nucleic acid nature and generation mechanisms. Their existence as a constituent of the naturally occurring complexes with proteins or membrane-bearing particles is discussed with regard to their homeostatic concentration and distribution in healthy donor blood which are significantly altered in cancer patients. Gene-target and whole-genome studies reveal significant differences in gene representation between extracellular DNA and genome DNA. Overrepresentation of regions with high transcription activity has led to proposal that extracellular DNA generation is strongly dependent on the parent genome functionality, which is associated with chromosome packaging and DNA methylation levels. EXPERT OPINION Recent studies provide evidence of the circulating nucleome organization complexity indicating that discovery of extracellular DNA generation and circulation patterns in healthy condition and cancer is essential to enable the development of proper approaches for the selection of valid diagnostic markers.
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Affiliation(s)
- Elena Y Rykova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Acad. Lavrentyev Prosp., Novosibirsk, Russia.
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Epithelial-specific methylation marker: a potential plasma biomarker in advanced non-small cell lung cancer. J Thorac Oncol 2012; 6:1818-25. [PMID: 21964525 DOI: 10.1097/jto.0b013e318226b46f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Under physiological conditions, leukocytes contribute the majority of circulating DNA in plasma. Therefore, detection of methylation at the SHP-1 promoter 2 (SHP1P2) in plasma, which represents epithelial tumor-derived circulating nucleic acids, may serve as a potential noninvasive biomarker for non-small cell lung cancer (NSCLC). MATERIALS AND METHOD A quantitative polymerase chain reaction-based assay was used to determine the level of SHP1P2 methylation in plasma. Blood samples were prospectively collected from 58 patients with advanced NSCLC, 20 patients with early NSCLC, and 52 healthy volunteers. RESULTS Most of the healthy volunteers exhibited undetectable levels of SHP1P2 methylation. In contrast, the pretreatment levels of SHP1P2 methylation in the patients with NSCLC were readily detectable, with a median value of 770 pg ml(-1) (0-26,500 pg ml(-1)), which was significantly higher than that of the healthy controls. Furthermore, the patients with advanced NSCLC who presented baseline levels of SHP1P2 methylation of less than 700 pg ml(-1) exhibited enhanced median progression-free survival (5.2 versus 2.6 months, p = 0.009) and improved median overall survival (12.6 versus 7.6 months, p = 0.01) compared with patients who exhibited SHP1P2 methylation levels greater than 700 pg ml(-1). From a multivariate analysis, the levels of SHP1P2 methylation were significantly associated with survival rates in advanced NSCLC. CONCLUSION Measurement of the level of SHP1P2 methylation in plasma serves as a potential noninvasive biomarker for the prognostic assessment of patients with lung cancer. This biomarker can be used to develop risk-adaptive treatments for patients with lung cancer.
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Genetic variations in plasma circulating DNA of HBV-related hepatocellular carcinoma patients predict recurrence after liver transplantation. PLoS One 2011; 6:e26003. [PMID: 21998744 PMCID: PMC3187841 DOI: 10.1371/journal.pone.0026003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 09/15/2011] [Indexed: 02/06/2023] Open
Abstract
Background Recurrence prediction of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) patients undergoing liver transplantation (LT) present a great challenge because of a lack of biomarkers. Genetic variations play an important role in tumor development and metastasis. Methods Oligonucleotide microarrays were used to evaluate the genetic characteristics of tumor DNA in 30 HBV-related HCC patients who were underwent LT. Recurrence-related single-nucleotide polymorphism were selected, and their prognostic value was assessed and validated in two independent cohorts of HCC patients (N = 102 and N = 77), using pretransplant plasma circulating DNA. Prognostic significance was assessed by Kaplan-Meier survival estimates and log-rank tests. Multivariate analyses were performed to evaluate prognosis-related factors. Results rs894151 and rs12438080 were significantly associated with recurrence (P = .003 and P = .004, respectively). Multivariate analyses demonstrated that the co-index of the 2 SNPs was an independent prognostic factor for recurrence (P = .040). Similar results were obtained in the third cohort (N = 77). Furthermore, for HCC patients (all the 3 cohorts) exceeding Milan criteria, the co-index was a prognostic factor for recurrence and survival (P<.001 and P = .002, respectively). Conclusions Our study demonstrated first that genetic variations of rs894151 and rs12438080 in pretransplant plasma circulating DNA are promising prognostic markers for tumor recurrence in HCC patients undergoing LT and identify a subgroup of patients who, despite having HCC exceeding Milan criteria, have a low risk of post-transplant recurrence.
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A Noninvasive System for Monitoring Resistance to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors with Plasma DNA. J Thorac Oncol 2011; 6:1639-48. [DOI: 10.1097/jto.0b013e31822956e8] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Turchaninova MA, Meshcheriakov AA, Rakhmankulova ZP, Rebrikov DV. [Characterization of circulating RNA in plasma as potential tool for breast cancer diagnostics]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:393-8. [PMID: 21899055 DOI: 10.1134/s1068162011030186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The representation patterns of 15 cytokines RNA in blood plasma and blood cells of patients with breast cancer and apparently healthy women were investigated. Relative levels of RNA IL-8 and IL-18 in plasma of breast cancer patients are significantly increased compared with control group. At the same time no obvious differences were found in relative concentrations of these transcripts in blood cells of patients and control groups. Relative concentration of IL-8 RNA was higher in blood plasma of locally advanced compared with early breast cancer patients.
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Wielscher M, Pulverer W, Peham J, Hofner M, Rappaport CF, Singer C, Jungbauer C, Nöhammer C, Weinhäusel A. Methyl-binding domain protein-based DNA isolation from human blood serum combines DNA analyses and serum-autoantibody testing. BMC Clin Pathol 2011; 11:11. [PMID: 21896199 PMCID: PMC3180258 DOI: 10.1186/1472-6890-11-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 09/06/2011] [Indexed: 01/12/2023] Open
Abstract
Background Circulating cell free DNA in serum as well as serum-autoantibodies and the serum proteome have great potential to contribute to early cancer diagnostics via non invasive blood tests. However, most DNA preparation protocols destroy the protein fraction and therefore do not allow subsequent protein analyses. In this study a novel approach based on methyl binding domain protein (MBD) is described to overcome the technical difficulties of combining DNA and protein analysis out of one single serum sample. Methods Serum or plasma samples from 98 control individuals and 54 breast cancer patients were evaluated upon silica membrane- or MBD affinity-based DNA isolation via qPCR targeting potential DNA methylation markers as well as by protein-microarrays for tumor-autoantibody testing. Results In control individuals, an average DNA level of 22.8 ± 25.7 ng/ml was detected applying the silica membrane based protocol and 8.5 ± 7.5 ng/ml using the MBD-approach, both values strongly dependent on the serum sample preparation methods used. In contrast to malignant and benign tumor serum samples, cell free DNA concentrations were significantly elevated in sera of metastasizing breast cancer patients. Technical evaluation revealed that serum upon MBD-based DNA isolation is suitable for protein-array analyses when data are consistent to untreated serum samples. Conclusion MBD affinity purification allows DNA isolations under native conditions retaining the protein function, thus for example enabling combined analyses of DNA methylation and autoantigene-profiles from the same serum sample and thereby improving minimal invasive diagnostics.
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Affiliation(s)
- Matthias Wielscher
- Molecular Medicine, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria.
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Diagnostic and prognostic value of metastasis inducer S100A4 transcripts in plasma of colon, rectal, and gastric cancer patients. J Mol Diagn 2011; 13:189-98. [PMID: 21354054 DOI: 10.1016/j.jmoldx.2010.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 09/29/2010] [Accepted: 10/05/2010] [Indexed: 12/22/2022] Open
Abstract
Early detection of tumors and metastases is critical for improving treatment strategies and patient outcomes. The development of molecular markers and simple tests that are clinically applicable for detection, prognostication, and therapy monitoring is strongly needed. The gene S100A4 has long been known to act as a metastasis inducer. High S100A4 levels in the primary tumor are prognostic for metachronous metastasis and correlate with reduced patient survival. We provide, for the first time, a plasma-based assay for transcript quantification of S100A4 in gastrointestinal patients' plasma. We conducted a study to define the diagnostic and prognostic power of S100A4 transcripts using 466 plasma samples from colon, rectal, and gastric cancer patients. Plasma was separated, RNA was isolated, and S100A4 mRNA was determined by quantitative RT-PCR. S100A4 transcripts were increased in cancer patients of each entity (P < 0.0001) and all disease stages (P < 0.05), compared with tumor-free volunteers (sensitivities of 96%, 74%, and 90% and specificities of 59%, 82%, and 71%, for colon, rectal, and gastric cancer patients, respectively). Prospectively analyzed follow-up patients who later experienced metastasis showed higher S100A4 levels than follow-up patients without metastasis. Disease-free survival was decreased in high S100A4-expressing follow-up colorectal cancer patients (P = 0.013). In summary, we developed a method for quantitative S100A4 transcript determination in plasma that allows clinical application routinely. We demonstrated the diagnostic and prognostic potential of this method for early defining cancer staging and patients' risk for metastasis.
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Ponomaryova AA, Rykova EY, Cherdyntseva NV, Choinzonov EL, Laktionov PP, Vlassov VV. Molecular genetic markers in diagnosis of lung cancer. Mol Biol 2011. [DOI: 10.1134/s0026893310061056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gahan PB, Stroun M. The virtosome-a novel cytosolic informative entity and intercellular messenger. Cell Biochem Funct 2011; 28:529-38. [PMID: 20941743 DOI: 10.1002/cbf.1690] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Studies on a range of prokaryote and eukaryote cells and tissues have shown that a newly synthesized DNA/RNA-lipoprotein complex is released in a regulated manner. This complex, termed a virtosome, is a novel cytosolic component of eukaryote cells. The released virtosomes can readily enter other cells where they can modify the biology of the recipient cells. Such modifications include immunological changes and transformation from normal to cancer cells. The virtosomes form a normal component of the circulating nucleic acids in plasma and serum currently used for clinical diagnostic purposes. Given the transformative powers of virtosomes released from tumour cells, the presence of such a complex in human plasma could readily offer the basis of an alternative mechanism for the initiation of metastases.
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Tamkovich SN, Vlassov VV, Laktionov PP. Circulating DNA in the blood and its application in medical diagnosis. Mol Biol 2011. [DOI: 10.1134/s0026893308010020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hofman VJ, Ilie MI, Bonnetaud C, Selva E, Long E, Molina T, Vignaud JM, Fléjou JF, Lantuejoul S, Piaton E, Butori C, Mourad N, Poudenx M, Bahadoran P, Sibon S, Guevara N, Santini J, Vénissac N, Mouroux J, Vielh P, Hofman PM. Cytopathologic detection of circulating tumor cells using the isolation by size of epithelial tumor cell method: promises and pitfalls. Am J Clin Pathol 2011; 135:146-56. [PMID: 21173137 DOI: 10.1309/ajcp9x8ozbeiqvvi] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Detection of circulating tumor cells (CTCs) morphologically may be a promising new approach in clinical oncology. We tested the reliability of a cytomorphologic approach to identify CTCs: 808 blood samples from patients with benign and malignant diseases and healthy volunteers were examined using the isolation by size of epithelial tumor cell (ISET) method. Cells having nonhematologic features (so-called circulating nonhematologic cells [CNHCs]) were classified into 3 categories: CNHCs with malignant features, CNHCs with uncertain malignant features, and CNHCs with benign features. CNHCs were found in 11.1% and 48.9% of patients with nonmalignant and malignant pathologies, respectively (P < .001). CNHCs with malignant features were observed in 5.3% and in 43.1% of patients with nonmalignant and malignant pathologies, respectively. Cytopathologic identification of CTCs using the ISET method represents a promising field for cytopathologists. The possibility of false-positive diagnosis stresses the need for using ancillary methods to improve this approach.
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Dobrzycka B, Terlikowski SJ, Kinalski M, Kowalczuk O, Niklinska W, Chyczewski L. Circulating free DNA and p53 antibodies in plasma of patients with ovarian epithelial cancers. Ann Oncol 2010; 22:1133-1140. [PMID: 21098618 DOI: 10.1093/annonc/mdq584] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study was conducted in order to evaluate the significance of circulating free DNA (CFDNA), blood plasma p53 antibodies (p53-Ab) and mutations of KRAS gene in the prognosis of ovarian epithelial cancers. PATIENTS AND METHODS A total of 126 patients were included in this study. KRAS mutations and CFDNA were detected by means of the PCR-restriction fragment length polymorphism (PCR-RFLP) and enriched by the PCR-RFLP method. Enzyme-linked immunosorbent assay was used to analyze plasma p53-Ab. RESULTS KRAS mutations were detected in 27 (21.4%) of examined tumors. The frequency of KRAS mutations was especially high in mucinous cancers (P < 0.001). CFDNA and p53-Ab were frequently detected in patients with serous cancers in high grade (P < 0.001). The overall survival rate was significantly lower for patients with serous tumors and CFDNA and p53-Ab-positive than negative tumors (P = 0.022 and P < 0.001, respectively). In mucinous ovarian cancer, a worse overall survival was correlated with the KRAS mutations (P = 0.03). CONCLUSIONS The results of the present study suggested that a presence of KRAS mutations in mucinous ovarian cancer and CFDNA and p53-Ab in serous tumors was correlated with the highest risk of cancer progression.
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Affiliation(s)
- B Dobrzycka
- Department of Obstetrics, Gynecology and Obstetrics/Gynecological Care, Medical University of Bialystok
| | - S J Terlikowski
- Department of Obstetrics, Gynecology and Obstetrics/Gynecological Care, Medical University of Bialystok.
| | - M Kinalski
- Department of Gynecology, District Hospital in Bialystok
| | | | | | - L Chyczewski
- Department of Clinical Molecular Biology; Department of Pathomorphology, Medical University of Bialystok, Bialystok, Poland
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