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Nam H, Lee E, Yang H, Lee K, Kwak T, Kim D, Kim H, Yang M, Yang Y, Son S, Nam YH, Minn I. PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity. Biol Methods Protoc 2024; 9:bpae041. [PMID: 38938409 PMCID: PMC11208725 DOI: 10.1093/biomethods/bpae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/29/2024] Open
Abstract
Real-time polymerase chain reaction (real-time PCR) is a powerful tool for the precise quantification of nucleic acids in various applications. In cancer management, the monitoring of circulating tumor DNA (ctDNA) from liquid biopsies can provide valuable information for precision care, including treatment selection and monitoring, prognosis, and early detection. However, the rare and heterogeneous nature of ctDNA has made its precise detection and quantification challenging, particularly for ctDNA containing hotspot mutations. We have developed a new real-time PCR tool, PROMER technology, which enables the precise and sensitive detection of ctDNA containing cancer-driven single-point mutations. The PROMER functions as both a PRObe and priMER, providing enhanced detection specificity. We validated PROMER technology using synthetic templates with known KRAS point mutations and demonstrated its sensitivity and linearity of quantification. Using genomic DNA from human cancer cells with mutant and wild-type KRAS, we confirmed that PROMER PCR can detect mutant DNA. Furthermore, we demonstrated the ability of PROMER technology to efficiently detect mutation-carrying ctDNA from the plasma of mice with human cancers. Our results suggest that PROMER technology represents a promising new tool for the precise detection and quantification of DNA containing point mutations in the presence of a large excess of wild-type counterpart.
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Affiliation(s)
- Hwanhee Nam
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Esder Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hichang Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Kyeyoon Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Taeho Kwak
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Dain Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hyemin Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Mihwa Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Younjoo Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Seungwan Son
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Young-Hyean Nam
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Il Minn
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21287, United States
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2
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Hosseini II, Hamidi SV, Capaldi X, Liu Z, Silva Pessoa MA, Mahshid S, Reisner W. Tunable nanofluidic device for digital nucleic acid analysis. NANOSCALE 2024. [PMID: 38682564 DOI: 10.1039/d3nr05553a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Nano/microfluidic-based nucleic acid tests have been proposed as a rapid and reliable diagnostic technology. Two key steps for many of these tests are target nucleic acid (NA) immobilization followed by an enzymatic reaction on the captured NAs to detect the presence of a disease-associated sequence. NA capture within a geometrically confined volume is an attractive alternative to NA surface immobilization that eliminates the need for sample pre-treatment (e.g. label-based methods such as lateral flow assays) or use of external actuators (e.g. dielectrophoresis) that are required for most nano/microfluidic-based NA tests. However, geometrically confined spaces hinder sample loading while making it challenging to capture, subsequently, retain and simultaneously expose target NAs to required enzymes. Here, using a nanofluidic device that features real-time confinement control via pneumatic actuation of a thin membrane lid, we demonstrate the loading of digital nanocavities by target NAs and exposure of target NAs to required enzymes/co-factors while the NAs are retained. In particular, as proof of principle, we amplified single-stranded DNAs (M13mp18 plasmid vector) in an array of nanocavities via two isothermal amplification approaches (loop-mediated isothermal amplification and rolling circle amplification).
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Affiliation(s)
- Imman I Hosseini
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Seyed Vahid Hamidi
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Xavier Capaldi
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Zezhou Liu
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
| | | | - Sara Mahshid
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Walter Reisner
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
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3
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Du S, Cao K, Yan Y, Wang Y, Wang Z, Lin D. Developments and current status of cell-free DNA in the early detection and management of hepatocellular carcinoma. J Gastroenterol Hepatol 2024; 39:231-244. [PMID: 37990622 DOI: 10.1111/jgh.16416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023]
Abstract
Nowadays, hepatocellular carcinoma (HCC) is still a major threat to human health globally, with a disappointing prognosis. Regular monitoring of patients at high risk, utilizing abdominal ultrasonography combined with alpha-fetoprotein (AFP) serum analysis, enables the early detection of potentially treatable tumors. However, the approach has limitations due to its lack of sensitivity. Meanwhile, the current standard procedure for obtaining a tumor biopsy in cases of HCC is invasive and lacks the ability to assess the dynamic progression of cancer or account for tumor heterogeneity. Hence, there is a pressing need to develop non-invasive, highly sensitive biomarkers for HCC which can improve the accuracy of early diagnosis, assess treatment response and accurately predict the prognosis. In contrast to the conventional method of tissue biopsy, liquid biopsy offers a non-invasive approach that can be readily repeated. As a liquid biopsy approach, the analysis of cell-free DNA (cfDNA) offers real-time insights that can accurately portray the tumor burden and provide a comprehensive depiction of the genetic profile associated with HCC. In this review, we present a comprehensive summary of the recent research findings pertaining to the significance and potential practicality of cfDNA analysis in the early detection and effective management of HCC.
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Affiliation(s)
- Sihao Du
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ke Cao
- Department of General Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yadong Yan
- Department of General Surgery, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yupeng Wang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zhenshun Wang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Dongdong Lin
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
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4
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Wang J, Ranjbaran M, Verma MS. Bacteroidales as a fecal contamination indicator in fresh produce industry: A baseline measurement. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119641. [PMID: 38064988 DOI: 10.1016/j.jenvman.2023.119641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024]
Abstract
Foodborne outbreaks caused by fecal contamination of fresh produce represent a serious concern to public health and the economy. As the consumption of fresh produce increases, public health officials and organizations have pushed for improvements in food safety procedures and environmental assessments to reduce the risk of contamination. Visual inspections and the establishment of "buffer zones" between animal feeding operations and producing fields are the current best practices for environmental assessments. However, a generalized distance guideline and visual inspections may not be enough to account for all environmental risk variables. Here, we report a baseline measurement surveying the background Bacteroidales concentration, as a quantitative fecal contamination indicator, in California's Salinas Valley. We collected a total of 1632 samples from two romaine lettuce commercial fields at the time of harvesting through two seasons in a year. The quantification of Bacteroidales concentration was performed using qPCR, revealing a notably low concentration (0-2.00 copies/cm2) in the commercial fields. To further enhance the applicability of our findings, we developed a user-friendly method for real-world fecal contamination risk assessment that seamlessly integrates with industry practices. Through the generation of heatmaps that visually illustrate varying risk levels across fields, this approach can identify site-specific risks and offer fresh produce stakeholders a more comprehensive understanding of their land. We anticipate this work can encourage the use of Bacteroidales in the fresh produce industry to monitor fecal contamination and prevent future foodborne outbreaks.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Mohit S Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA.
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Spiliopoulou P, Holanda Lopes CD, Spreafico A. Promising and Minimally Invasive Biomarkers: Targeting Melanoma. Cells 2023; 13:19. [PMID: 38201222 PMCID: PMC10777980 DOI: 10.3390/cells13010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
The therapeutic landscape of malignant melanoma has been radically reformed in recent years, with novel treatments emerging in both the field of cancer immunotherapy and signalling pathway inhibition. Large-scale tumour genomic characterization has accurately classified malignant melanoma into four different genomic subtypes so far. Despite this, only somatic mutations in BRAF oncogene, as assessed in tumour biopsies, has so far become a validated predictive biomarker of treatment with small molecule inhibitors. The biology of tumour evolution and heterogeneity has uncovered the current limitations associated with decoding genomic drivers based only on a single-site tumour biopsy. There is an urgent need to develop minimally invasive biomarkers that accurately reflect the real-time evolution of melanoma and that allow for streamlined collection, analysis, and interpretation. These will enable us to face challenges with tumour tissue attainment and process and will fulfil the vision of utilizing "liquid biopsy" to guide clinical decisions, in a manner akin to how it is used in the management of haematological malignancies. In this review, we will summarize the most recent published evidence on the role of minimally invasive biomarkers in melanoma, commenting on their future potential to lead to practice-changing discoveries.
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Affiliation(s)
- Pavlina Spiliopoulou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | | | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
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Masui S, Kanno Y, Nisisako T. Understanding droplet breakup in a post-array device with sheath-flow configuration. LAB ON A CHIP 2023; 23:4959-4966. [PMID: 37873662 DOI: 10.1039/d3lc00573a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Microfluidic post-array devices have the potential to generate quasi-monodisperse emulsion droplets with high throughput and dispersed phase fractions by splitting droplets with regularly arranged posts. However, the lack of understanding of post-array devices makes it challenging to predict droplet size and quantitatively evaluate the influence of post geometry, hindering their widespread application. Therefore, we investigated the characteristics of droplet breakup through a post array using a series of devices with sheath-flow configurations, in which the dispersed and continuous flow rates could be flexibly tuned. Using a poly(dimethylsiloxane)-glass device fabricated via soft lithography, we found that the volume ratio of the dispersed phase to the continuous phase significantly affects the droplet size, even when the viscosity ratio is close to one. For the first time, we demonstrated that the effective capillary number calculated from the emulsion viscosity and effect of the dispersed phase fraction consistently describes various experimental results. Furthermore, our flow observations and droplet diameter measurement showed two breakup modes: the size-constant obstruction and shear-induced modes with a power-law correlation similar to droplet splitting in a T-junction. Thus, the power-law correlation in microfluidic droplet splitting successfully expresses the droplet generation characteristics in post-array devices. A combination of effective viscosity correction and curve fitting allowed us to evaluate the influence of the material and post-geometry on droplet generation characteristics. This study contributes to the understanding of droplet breakup in post-array devices and extends their unique droplet generation properties to include high-throughput, high-fraction, robust, and continuous emulsification processes.
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Affiliation(s)
- Shuzo Masui
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
| | - Yusuke Kanno
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
| | - Takasi Nisisako
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
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7
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Chiang CL, Ho HL, Yeh YC, Lee CC, Huang HC, Shen CI, Luo YH, Chen YM, Chiu CH, Chou TY. Efficacy of different platforms in detecting EGFR mutations using cerebrospinal fluid cell-free DNA from non-small-cell lung cancer patients with leptomeningeal metastases. Thorac Cancer 2023; 14:1251-1259. [PMID: 36977550 PMCID: PMC10175033 DOI: 10.1111/1759-7714.14866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Cell-free tumor DNA (ctDNA) obtained through liquid biopsy is useful for the molecular analysis of advanced non-small-cell lung cancer (NSCLC). Few studies have directly compared analysis platforms in terms of their diagnostic performance in analyzing ctDNA obtained from the cerebrospinal fluid (CSF) of patients with leptomeningeal metastasis (LM). METHODS We prospectively analyzed patients with epidermal growth factor receptor (EGFR)-mutant NSCLC who were subjected to CSF analysis for suspected LM. To detect EGFR mutations, CSF ctDNA was analyzed using the cobas EGFR Mutation Test and droplet digital polymerase chain reaction (ddPCR). CSF samples from osimertinib-refractory patients with LM were also subjected to next-generation sequencing (NGS). RESULTS Significantly higher rates of valid results (95.1% vs. 78%, respectively, p = 0.04) and EGFR common mutation detection (94.3% vs. 77.1%, respectively, p = 0.047) were obtained through ddPCR than through the cobas EGFR Mutation Test. The sensitivities of ddPCR and cobas were 94.3% and 75.6%, respectively. The concordance rate for EGFR mutation detection through ddPCR and the cobas EGFR Mutation Test was 75.6% and that for EGFR mutation detection in CSF and plasma ctDNA was 28.1%. In osimertinib-resistant CSF samples, all original EGFR mutations were detected through NGS. MET amplification and CCDC6-RET fusion were demonstrated in one patient each (9.1%). CONCLUSIONS The cobas EGFR Mutation Test, ddPCR, and NGS appear to be feasible methods for analyzing CSF ctDNA in patients with NSCLC and LM. In addition, NGS may provide comprehensive information regarding the mechanisms underlying osimertinib resistance.
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Affiliation(s)
- Chi-Lu Chiang
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsiang-Ling Ho
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Chen Yeh
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Cheng-Chia Lee
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsu-Ching Huang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-I Shen
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yung-Hung Luo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yuh-Min Chen
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chao-Hua Chiu
- Taipei Cancer Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Teh-Ying Chou
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Pathology, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
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Schlenker F, Juelg P, Lüddecke J, Paust N, Zengerle R, Hutzenlaub T. Nanobead handling on a centrifugal microfluidic LabDisk for automated extraction of cell-free circulating DNA with high recovery rates. Analyst 2023; 148:932-941. [PMID: 36722841 DOI: 10.1039/d2an01820a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
cfDNA is an emerging biomarker with promising uses for the monitoring of cancer or infectious disease diagnostics. This work demonstrates a new concept for an automated cfDNA extraction with nanobeads as the solid phase in a centrifugal microfluidic LabDisk. By using a combination of centrifugal and magnetic forces, we retain the nanobeads in one incubation chamber while sequentially adding, incubating and removing the sample and pre-stored buffers for extraction. As the recovery rate of the typically low concentration of cfDNA is of high importance to attain sufficient amounts for analysis, optimal beadhandling is paramount. The goal is that the cfDNA in the sample adsorbs to the solid phase completely during the binding step, is retained during washing and completely removed during elution. In this work, we improved beadhandling by optimizing the incubation chamber geometry and both frequency and temperature protocols, to maximize recovery rates. For characterization of the extraction performance, synthetic mutant DNA was spiked into human plasma samples. The LabDisk showed better reproducibility in DNA recovery rates with a standard deviation of ±13% compared to a manual approach using spin-columns (±17%) or nanobeads (±26%). The extraction of colorectal cancer samples with both the developed LabDisk and a robotic automation instrument resulted in comparable allele frequencies. Consequently, we present a highly attractive solution for an automated liquid biopsy cfDNA extraction in a small benchtop device.
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Affiliation(s)
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Jan Lüddecke
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nils Paust
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Tobias Hutzenlaub
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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Chen G, Zhang J, Fu Q, Taly V, Tan F. Integrative analysis of multi-omics data for liquid biopsy. Br J Cancer 2023; 128:505-518. [PMID: 36357703 PMCID: PMC9938261 DOI: 10.1038/s41416-022-02048-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
The innovation of liquid biopsy holds great potential to revolutionise cancer management through early diagnosis and timely treatment of cancer. Integrative analysis of different tumour-derived omics data (such as genomics, epigenetics, fragmentomics, and proteomics) from body fluids for cancer detection and monitoring could outperform the analysis of single modality data alone. In this review, we focussed on the discussion of early cancer detection and molecular residual disease surveillance based on multi-omics data of blood. We summarised diverse types of tumour-derived components, current popular platforms for profiling cancer-associated signals, machine learning approaches for joint analysis of liquid biopsy data, as well as multi-omics-based early detection of cancers, molecular residual disease monitoring, and treatment response surveillance. We also discussed the challenges and future directions of multi-omics-based liquid biopsy. With the development of both experimental protocols and computational methods dedicated to liquid biopsy, the implementation of multi-omics strategies into the clinical workflow will likely benefit the clinical management of cancers including decision-making guidance and patient outcome improvement.
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Affiliation(s)
- Geng Chen
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China.
- Center for Bioinformatics and Computational Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China.
| | - Jing Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China
| | - Qiaoting Fu
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, 200443, Shanghai, China
| | - Valerie Taly
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe labélisée Ligue Nationale contre le cancer, Centre de Recherche des Cordeliers, Paris, France.
| | - Fei Tan
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China.
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, 200443, Shanghai, China.
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10
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Zhang H, Hu Y, Wang Y, Song X, Hu Y, Ma L, Yang X, Li K, Qin N, Wang J, Lv J, Li X, Zhang X, Zhang Q, Wu Y, Yao G, Zhang S. Application of ddPCR in detection of the status and abundance of EGFR T790M mutation in the plasma samples of non-small cell lung cancer patients. Front Oncol 2023; 12:942123. [PMID: 36776375 PMCID: PMC9909534 DOI: 10.3389/fonc.2022.942123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023] Open
Abstract
Background/Objective The third-generation epidermal growth factor receptor (EGFR) -tyrosine kinase inhibitor (TKIs), such as osimertinib, designed for targeting the acquired drug-resistant mutation of EGFR T790M, was approved as the first-line therapy for advanced EGFR-mutated non-small cell lung cancer (NSCLC). Thus, detection of the EGFR T790M mutation for NSCLC is crucial. However, tissue samples are often difficult to obtain, especially in patients at advanced stages. This study assessed the performances of droplet digital polymerase chain reaction (ddPCR) and next-generation sequencing (NGS) in detecting EGFR T790M status and abundance in the plasma ctDNA samples of patients with NSCLC. We also explored the association between T790M status and abundance and the response to third-generation EGFR-TKIs. Methods A total of 201 plasma samples with matched tissues, 821 plasma samples, and 56 patients who received third-generation EGFR-TKIs with response evaluation were included in this study. ddPCR and NGS were used to detect the mutation status and abundance of T790M in the tissues and/or blood samples. Results The results showed that the sensitivity and the specificity of EGFR T790M mutation status detected by ddPCR in plasma samples were 81.82% and 91.85%, respectively, compared with the tissue samples, with a consistency coefficient of 0.740. Among the 821 plasma samples, the positive rates of EGFR T790M detected by ddPCR and NGS were 34.2% (281/821) and 22.5% (185/821), respectively. With NGS results as the reference, the sensitivity and the specificity of ddPCR were 100% and 84.91%, respectively, and the consistency coefficient of the two methods was 0.717. In addition, we found that a higher EGFR T790M abundance was linked to a higher treatment response rate to the third-generation EGFR-TKIs regardless of the classification of the median value of 0.43% (P = 0.016) or average value of 3.16% (P = 0.010). Conclusion Taking these data together, this study reveals that ddPCR is an alternatively potent method for the detection of EGFR T790M in the plasma samples of NSCLC patients.
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Affiliation(s)
- Hui Zhang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yi Hu
- Department of Medical Oncology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yan Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xia Song
- Department of Respiratory, Shanxi Cancer Hospital, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, China
| | - Ying Hu
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Li Ma
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xinjie Yang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Kun Li
- Department of Pathology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Na Qin
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jinghui Wang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jialin Lv
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xi Li
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xinyong Zhang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Quan Zhang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuhua Wu
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Guangyin Yao
- Department of Medicine, Shanghai Yuanqi Biomedical Technology Co. Ltd., Shanghai, China
| | - Shucai Zhang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,*Correspondence: Shucai Zhang,
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11
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Guo Q, Wang L, Liang X, Zhao M, Huang X, Xu W, Lou J, Qiao L. Comparative analysis of QS3D versus droplet digital PCR for quantitative measures of EGFR T790M mutation from identical plasma. Heliyon 2022; 8:e11339. [PMID: 36387507 PMCID: PMC9647353 DOI: 10.1016/j.heliyon.2022.e11339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/07/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Objectives The capacity of QuantStudio™ 3D (QS3D) and droplet digital PCR (dPCR) for the detection of plasma Epidermal Growth Factor Receptor (EGFR) mutations have been widely reported. Few comparative studies on the quantitative test of the identical DNA material, however, are carried out. Here we compared the performance of the two methods in detecting EGFR T790M mutation in cell-free DNA (cfDNA) from the same lung cancer patients. Methods We recruited 72 non-small cell lung cancer (NSCLC) patients who initially respond to tyrosine kinase inhibitor treatment but subsequently developed resistance. Two tubes of 10mL anticoagulant blood were collected and cfDNA was isolated from plasma. Identical cfDNA samples were analyzed for T790M mutation using QS3D and droplet dPCR in parallel. Results T790M mutation was detected in 15 and 21 cfDNA samples by QS3D and droplet digital PCR, respectively. The 6 discordant samples showed low mutation abundance (∼0.1%) and the discrepancy is caused by the stricter threshold settings for QS3D dPCR. The overall agreement between the two methods was 91.7% (66/72). The median allele frequencies for QS3D dPCR and droplet dPCR to detect T790M mutation was 2.01% and 2.62%, respectively. There was no significance in mutation abundance detected by both methods. Both methods are highly correlated with allele frequencies and copy numbers in T790M wild type and mutant, with R2 of 0.98, 0.92 and 0.95, respectively. Conclusion Our study demonstrated that QS3D dPCR are highly consistent with droplet PCR for quantitative determination of EGFR T790M mutation in plasma cfDNA.
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12
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Fang X, Yu S, Jiang Y, Xiang Y, Lu K. Circulating tumor DNA detection in MRD assessment and diagnosis and treatment of non-small cell lung cancer. Front Oncol 2022; 12:1027664. [PMID: 36387176 PMCID: PMC9646858 DOI: 10.3389/fonc.2022.1027664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022] Open
Abstract
Circulating tumor DNA (ctDNA) has contributed immensely to the management of hematologic malignancy and is now considered a valuable detection tool for solid tumors. ctDNA can reflect the real-time tumor burden and be utilized for analyzing specific cancer mutations via liquid biopsy which is a non-invasive procedure that can be used with a relatively high frequency. Thus, many clinicians use ctDNA to assess minimal residual disease (MRD) and it serves as a prognostic and predictive biomarker for cancer therapy, especially for non-small cell lung cancer (NSCLC). Advanced methods have been developed to detect ctDNA, and recent clinical trials have shown the rationality and feasibility of ctDNA for identifying mutations and guiding treatments in NSCLC. Here, we have reviewed recently developed ctDNA detection methods and the importance of sequence analyses of ctDNA in NSCLC.
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13
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Ho HL, Wang FY, Chiang CL, Tsai CM, Chiu CH, Chou TY. Dynamic Assessment of Tissue and Plasma EGFR-Activating and T790M Mutations with Droplet Digital PCR Assays for Monitoring Response and Resistance in Non-Small Cell Lung Cancers Treated with EGFR-TKIs. Int J Mol Sci 2022; 23:ijms231911353. [PMID: 36232650 PMCID: PMC9569685 DOI: 10.3390/ijms231911353] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Assessing tumor EGFR mutation status is necessary for the proper management of patients with advanced non–small cell lung cancer (NSCLC). We evaluated the impact of dynamic analyses of the plasma and tissue EGFR mutation using ultra-sensitive droplet digital PCR (ddPCR) assays to manage NSCLC patients treated with EGFR tyrosine kinase inhibitors (EGFR-TKIs). Paired tumor tissues and plasma samples from 137 EGFR-mutated lung adenocarcinoma patients prior to the first-line EGFR-TKIs treatment (at baseline) and at disease progression were subjected to EGFR mutation analysis using ddPCR, together with the analyses of the clinicopathological characteristics and treatment outcomes. Patients with EGFR-activating mutations detected in baseline plasma were associated with bone metastasis (p = 0.002) and had shorter progression-free survival (12.9 vs. 17.7 months, p = 0.02) and overall survival (24.0 vs. 39.4 months, p = 0.02) compared to those without. Pre-treatment EGFR T790M mutation found in baseline tumor tissues of 28 patients (20.4%; 28/137) was significantly associated with brain metastasis (p = 0.005) and a shorter brain metastasis-free survival (p = 0.001). The presence of EGFR T790M mutations in baseline tumor tissues did not correlate with the emergence of acquired EGFR T790M mutations detected at progression. At disease progression, acquired EGFR T790M mutations were detected in 26.6% (21/79) of the plasma samples and 42.9% (15/35) of the rebiopsy tissues, with a concordance rate of 71.4% (25/35). The dynamic monitoring of tissue and plasma EGFR mutation status at baseline and progression using ddPCR has a clinical impact on the evaluation of EGFR-TKIs treatment efficacy and patient outcomes, as well as the emergence of resistance in NSCLC.
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Affiliation(s)
- Hsiang-Ling Ho
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Correspondence: (H.-L.H.); (T.-Y.C.)
| | - Fang-Yu Wang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Chi-Lu Chiang
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chun-Ming Tsai
- Department of Oncology, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Chao-Hua Chiu
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Taipei Cancer Center and Taipei Medical University Hospital, Taipei Medical University, Taipei 110301, Taiwan
| | - Teh-Ying Chou
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Correspondence: (H.-L.H.); (T.-Y.C.)
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14
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Onukwugha NE, Kang YT, Nagrath S. Emerging micro-nanotechnologies for extracellular vesicles in immuno-oncology: from target specific isolations to immunomodulation. LAB ON A CHIP 2022; 22:3314-3339. [PMID: 35980234 PMCID: PMC9474625 DOI: 10.1039/d2lc00232a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Extracellular vesicles (EVs) have been hypothesized to incorporate a variety of crucial roles ranging from intercellular communication to tumor pathogenesis to cancer immunotherapy capabilities. Traditional EV isolation and characterization techniques cannot accurately and with specificity isolate subgroups of EVs, such as tumor-derived extracellular vesicles (TEVs) and immune-cell derived EVs, and are plagued with burdensome steps. To address these pivotal issues, multiplex microfluidic EV isolation/characterization and on-chip EV engineering may be imperative towards developing the next-generation EV-based immunotherapeutics. Henceforth, our aim is to expound the state of the art in EV isolation/characterization techniques and their limitations. Additionally, we seek to elucidate current work on total analytical system based technologies for simultaneous isolation and characterization and to summarize the immunogenic capabilities of EV subgroups, both innate and adaptive. In this review, we discuss recent state-of-art microfluidic/micro-nanotechnology based EV screening methods and EV engineering methods towards therapeutic use of EVs in immune-oncology. By venturing in this field of EV screening and immunotherapies, it is envisioned that transition into clinical settings can become less convoluted for clinicians.
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Affiliation(s)
- Nna-Emeka Onukwugha
- Department of Chemical Engineering and Biointerface Institute, University of Michigan, 2800 Plymouth Road, NCRC B10-A184, Ann Arbor, MI 48109, USA.
| | - Yoon-Tae Kang
- Department of Chemical Engineering and Biointerface Institute, University of Michigan, 2800 Plymouth Road, NCRC B10-A184, Ann Arbor, MI 48109, USA.
| | - Sunitha Nagrath
- Department of Chemical Engineering and Biointerface Institute, University of Michigan, 2800 Plymouth Road, NCRC B10-A184, Ann Arbor, MI 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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16
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R Peter M, Bilenky M, Shi Y, Pu J, Kamdar S, R Hansen A, E Fleshner N, S Sridhar S, M Joshua A, Hirst M, Xu W, Bapat B. A novel methylated cell-free DNA marker panel to monitor treatment response in metastatic prostate cancer. Epigenomics 2022; 14:811-822. [PMID: 35818933 DOI: 10.2217/epi-2022-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study examined circulating cell-free DNA (cfDNA) biomarkers associated with androgen treatment resistance in metastatic castration resistance prostate cancer (mCRPC). Materials & methods: We designed a panel of nine candidate cfDNA methylation markers using droplet digital PCR (Methyl-ddPCR) and assessed methylation levels in sequentially collected cfDNA samples from patients with mCRPC. Results: Increased cfDNA methylation in eight out of nine markers during androgen-targeted treatment correlated with a faster time to clinical progression. Cox proportional hazards modeling and logistic regression analysis further confirmed that higher cfDNA methylation during treatment was significantly associated with clinical progression. Conclusion: Overall, our findings have revealed a novel methylated cfDNA marker panel that could aid in the clinical management of metastatic prostate cancer.
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Affiliation(s)
- Madonna R Peter
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Misha Bilenky
- Canada's Michael Smith Genome Science Center, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Yuliang Shi
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Jiajie Pu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Shivani Kamdar
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Aaron R Hansen
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Neil E Fleshner
- Division of Urology, Department of Surgical Oncology, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Srikala S Sridhar
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Anthony M Joshua
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada.,Department of Medical Oncology, Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Martin Hirst
- Canada's Michael Smith Genome Science Center, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.,Department of Microbiology & Immunology & Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Bharati Bapat
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
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17
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Temraz S, Nasr R, Mukherji D, Kreidieh F, Shamseddine A. Liquid Biopsy Derived Circulating Tumor Cells and Circulating Tumor DNA as Novel Biomarkers in Hepatocellular Carcinoma. Expert Rev Mol Diagn 2022; 22:507-518. [PMID: 35758097 DOI: 10.1080/14737159.2022.2094706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The diagnosis of hepatocellular carcinoma (HCC) is made at a relatively advanced stage resulting in poor prognosis. Alpha-fetoprotein and liver ultrasound have limited accuracy as biomarkers in HCC. Liver biopsy provides information on tumor biology; however, it is invasive and holds high threat of tumor seeding. Thus, more accurate and less invasive approaches are needed. AREAS COVERED Highly sensitive liquid biopsy assays have made possible the detection and analysis of cells or organelles such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and tumor-derived exosomes. Here, we focus on CTCs and ctDNA components of liquid biopsy and their clinical application as diagnostic, prognostic and predictive biomarkers in HCC. Unlike tissue biopsy, liquid biopsy involves attaining a sample at several time frames in an easy and a non-invasive manner. They have been efficacious in detecting and classifying cancer, in predicting treatment response, in monitoring disease relapse and in identifying mechanisms of resistance to targeted therapies. EXPERT OPINION Although interesting and highly promising, liquid biopsy techniques still have many obstacles to overcome before their wide spread clinical application sees the light. It is expected that these techniques will be incorporated into traditional methodologies for better diagnostic, predictive and prognostic results.
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Affiliation(s)
- Sally Temraz
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiology, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Deborah Mukherji
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Firas Kreidieh
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Ali Shamseddine
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
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18
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Ren L, Ming Z, Zhang W, Liao Y, Tang X, Yan B, Lv H, Xiao X. Shared-probe system: An accurate, low-cost and general enzyme-assisted DNA probe system for detection of genetic mutation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Kasi PM, Fehringer G, Taniguchi H, Starling N, Nakamura Y, Kotani D, Powles T, Li BT, Pusztai L, Aushev VN, Kalashnikova E, Sharma S, Malhotra M, Demko ZP, Aleshin A, Rodriguez A, Billings PR, Grothey A, Taieb J, Cunningham D, Yoshino T, Kopetz S. Impact of Circulating Tumor DNA-Based Detection of Molecular Residual Disease on the Conduct and Design of Clinical Trials for Solid Tumors. JCO Precis Oncol 2022; 6:e2100181. [PMID: 35263168 PMCID: PMC8926064 DOI: 10.1200/po.21.00181] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Earlier detection of cancer recurrence using circulating tumor DNA (ctDNA) to detect molecular residual disease (MRD) has the potential to dramatically affect cancer management. We review evidence supporting the use of ctDNA as a biomarker for detection of MRD and highlight the potential impact that ctDNA testing could have on the conduct of clinical trials.
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Affiliation(s)
- Pashtoon M Kasi
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA
| | | | - Hiroya Taniguchi
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Naureen Starling
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Thomas Powles
- Barts Cancer Institute, Queen Mary University of London ECMC, Barts Health, London, United Kingdom
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT
| | | | | | | | | | | | | | | | | | - Axel Grothey
- West Cancer Center and Research Institute, Germantown, TN
| | - Julien Taieb
- Georges Pompidou European Hospital, SIRIC-CARPEM, Université de Paris, Paris, France
| | - David Cunningham
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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20
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The future of ctDNA-defined minimal residual disease: Personalizing adjuvant therapy in CRC. Clin Colorectal Cancer 2022; 21:89-95. [DOI: 10.1016/j.clcc.2022.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022]
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21
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Fan Y, Chen J, Liu M, Xu X, Zhang Y, Yue P, Cao W, Ji Z, Su X, Wen S, Kong J, Zhou G, Li B, Dong Y, Liu A, Bao F. Application of Droplet Digital PCR to Detection of Mycobacterium tuberculosis and Mycobacterium leprae Infections: A Narrative Review. Infect Drug Resist 2022; 15:1067-1076. [PMID: 35313727 PMCID: PMC8934166 DOI: 10.2147/idr.s349607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (MTB) infection, which has seriously endangered human health for many years. With the emergence of multidrug-resistant and extensively drug-resistant MTB, the prevention and treatment of TB has become a pressing need. Early diagnosis, drug resistance monitoring, and control of disease transmission are critical aspects in the prevention and treatment of TB. However, the currently available diagnostic technologies and drug sensitivity tests are time consuming, and thus, it is difficult to achieve the goal of early diagnosis and detection drug sensitivity, which results in limited control of disease transmission. The development of molecular testing technology has gradually achieved the vision of rapid and accurate diagnosis of TB. Droplet digital PCR (ddPCR) is an excellent nucleic acid quantification method with high sensitivity and no need for a calibration curve. Herein, we review the application of ddPCR in TB diagnosis and drug resistance detection and transmission monitoring.
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Affiliation(s)
- Yuxin Fan
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Jingjing Chen
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Meixiao Liu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Xin Xu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Yu Zhang
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Peng Yue
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Wenjing Cao
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Zhenhua Ji
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Xuan Su
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Shiyuan Wen
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Jing Kong
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Guozhong Zhou
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Bingxue Li
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Yan Dong
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Aihua Liu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Correspondence: Aihua Liu; Fukai Bao, The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China, Email ;
| | - Fukai Bao
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
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22
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Wu X, Chan C, Springs SL, Lee YH, Lu TK, Yu H. A warm-start digital CRISPR/Cas-based method for the quantitative detection of nucleic acids. Anal Chim Acta 2022; 1196:339494. [DOI: 10.1016/j.aca.2022.339494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/03/2022] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
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23
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Saha S, Araf Y, Promon SK. Circulating tumor DNA in cancer diagnosis, monitoring, and prognosis. J Egypt Natl Canc Inst 2022; 34:8. [PMID: 35187602 DOI: 10.1186/s43046-022-00109-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/29/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has become one of the crucial components for cancer detection with the increase of precision medicine practice. ctDNA has great potential as a blood-based biomarker for the detection and treatment of cancer in its early stages. The purpose of this article was to discuss ctDNA and how it can be utilized to detect cancer. The benefits and drawbacks of this cancer detection technology, as well as the field's future possibilities in various cancer management scenarios, are discussed. MAIN TEXT: ctDNA has clinical applications in disease diagnosis and monitoring. It can be used to identify mutations of interest and genetic heterogeneity. Another use of ctDNA is to monitor the effects of therapy by detecting mutation-driven resistance. Different technologies are being used for the detection of ctDNA. Next-generation sequencing, digital PCR, real-time PCR, and mass spectrometry are used. Using dPCR makes it possible to partition and analyze individual target sequences from a complex mixture. Mass-spectrometry technology enables accurate detection and quantification of ctDNA mutations at low frequency. Surface-enhanced Raman spectroscopy (SERS) and UltraSEEK are two systems based on this technology. There is no unified standard for detecting ctDNA as it exists in a low concentration in blood. As there is no defined approach, false positives occur in several methods due to inadequate sensitivities. Techniques used in ctDNA are costly and there is a limitation in clinical settings. SHORT CONCLUSION A detailed investigation is urgently needed to increase the test's accuracy and sensitivity. To find a standard marker for all forms of cancer DNA, more study is needed. Low concentrations of ctDNA in a sample require improved technology to provide the precision that low concentrations of ctDNA in a sample afford.
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Affiliation(s)
- Sudeepto Saha
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Salman Khan Promon
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh.
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24
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Mair R, Mouliere F. Cell-free DNA technologies for the analysis of brain cancer. Br J Cancer 2022; 126:371-378. [PMID: 34811503 PMCID: PMC8811068 DOI: 10.1038/s41416-021-01594-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/08/2022] Open
Abstract
Survival for glioma patients has shown minimal improvement over the past 20 years. The ability to detect and monitor gliomas relies primarily upon imaging technologies that lack sensitivity and specificity, especially during the post-surgical treatment phase. Treatment-response monitoring with an effective liquid-biopsy paradigm may also provide the most facile clinical scenario for liquid-biopsy integration into brain-tumour care. Conceptually, liquid biopsy is advantageous when compared with both tissue sampling (less invasive) and imaging (more sensitive and specific), but is hampered by technical and biological problems. These problems predominantly relate to low concentrations of tumour-derived DNA in the bloodstream of glioma patients. In this review, we highlight methods by which the neuro-oncological scientific and clinical communities have attempted to circumvent this limitation. The use of novel biological, technological and computational approaches will be explored. The utility of alternate bio-fluids, tumour-guided sequencing, epigenomic and fragmentomic methods may eventually be leveraged to provide the biological and technological means to unlock a wide range of clinical applications for liquid biopsy in glioma.
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Affiliation(s)
- Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, Cambridge, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE, Cambridge, UK.
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ, Cambridge, UK.
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, 1081 HV, Amsterdam, The Netherlands.
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Crocetto F, Barone B, Ferro M, Busetto GM, La Civita E, Buonerba C, Di Lorenzo G, Terracciano D, Schalken JA. Liquid biopsy in bladder cancer: State of the art and future perspectives. Crit Rev Oncol Hematol 2022; 170:103577. [PMID: 34999017 DOI: 10.1016/j.critrevonc.2022.103577] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 01/01/2023] Open
Abstract
Bladder cancer is the most common malignancy of the urinary tract. Cystoscopy represents the gold standard in the diagnosis of suspicious bladder lesions. However, the procedure is invasive and burdened by pain, discomfort and infective complications. Cytology, which represents an alternative diagnostic possibility is limited by poor sensitivity. Considering the limitations of both procedures, and the necessity to perform multiple evaluations in patients who are in follow-up for bladder cancer, an improved non-invasive methodology is required in the clinical management of this disease. Liquid biopsy, e.g. the detection of clinical biomarkers in urine, represent a promising novel and non-invasive approach that could overcome those limitations and be integrated into the current clinical practice. The aim of this review is to summarize the state of the art of this approach and the latest novelties regarding detection, prognosis and surveillance of bladder cancer.
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Affiliation(s)
- Felice Crocetto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples "Federico II", Naples, Italy
| | - Biagio Barone
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples "Federico II", Naples, Italy.
| | - Matteo Ferro
- Department of Urology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Gian Maria Busetto
- Urology and Renal Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy
| | - Carlo Buonerba
- Oncology Unit, Hospital "Andrea Tortora", ASL Salerno, Pagani, Italy
| | - Giuseppe Di Lorenzo
- Oncology Unit, Hospital "Andrea Tortora", ASL Salerno, Pagani, Italy; Department of Medicine and Health Science, University of Molise, Campobasso, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy
| | - Jack A Schalken
- Department of Urology, Radboud University Medical Center, Nijmegen, Netherlands
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Jo D, Kim SY, Kang HW, Pyo SH, Jeong NK, Bae NH, Lee SJ, Kim YT, Lee KG. Micro-injection Molded Droplet Generation System for Digital PCR Application. BIOCHIP JOURNAL 2022; 16:433-440. [PMID: 36091641 PMCID: PMC9446600 DOI: 10.1007/s13206-022-00079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 12/29/2022]
Abstract
Sensitive, effective, and quantitative analysis of infectious pathogens is an important task for the prevention of human health threats. Herein, we present an advanced approach to producing gene-encapsulated microdroplets for quantitative analysis using a micropatterned metal mold and injection molding technique with an automatically operated system. An injection molded microdroplet generation device was successfully fabricated with a minimum channel width of 30 μm and optimized to produce 100 μm diameter droplets. The optimized microchannel design and flow rate also enable the production of stable numbers of microdroplets (~ 16,000 droplets). To verify the applicability of our device and system to droplet-based digital PCR analysis, Escherichia coli (E. coli) O157:H7 was selected as a model bacterial pathogen, and the stx2 gene was amplified in the microdroplets. The generated microdroplets exhibit both chemical and mechanical stability, and our results are similar to those obtained by a commercially available method. Accordingly, the usefulness of the microdroplet generative device and system is confirmed as a simple, fast, and reliable tool for the quantitative molecular analysis of infectious diseases.
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Affiliation(s)
- Daae Jo
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - So Young Kim
- Bio R&D Lab, BioTNS Co.Ltd, 19-12 Daehak-ro 76 beonan-gil, Daejeon, 34141 Republic of Korea
- Department of Biology, Soon Chun Hyang University, 22 Soonchunhyang-ro, Chungcheongnam-do, Asan-si, 31538 Republic of Korea
| | - Hyeon Woo Kang
- Bio R&D Lab, BioTNS Co.Ltd, 19-12 Daehak-ro 76 beonan-gil, Daejeon, 34141 Republic of Korea
- Department of Biology, Soon Chun Hyang University, 22 Soonchunhyang-ro, Chungcheongnam-do, Asan-si, 31538 Republic of Korea
| | - Sung Han Pyo
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Nam Kyu Jeong
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Nam ho Bae
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Seok Jae Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering and Biotechnology, Tech University of Korea, 237 Sangidaehak-ro, Siheung-si, Gyeonggi-do 15073 Republic of Korea
| | - Kyoung G. Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
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Romero-Peña M, Ng EK, Ghosh S. Development of thermally stable coarse water-in-oil emulsions as potential DNA bioreactors. J DISPER SCI TECHNOL 2021. [DOI: 10.1080/01932691.2020.1794886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Maria Romero-Peña
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Canada
- Facultad de Ingeniería en Mecánica y Ciencias de la Producción, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | | | - Supratim Ghosh
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Canada
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Wang Z, Chen Y, Deng H, Zhen X, Xiong J, Hu Y. Quantification of intrahepatic cccDNA in HBV associated hepatocellular carcinoma by improved ddPCR method. J Virol Methods 2021; 299:114334. [PMID: 34688781 DOI: 10.1016/j.jviromet.2021.114334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/26/2022]
Abstract
The quantification of intrahepatic covalently closed circular DNA (cccDNA) is important for assessing the efficiency of anti-HBV therapy. Exonuclease treatment is essential before real-time quantitative PCR (qPCR) or droplet digital PCR (ddPCR) measurement to improve the specificity of cccDNA quantification. In this research, we compared the limit of detection (LOD) of qPCR and ddPCR and evaluated the digestion efficiency of three exonuclease treatments, PSAD, exonuclease III and T5 exonuclease, when measuring cccDNA in cells or clinical samples by ddPCR. We demonstrated that the LOD of ddCPR was 5.9 copies/reaction, which was much lower than that of qPCR (54.9 copies/reaction), indicating that ddPCR is more sensitive than qPCR. Meanwhile, compared to PSAD or Exo III, UNG and T5 exonuclease treatment combined with ddPCR is more effective in detecting intrahepatic cccDNA in clinical samples. Finally, the median intrahepatic cccDNA was 2.6 copies/104 cells in 26 pairs of HCC samples determined by the improved ddPCR method. Therefore, we developed an optimized ddPCR method, which can be used for the absolute quantification of low levels of intrahepatic cccDNA more precisely.
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Affiliation(s)
- Zhuo Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, 109# Chongqing Medical University, 1 Yi Xue Yuan Road, Yuzhong District, Chongqing, 400016, China
| | - YanMeng Chen
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, 109# Chongqing Medical University, 1 Yi Xue Yuan Road, Yuzhong District, Chongqing, 400016, China
| | - Haijun Deng
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, 109# Chongqing Medical University, 1 Yi Xue Yuan Road, Yuzhong District, Chongqing, 400016, China
| | - Xiaochuan Zhen
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, 109# Chongqing Medical University, 1 Yi Xue Yuan Road, Yuzhong District, Chongqing, 400016, China
| | - Jing Xiong
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, 109# Chongqing Medical University, 1 Yi Xue Yuan Road, Yuzhong District, Chongqing, 400016, China
| | - Yuan Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, 109# Chongqing Medical University, 1 Yi Xue Yuan Road, Yuzhong District, Chongqing, 400016, China.
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Kamińska P, Buszka K, Zabel M, Nowicki M, Alix-Panabières C, Budna-Tukan J. Liquid Biopsy in Melanoma: Significance in Diagnostics, Prediction and Treatment Monitoring. Int J Mol Sci 2021; 22:9714. [PMID: 34575876 PMCID: PMC8468624 DOI: 10.3390/ijms22189714] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/25/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy is a common term referring to circulating tumor cells and other biomarkers, such as circulating tumor DNA (ctDNA) or extracellular vesicles. Liquid biopsy presents a range of clinical advantages, such as the low invasiveness of the blood sample collection and continuous control of the tumor progression. In addition, this approach enables the mechanisms of drug resistance to be determined in various methods of cancer treatment, including immunotherapy. However, in the case of melanoma, the application of liquid biopsy in patient stratification and therapy needs further investigation. This review attempts to collect all of the relevant and recent information about circulating melanoma cells (CMCs) related to the context of malignant melanoma and immunotherapy. Furthermore, the biology of liquid biopsy analytes, including CMCs, ctDNA, mRNA and exosomes, as well as techniques for their detection and isolation, are also described. The available data support the notion that thoughtful selection of biomarkers and technologies for their detection can contribute to the development of precision medicine by increasing the efficacy of cancer diagnostics and treatment.
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Affiliation(s)
- Paula Kamińska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Karolina Buszka
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Maciej Zabel
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Góra, 65-046 Zielona Góra, Poland;
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, 34093 Montpellier, France;
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Joanna Budna-Tukan
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
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Selvarajah S, Plante S, Speevak M, Vaags A, Hamelinck D, Butcher M, McCready E, Grafodatskaya D, Blais N, Tran-Thanh D, Weng X, Nassabein R, Greer W, Walton RN, Lo B, Demetrick D, Santos S, Sadikovic B, Zhang X, Zhang T, Spence T, Stockley T, Feilotter H, Joubert P. A Pan-Canadian Validation Study for the Detection of EGFR T790M Mutation Using Circulating Tumor DNA From Peripheral Blood. JTO Clin Res Rep 2021; 2:100212. [PMID: 34590051 PMCID: PMC8474449 DOI: 10.1016/j.jtocrr.2021.100212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/23/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Genotyping circulating tumor DNA (ctDNA) is a promising noninvasive clinical tool to identify the EGFR T790M resistance mutation in patients with advanced NSCLC with resistance to EGFR inhibitors. To facilitate standardization and clinical adoption of ctDNA testing across Canada, we developed a 2-phase multicenter study to standardize T790M mutation detection using plasma ctDNA testing. METHODS In phase 1, commercial reference standards were distributed to participating clinical laboratories, to use their existing platforms for mutation detection. Baseline performance characteristics were established using known and blinded engineered plasma samples spiked with predetermined concentrations of T790M, L858R, and exon 19 deletion variants. In phase II, peripheral blood collected from local patients with known EGFR activating mutations and progressing on treatment were assayed for the presence of EGFR variants and concordance with a clinically validated test at the reference laboratory. RESULTS All laboratories in phase 1 detected the variants at 0.5 % and 5.0 % allele frequencies, with no false positives. In phase 2, the concordance with the reference laboratory for detection of both the primary and resistance mutation was high, with next-generation sequencing and droplet digital polymerase chain reaction exhibiting the best overall concordance. Data also suggested that the ability to detect mutations at clinically relevant limits of detection is generally not platform-specific, but rather impacted by laboratory-specific practices. CONCLUSIONS Discrepancies among sending laboratories using the same assay suggest that laboratory-specific practices may impact performance. In addition, a negative or inconclusive ctDNA test should be followed by tumor testing when possible.
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Affiliation(s)
- Shamini Selvarajah
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sophie Plante
- Institut Universitaire de Cardiologie et de Pneumologie de Québec-Université Laval, Québec, Quebec, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Vaags
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Darren Hamelinck
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Martin Butcher
- Department of Oncology, McMaster University, Hamilton, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Normand Blais
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Danh Tran-Thanh
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Xiaoduan Weng
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Rami Nassabein
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Wenda Greer
- Queen Elizabeth II Health Sciences Center, Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Bryan Lo
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Doug Demetrick
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Xiao Zhang
- Laboratory Genetics, Kingston Health Sciences Center, Kingston, Ontario, Canada
| | - Tong Zhang
- Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada
| | - Tara Spence
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Tracy Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada
| | - Harriet Feilotter
- Laboratory Genetics, Kingston Health Sciences Center, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec-Université Laval, Québec, Quebec, Canada
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Sallustio F, Curci C, Solimando AG, Leone P, Pontrelli P, Gesualdo L, Vacca A, Racanelli V, Gallone A. Identification and monitoring of Copy Number Variants (CNV) in monoclonal gammopathy. Cancer Biol Ther 2021; 22:404-412. [PMID: 34288806 DOI: 10.1080/15384047.2021.1946458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Monoclonal gammopathy of undetermined significance (MGUS) represents the pre-clinical stage of Multiple Myeloma (MM) with the 5% of MGUS progresses to MM. Although the progression from MGUS to MM has not been completely characterized, it is possible to monitor the DNA modifications of patients diagnosed with MGUS to detect early specific genomic abnormalities, including copy number variations (CNV). The CNVs of chromosome 1q and chromosome 13q are associated with a worse prognosis in MM.In the present study, we showed that it is possible to monitor the 1q21 gain and 13q deletion frequencies in gDNA using digital PCR. The CNV analysis of three cell lines with a well-characterized cytogenetic profile were compared with measures performed by a real-time PCR approach and with a digital PCR approach. Then, we analyzed CNVs in CD138+ plasma cells isolated from bone marrow of MGUS and MM patients.Our results show that digital PCR and targeted DNA monitoring represent a specific and accurate technique for the early detection of specific genomic abnormalities both in MM and in MGUS patients.Our results could represent a remarkable advancement in MM and MGUS diagnosis and in CNV analysis for the evaluation of the risk of progression from MGUS to MM.
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Affiliation(s)
- Fabio Sallustio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Curci
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, Internal Medicine Unit "G. Baccelli", University of Bari Aldo Moro, Bari, Italy.,IRCCS Istituto Tumori Giovanni Paolo II of Bari, Italy
| | - Patrizia Leone
- Department of Biomedical Sciences and Human Oncology, Internal Medicine Unit "G. Baccelli", University of Bari Aldo Moro, Bari, Italy
| | - Paola Pontrelli
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Loreto Gesualdo
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Angelo Vacca
- Department of Biomedical Sciences and Human Oncology, Internal Medicine Unit "G. Baccelli", University of Bari Aldo Moro, Bari, Italy
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, Internal Medicine Unit "G. Baccelli", University of Bari Aldo Moro, Bari, Italy
| | - Anna Gallone
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Bari, Italy
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Li Y, Zheng Y, Wu L, Li J, Ji J, Yu Q, Dai W, Feng J, Wu J, Guo C. Current status of ctDNA in precision oncology for hepatocellular carcinoma. J Exp Clin Cancer Res 2021; 40:140. [PMID: 33902698 PMCID: PMC8074474 DOI: 10.1186/s13046-021-01940-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/06/2021] [Indexed: 01/12/2023] Open
Abstract
The conventional method used to obtain a tumor biopsy for hepatocellular carcinoma (HCC) is invasive and does not evaluate dynamic cancer progression or assess tumor heterogeneity. It is thus imperative to create a novel non-invasive diagnostic technique for improvement in cancer screening, diagnosis, treatment selection, response assessment, and predicting prognosis for HCC. Circulating tumor DNA (ctDNA) is a non-invasive liquid biopsy method that reveals cancer-specific genetic and epigenetic aberrations. Owing to the development of technology in next-generation sequencing and PCR-based assays, the detection and quantification of ctDNA have greatly improved. In this publication, we provide an overview of current technologies used to detect ctDNA, the ctDNA markers utilized, and recent advances regarding the multiple clinical applications in the field of precision medicine for HCC.
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Affiliation(s)
- Yan Li
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Yuanyuan Zheng
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Liwei Wu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Jingjing Li
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Jie Ji
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Qiang Yu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Weiqi Dai
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Jiao Feng
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China.
| | - Jianye Wu
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China.
| | - Chuanyong Guo
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China.
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China.
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Oversoe SK, Clement MS, Weber B, Grønbæk H, Hamilton-Dutoit SJ, Sorensen BS, Kelsen J. Combining tissue and circulating tumor DNA increases the detection rate of a CTNNB1 mutation in hepatocellular carcinoma. BMC Cancer 2021; 21:376. [PMID: 33827453 PMCID: PMC8028749 DOI: 10.1186/s12885-021-08103-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Background and aims Studies suggest that mutations in the CTNNB1 gene are predictive of response to immunotherapy, an emerging therapy for advanced hepatocellular carcinoma (HCC). Analysis of circulating tumor DNA (ctDNA) offers the possibility of serial non-invasive mutational profiling of tumors. Combining tumor tissue and ctDNA analysis may increase the detection rate of mutations. This study aimed to evaluate the frequency of the CTNNB1 p.T41A mutation in ctDNA and tumor samples from HCC patients and to evaluate the concordance rates between plasma and tissue. We further evaluated changes in ctDNA after various HCC treatment modalities and the impact of the CTNNB1 p.T41A mutation on the clinical course of HCC. Methods We used droplet digital PCR to analyze plasma from 95 patients and the corresponding tumor samples from 37 patients during 3 years follow up. Results In tumor tissue samples, the mutation rate was 8.1% (3/37). In ctDNA from HCC patients, the CTNNB1 mutation rate was 9.5% (9/95) in the pre-treatment samples. Adding results from plasma analysis to the subgroup of patients with available tissue samples, the mutation detection rate increased to 13.5% (5/37). There was no difference in overall survival according to CTNNB1 mutational status. Serial testing of ctDNA suggested a possible clonal evolution of HCC or arising multicentric tumors with separate genetic profiles in individual patients. Conclusion Combining analysis of ctDNA and tumor tissue increased the detection rate of CTNNB1 mutation in HCC patients. A liquid biopsy approach may be useful in a tailored therapy of HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08103-0.
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Affiliation(s)
- Stine Karlsen Oversoe
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark. .,Department of Internal Medicine, Randers Regional Hospital, Randers, Denmark.
| | | | - Britta Weber
- Department of Clinical Oncology and Danish Centre of Particle Therapy, Aarhus University Hospital, Aarhus, Denmark
| | - Henning Grønbæk
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Kelsen
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
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Huerta M, Roselló S, Sabater L, Ferrer A, Tarazona N, Roda D, Gambardella V, Alfaro-Cervelló C, Garcés-Albir M, Cervantes A, Ibarrola-Villava M. Circulating Tumor DNA Detection by Digital-Droplet PCR in Pancreatic Ductal Adenocarcinoma: A Systematic Review. Cancers (Basel) 2021; 13:cancers13050994. [PMID: 33673558 PMCID: PMC7956845 DOI: 10.3390/cancers13050994] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/11/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Pancreatic cancer is a digestive tumor that is most difficult to treat and carries one of the worst prognoses. The anatomical location of the pancreas makes it very difficult to obtain enough tumor material to establish a molecular diagnosis, so knowing the biology of this tumor and implementing new targeted-therapies is still a pending issue. The use of liquid biopsy, a blood sample test to detect circulating-tumor DNA fragments (ctDNA), is key to overcoming this difficulty and improving the evolution of this tumor. Liquid biopsies are equally representative of the tissue from which they come and allow relevant molecular and diagnostic information to be obtained in a faster and less invasive way. One challenge related to ctDNA is the lack of consistency in the study design. Moreover, ctDNA accounts for only a small percentage of the total cell-free circulating DNA and prior knowledge about particular mutations is usually required. Thus, our aim was to understand the current role and future perspectives of ctDNA in pancreatic cancer using digital-droplet PCR technology. Abstract Pancreatic cancer (PC) is one of the most devastating malignant tumors, being the seventh leading cause of cancer-related death worldwide. Researchers and clinicians are endeavoring to develop strategies for the early detection of the disease and the improvement of treatment results. Adequate biopsy is still challenging because of the pancreas’s poor anatomic location. Recently, circulating tumor DNA (ctDNA) could be identified as a liquid biopsy tool with huge potential as a non-invasive biomarker in early diagnosis, prognosis and management of PC. ctDNA is released from apoptotic and necrotic cancer cells, as well as from living tumor cells and even circulating tumor cells, and it can reveal genetic and epigenetic alterations with tumor-specific and individual mutation and methylation profiles. However, ctDNA sensibility remains a limitation and the accuracy of ctDNA as a biomarker for PC is relatively low and cannot be currently used as a screening or diagnostic tool. Increasing evidence suggests that ctDNA is an interesting biomarker for predictive or prognosis studies, evaluating minimal residual disease, longitudinal follow-up and treatment management. Promising results have been published and therefore the objective of our review is to understand the current role and the future perspectives of ctDNA in PC.
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Affiliation(s)
- Marisol Huerta
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain; (M.H.); (S.R.); (A.F.); (N.T.); (D.R.); (V.G.); (A.C.)
| | - Susana Roselló
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain; (M.H.); (S.R.); (A.F.); (N.T.); (D.R.); (V.G.); (A.C.)
- CIBERONC, Medical Oncology Unit, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain
| | - Luis Sabater
- Liver, Biliary and Pancreatic Unit, Department of Surgery, Hospital Clínico Universitario of Valencia, University of Valencia, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (L.S.); (M.G.-A.)
| | - Ana Ferrer
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain; (M.H.); (S.R.); (A.F.); (N.T.); (D.R.); (V.G.); (A.C.)
- CIBERONC, Medical Oncology Unit, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain; (M.H.); (S.R.); (A.F.); (N.T.); (D.R.); (V.G.); (A.C.)
- CIBERONC, Medical Oncology Unit, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain
| | - Desamparados Roda
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain; (M.H.); (S.R.); (A.F.); (N.T.); (D.R.); (V.G.); (A.C.)
- CIBERONC, Medical Oncology Unit, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain
| | - Valentina Gambardella
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain; (M.H.); (S.R.); (A.F.); (N.T.); (D.R.); (V.G.); (A.C.)
- CIBERONC, Medical Oncology Unit, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain
| | - Clara Alfaro-Cervelló
- Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain;
| | - Marina Garcés-Albir
- Liver, Biliary and Pancreatic Unit, Department of Surgery, Hospital Clínico Universitario of Valencia, University of Valencia, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (L.S.); (M.G.-A.)
| | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain; (M.H.); (S.R.); (A.F.); (N.T.); (D.R.); (V.G.); (A.C.)
- CIBERONC, Medical Oncology Unit, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain
| | - Maider Ibarrola-Villava
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain; (M.H.); (S.R.); (A.F.); (N.T.); (D.R.); (V.G.); (A.C.)
- CIBERONC, Medical Oncology Unit, INCLIVA Biomedical Research Institute, University of Valencia, 46010 Valencia, Spain
- Correspondence: ; Tel.: +34-963-862-894
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Gallardo-Gómez M, De Chiara L, Álvarez-Chaver P, Cubiella J. Colorectal cancer screening and diagnosis: omics-based technologies for development of a non-invasive blood-based method. Expert Rev Anticancer Ther 2021; 21:723-738. [PMID: 33507120 DOI: 10.1080/14737140.2021.1882858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Colorectal cancer (CRC) is one of the most important health problems in the Western world. In order to reduce the burden of the disease, two strategies are proposed: screening and prompt detection in symptomatic patients. Although diagnosis and prevention are mainly based on colonoscopy, fecal hemoglobin detection has been widely implemented as a noninvasive strategy. Various studies aiming to discover blood-based biomarkers have recently emerged.Areas covered: The burgeoning omics field provides diverse high-throughput approaches for CRC blood-based biomarker discovery. In this review, we appraise the most robust and commonly used technologies within the fields of genomics, transcriptomics, epigenomics, proteomics, and metabolomics, together with their targeted validation approaches. We summarize the transference process from the discovery phase until clinical translation. Finally, we review the best candidate biomarkers and their potential clinical applicability.Expert opinion: Some available biomarkers are promising, especially in the field of epigenomics: DNA methylation and microRNA. Transference requires the joint collaboration of basic researchers, intellectual property experts, technology transfer officers and clinicians. Blood-based biomarkers will be selected not only based on their diagnostic accuracy and cost but also on their reliability, applicability to clinical analysis laboratories and their acceptance by the population.
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Affiliation(s)
- María Gallardo-Gómez
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Loretta De Chiara
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Paula Álvarez-Chaver
- Proteomics Unit, Service of Structural Determination, Proteomics and Genomics, Center for Scientific and Technological Research Support (CACTI), University of Vigo, Vigo, Spain
| | - Joaquin Cubiella
- Department of Gastroenterology, Hospital Universitario De Ourense, Ourense, Spain.,Instituto De Investigación Sanitaria Galicia Sur, Ourense, Spain.,Centro De Investigación Biomédica En Red Enfermedades Hepáticas Y Digestivas, Ourense, Spain
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36
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Centrifugal Microfluidic Integration of 4-Plex ddPCR Demonstrated by the Quantification of Cancer-Associated Point Mutations. Processes (Basel) 2021. [DOI: 10.3390/pr9010097] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We present the centrifugal microfluidic implementation of a four-plex digital droplet polymerase chain reaction (ddPCR). The platform features 12 identical ddPCR units on a LabDisk cartridge, each capable of generating droplets with a diameter of 82.7 ± 9 µm. By investigating different oil–surfactant concentrations, we identified a robust process for droplet generation and stabilization. We observed high droplet stability during thermocycling and endpoint fluorescence imaging, as is required for ddPCRs. Furthermore, we introduce an automated process for four-color fluorescence imaging using a commercial cell analysis microscope, including a customized software pipeline for ddPCR image evaluation. The applicability of ddPCRs is demonstrated by the quantification of three cancer-associated KRAS point mutations (G12D, G12V and G12A) in a diagnostically relevant wild type DNA background. The four-plex assay showed high sensitivity (3.5–35 mutant DNA copies in 15,000 wild type DNA copies) and linear performance (R² = 0.99) across all targets in the LabDisk.
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Paramathas S, Guha T, Pugh TJ, Malkin D, Villani A. Considerations for the use of circulating tumor DNA sequencing as a screening tool in cancer predisposition syndromes. Pediatr Blood Cancer 2020; 67:e28758. [PMID: 33047872 DOI: 10.1002/pbc.28758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022]
Abstract
Liquid biopsy, specifically circulating tumor DNA (ctDNA) detection, has started to revolutionize the clinical management of patients with cancer by surpassing many limitations of traditional tissue biopsies, particularly for serial testing. ctDNA sequencing has been successfully utilized for cancer detection, prognostication, and assessment of disease response and evolution. While the applications of ctDNA analysis are growing, the majority of studies to date have primarily evaluated its use as a tool for tracking a known cancer, and in most cases at advanced stage. Herein, we discuss the potential application of ctDNA for surveillance and early cancer detection in patients with a cancer predisposition syndrome.
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Affiliation(s)
- Sangeetha Paramathas
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Tanya Guha
- Institute of Medical Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Centre, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Anita Villani
- Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
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38
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Hosen MI, Forey N, Durand G, Voegele C, Bilici S, Avogbe PH, Delhomme TM, Foll M, Manel A, Vian E, Meziani S, De Tilly B, Polo G, Lole O, Francois P, Boureille A, Pisarev E, Salas AROSE, Monteiro-Reis S, Henrique R, Byrnes G, Jeronimo C, Scelo G, McKay JD, Calvez-Kelm FL, Zvereva M. Development of Sensitive Droplet Digital PCR Assays for Detecting Urinary TERT Promoter Mutations as Non-Invasive Biomarkers for Detection of Urothelial Cancer. Cancers (Basel) 2020; 12:E3541. [PMID: 33260905 PMCID: PMC7761513 DOI: 10.3390/cancers12123541] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Somatic mutations in the telomerase reverse transcriptase (TERT) promoter regions are frequent events in urothelial cancer (UC) and their detection in urine (supernatant cell-free DNA or DNA from exfoliated cells) could serve as putative non-invasive biomarkers for UC detection and monitoring. However, detecting these tumor-borne mutations in urine requires highly sensitive methods, capable of measuring low-level mutations. In this study, we developed sensitive droplet digital PCR (ddPCR) assays for detecting TERT promoter mutations (C228T, C228A, CC242-243TT, and C250T). We tested the C228T and C250T ddPCR assays on all samples with sufficient quantity of urinary DNA (urine supernatant cell-free DNA (US cfDNA) or urine pellet cellular DNA (UP cellDNA)) from the DIAGURO (n = 89/93 cases and n = 92/94 controls) and from the IPO-PORTO (n = 49/50 cases and n = 50/50 controls) series that were previously screened with the UroMuTERT assay and compared the performance of the two approaches. In the DIAGURO series, the sensitivity and specificity of the ddPCR assays for detecting UC using either US cfDNA or UP cellDNA were 86.8% and 92.4%. The sensitivity was slightly higher than that of the UroMuTERT assay in the IPO-PORTO series (67.4% vs. 65.3%, respectively), but not in the DIAGURO series (86.8% vs. 90.7%). The specificity was 100% in the IPO-PORTO controls for both the UroMuTERT and ddPCR assays, whereas in the DIAGURO series, the specificity dropped for ddPCR (92.4% versus 95.6%). Overall, an almost perfect agreement between the two methods was observed for both US cfDNA (n = 164; kappa coefficient of 0.91) and UP cellDNA (n = 280; kappa coefficient of 0.94). In a large independent series of serial urine samples from DIAGURO follow-up BC cases (n = 394), the agreement between ddPCR and UroMuTERT was (i) strong (kappa coefficient of 0.87), regardless of urine DNA types (kappa coefficient 0.89 for US cfDNA and 0.85 for UP cellDNA), (ii) the highest for samples with mutant allelic fractions (MAFs) > 2% (kappa coefficient of 0.99) and (iii) only minimal for the samples with the lowest MAFs (< 0.5%; kappa coefficient 0.32). Altogether, our results indicate that the two methods (ddPCR and UroMuTERT) for detecting urinary TERT promoter mutations are comparable and that the discrepancies relate to the detection of low-allelic fraction mutations. The simplicity of the ddPCR assays makes them suitable for implementation in clinical settings.
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Affiliation(s)
- Md Ismail Hosen
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh
| | - Nathalie Forey
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Catherine Voegele
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Selin Bilici
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Patrice Hodonou Avogbe
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Tiffany Myriam Delhomme
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | | | - Emmanuel Vian
- Department of Urology, Protestant Clinic of Lyon, 69300 Caluire-et-Cuire, France; (E.V.); (B.D.T.); (G.P.)
| | - Sonia Meziani
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Berengere De Tilly
- Department of Urology, Protestant Clinic of Lyon, 69300 Caluire-et-Cuire, France; (E.V.); (B.D.T.); (G.P.)
| | - Gilles Polo
- Department of Urology, Protestant Clinic of Lyon, 69300 Caluire-et-Cuire, France; (E.V.); (B.D.T.); (G.P.)
| | - Olesia Lole
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Pauline Francois
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Antoine Boureille
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Eduard Pisarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Andrei R. O. S. E. Salas
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
- Santa Casa de Sao Paulo School of Medical Sciences, Sao Paulo 01221-020, Brazil
| | - Sara Monteiro-Reis
- Portuguese Oncology Institute of Porto, Research Center (CI-IPOP), 4200-072 Porto, Portugal; (S.M.-R.); (R.H.); (C.J.)
| | - Rui Henrique
- Portuguese Oncology Institute of Porto, Research Center (CI-IPOP), 4200-072 Porto, Portugal; (S.M.-R.); (R.H.); (C.J.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4099-002 Porto, Portugal
| | - Graham Byrnes
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Carmen Jeronimo
- Portuguese Oncology Institute of Porto, Research Center (CI-IPOP), 4200-072 Porto, Portugal; (S.M.-R.); (R.H.); (C.J.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4099-002 Porto, Portugal
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
- Department of Medical Sciences, University of Turin, 8-10124 Turin, Italy
| | - James D. McKay
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Florence Le Calvez-Kelm
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
| | - Maria Zvereva
- International Agency for Research on Cancer (IARC), 69372 Lyon, France; (M.I.H.); (N.F.); (G.D.); (C.V.); (S.B.); (P.H.A.); (T.M.D.); (M.F.); (S.M.); (O.L.); (P.F.); (A.B.); (A.R.O.S.E.S.); (G.B.); (G.S.); (J.D.M.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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Shen T, Li SF, Wang JL, Zhang T, Zhang S, Chen HT, Xiao QY, Ren WH, Liu C, Peng B, Ji XN, Yang Y, Lu PX, Chen TY, Yu L, Ji Y, Jiang DK. TP53 R249S mutation detected in circulating tumour DNA is associated with Prognosis of hepatocellular carcinoma patients with or without hepatectomy. Liver Int 2020; 40:2834-2847. [PMID: 32594568 DOI: 10.1111/liv.14581] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/19/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Somatic mutation R249S in TP53 is highly common in hepatocellular carcinoma (HCC). We aim to investigate the effects of R249S in ctDNA on the prognosis of HCC. METHODS We analysed three cohorts including 895 HCC patients. TP53 mutation spectrum was examined by direct sequencing of genomic DNA from tissue specimens in HCC patients with hepatectomy (Cohort 1, N = 260). R249S and other recurrent missense mutations were assessed for their biological functions and associations with overall survival (OS) and progression-free survival (PFS) of HCC patients in Cohort 1. R249S within circulating tumour DNA (ctDNA) was detected through droplet digital polymerase chain reaction (ddPCR) and its association with OS and PRS was analysed in HCC patients with (Cohort 2, N = 275) or without (Cohort 3, N = 360) hepatectomy. RESULTS In Cohort 1, R249S occupied 60.28% of all TP53 mutations. Overexpression of R249S induced more serious malignant phenotypes than those of the other three identified TP53 recurrent missense mutations. Additionally, R249S, but not other missense mutations, was significantly associated with worse OS (P = .006) and PFS (P = .01) of HCC patients. Consistent with the results in Cohort 1, HCC patients in Cohorts 2 and 3 with R249S had worse OS (P = 8.291 × 10-7 and 2.608 × 10-7 in Cohorts 2 and 3, respectively) and PFS (P = 5.115 × 10-7 and 5.900 × 10-13 in Cohorts 2 and 3, respectively) compared to those without this mutation. CONCLUSIONS TP53 R249S mutation in ctDNA may serve as a promising prognosis biomarker for HCC patients with or without hepatectomy.
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Affiliation(s)
- Ting Shen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, GuangZhou, China
| | - Shan-Feng Li
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, GuangZhou, China
| | - Jia-Lin Wang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, GuangZhou, China
| | - Ting Zhang
- Institute of Cancer, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Song Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, and Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hai-Tao Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, GuangZhou, China
| | - Qian-Yi Xiao
- School of public health, Fudan University, Shanghai, China
| | - Wei-Hua Ren
- Central Laboratory, First Affiliated Hospital, Henan University of Science and Technology, luoyang, China
| | - Chao Liu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, and Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Peng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, and Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiao-Na Ji
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, and Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yang Yang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, and Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Pei-Xin Lu
- Qidong Liver Cancer Institute, Qidong people's hospital, Qidong, China
| | - Tao-Yang Chen
- Qidong Liver Cancer Institute, Qidong people's hospital, Qidong, China
| | - Long Yu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, and Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuan Ji
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - De-Ke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, GuangZhou, China
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Lam D, Clark S, Stirzaker C, Pidsley R. Advances in Prognostic Methylation Biomarkers for Prostate Cancer. Cancers (Basel) 2020; 12:E2993. [PMID: 33076494 PMCID: PMC7602626 DOI: 10.3390/cancers12102993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/24/2022] Open
Abstract
There is a major clinical need for accurate biomarkers for prostate cancer prognosis, to better inform treatment strategies and disease monitoring. Current clinically recognised prognostic factors, including prostate-specific antigen (PSA) levels, lack sensitivity and specificity in distinguishing aggressive from indolent disease, particularly in patients with localised intermediate grade prostate cancer. There has therefore been a major focus on identifying molecular biomarkers that can add prognostic value to existing markers, including investigation of DNA methylation, which has a known role in tumorigenesis. In this review, we will provide a comprehensive overview of the current state of DNA methylation biomarker studies in prostate cancer prognosis, and highlight the advances that have been made in this field. We cover the numerous studies into well-established candidate genes, and explore the technological transition that has enabled hypothesis-free genome-wide studies and the subsequent discovery of novel prognostic genes.
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Affiliation(s)
- Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
| | - Susan Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
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Circular RNAs in cancer: limitations in functional studies and diagnostic potential. Semin Cancer Biol 2020; 75:49-61. [PMID: 33035655 DOI: 10.1016/j.semcancer.2020.10.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/15/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) are a large class of noncoding RNAs, generated from a process called back-splicing, that possess critical regulatory functions in many cellular events. A large body of literature has reported various circRNA functions and their underlying mechanisms, including sponging miRNA, exerting transcriptional and translational regulation, interacting with proteins, and translating into peptides and proteins. CircRNA dysregulation has been implicated in many cancers, including lung, breast, liver, gastric, colorectal, and ovarian cancer. They are detectable in bodily fluids and relatively stable, making them potential cancer biomarker candidates. Furthermore, targeting circRNA expression levels is a potential therapeutic approach for treating cancers. In this review, we describe the functional mechanisms of circRNAs and discuss limitations of current mechanism studies. Following this, we outline the potential of circRNAs to be effective biomarkers in various cancers and present circRNA-based therapeutic approaches. Finally, we discuss challenges in using circRNAs as diagnostic and therapeutic tools and propose future research directions.
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Moniri A, Miglietta L, Malpartida-Cardenas K, Pennisi I, Cacho-Soblechero M, Moser N, Holmes A, Georgiou P, Rodriguez-Manzano J. Amplification Curve Analysis: Data-Driven Multiplexing Using Real-Time Digital PCR. Anal Chem 2020; 92:13134-13143. [PMID: 32946688 DOI: 10.1021/acs.analchem.0c02253] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Information about the kinetics of PCR reactions is encoded in the amplification curve. However, in digital PCR (dPCR), this information is typically neglected by collapsing each amplification curve into a binary output (positive/negative). Here, we demonstrate that the large volume of raw data obtained from real-time dPCR instruments can be exploited to perform data-driven multiplexing in a single fluorescent channel using machine learning methods, by virtue of the information in the amplification curve. This new approach, referred to as amplification curve analysis (ACA), was shown using an intercalating dye (EvaGreen), reducing the cost and complexity of the assay and enabling the use of melting curve analysis for validation. As a case study, we multiplexed 3 carbapenem-resistant genes to show the impact of this approach on global challenges such as antimicrobial resistance. In the presence of single targets, we report a classification accuracy of 99.1% (N = 16188), which represents a 19.7% increase compared to multiplexing based on the final fluorescent intensity. Considering all combinations of amplification events (including coamplifications), the accuracy was shown to be 92.9% (N = 10383). To support the analysis, we derived a formula to estimate the occurrence of coamplification in dPCR based on multivariate Poisson statistics and suggest reducing the digital occupancy in the case of multiple targets in the same digital panel. The ACA approach takes a step toward maximizing the capabilities of existing real-time dPCR instruments and chemistries, by extracting more information from data to enable data-driven multiplexing with high accuracy. Furthermore, we expect that combining this method with existing probe-based assays will increase multiplexing capabilities significantly. We envision that once emerging point-of-care technologies can reliably capture real-time data from isothermal chemistries, the ACA method will facilitate the implementation of dPCR outside of the lab.
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Affiliation(s)
- Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Luca Miglietta
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Ivana Pennisi
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K.,Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London W2 1NY, U.K
| | - Miguel Cacho-Soblechero
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Alison Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, U.K
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, U.K
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Pessoa LS, Heringer M, Ferrer VP. ctDNA as a cancer biomarker: A broad overview. Crit Rev Oncol Hematol 2020; 155:103109. [PMID: 33049662 DOI: 10.1016/j.critrevonc.2020.103109] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in fluids has gained attention because ctDNA seems to identify tumor-specific abnormalities, which could be used for diagnosis, follow-up of treatment, and prognosis: the so-called liquid biopsy. Liquid biopsy is a minimally invasive approach and presents the sum of ctDNA from primary and secondary tumor sites. It has been possible not only to quantify the amount of ctDNA but also to identify (epi)genetic changes. Specific mutations in genes have been identified in the plasma of patients with several types of cancer, which highlights ctDNA as a possible cancer biomarker. However, achieving detectable concentrations of ctDNA in body fluids is not an easy task. ctDNA fragments present a short half-life, and there are no cut-off values to discriminate high and low ctDNA concentrations. Here, we discuss the use of ctDNA as a cancer biomarker, the main methodologies, the inherent difficulties, and the clinical predictive value of ctDNA.
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Affiliation(s)
- Luciana Santos Pessoa
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil; Center for Experimental Surgery, Graduate Program in Surgical Sciences, Department of Surgery, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manoela Heringer
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil.
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Kolenda T, Guglas K, Baranowski D, Sobocińska J, Kopczyńska M, Teresiak A, Bliźniak R, Lamperska K. cfRNAs as biomarkers in oncology - still experimental or applied tool for personalized medicine already? Rep Pract Oncol Radiother 2020; 25:783-792. [PMID: 32904167 PMCID: PMC7451588 DOI: 10.1016/j.rpor.2020.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/13/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
Currently, the challenges of contemporary oncology are focused mainly on the development of personalized medicine and precise treatment, which could be achieved through the use of molecular biomarkers. One of the biological molecules with great potential are circulating free RNAs (cfRNAs) which are present in various types of body fluids, such as blood, serum, plasma, and saliva. Also, different types of cfRNA particles can be distinguished depending on their length and function: microRNA (miRNA), PIWI-interacting RNA (piRNA), tRNA-derived RNA fragments (tRFs), circular RNA (circRNA), long non-coding RNA (lncRNA), and messenger RNA (mRNA). Moreover, cfRNAs occur in various forms: as a free molecule alone, in membrane vesicles, such as exosomes, or in complexes with proteins and lipids. One of the modern approaches for monitoring patient's condition is a "liquid biopsy" that provides a non-invasive and easily available source of circulating RNAs. Both the presence of specific cfRNA types as well as their concentration are dependent on many factors including cancer type or even reaction to treatment. Despite the possibility of using circulating free RNAs as biomarkers, there is still a lack of validated diagnostic panels, defined protocols for sampling, storing as well as detection methods. In this work we examine different types of cfRNAs, evaluate them as possible biomarkers, and analyze methods of their detection. We believe that further research on cfRNA and defining diagnostic panels could lead to better and faster cancer identification and improve treatment monitoring.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Dawid Baranowski
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
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Veyer D, Kernéis S, Poulet G, Wack M, Robillard N, Taly V, L'Honneur AS, Rozenberg F, Laurent-Puig P, Bélec L, Hadjadj J, Terrier B, Péré H. Highly sensitive quantification of plasma SARS-CoV-2 RNA shelds light on its potential clinical value. Clin Infect Dis 2020; 73:e2890-e2897. [PMID: 32803231 PMCID: PMC7454373 DOI: 10.1093/cid/ciaa1196] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 01/08/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) is a global public health problem that has already caused more than 662,000 deaths worldwide. Although the clinical manifestations of COVID-19 are dominated by respiratory symptoms, some patients present other severe damage such as cardiovascular, renal and liver injury or/and multiple organ failure, suggesting a spread of the SARS-CoV-2 in blood. Recent ultrasensitive polymerase chain reaction (PCR) technology now allows absolute quantification of nucleic acids in plasma. We herein intended to use the droplet-based digital PCR technology to obtain sensitive detection and precise quantification of plasma SARS-CoV-2 viral load (SARS-CoV-2 RNAaemia) in hospitalized COVID-19 patients. Methods Fifty-eight consecutive COVID-19 patients with pneumonia 8 to 12 days after onset of symptoms and 12 healthy controls were analyzed. Disease severity was categorized as mild-to-moderate in 17 patients, severe in 16 patients and critical in 26 patients. Plasma SARS-CoV-2 RNAaemia was quantified by droplet digital Crystal Digital PCR™ next-generation technology (Stilla Technologies, Villejuif, France). Results Overall, SARS-CoV-2 RNAaemia was detected in 43 (74.1%) patients. Prevalence of positive SARS-CoV-2 RNAaemia correlated with disease severity, ranging from 53% in mild-to-moderate patients to 88% in critically ill patients (p=0.036). Levels of SARS-CoV-2 RNAaemia were associated with severity (p=0.035). Among nine patients who experienced clinical deterioration during follow-up, eight had positive SARS-CoV-2 RNAaemia at baseline while only one critical patient with undetectable SARS-CoV-2 RNAaemia at the time of analysis died at day 27. Conclusion SARS-CoV-2 RNAaemia measured by droplet-based digital PCR constitutes a promising prognosis biomarker in COVID-19 patients
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Affiliation(s)
- David Veyer
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Microbiologie (Unité de virologie), Hôpital Européen Georges Pompidou, Paris, France.,Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Solen Kernéis
- Equipe Mobile d'Infectiologie, AP-HP, APHP.CUP, Hôpital Cochin, F-75014 Paris, France.,Université de Paris, INSERM, IAME, F-75006 Paris, France.,Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), F-75015 Paris, France
| | - Geoffroy Poulet
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Personalized Medicine Pharmacogenomics, therapeutic optimization, eDIAG plateform, laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Maxime Wack
- Eurofins-Biomnis, Lyon.,Département d'Informatique Médicale, Biostatistiques et Santé Publique, Hôpital Européen Georges Pompidou, AP-HP CUP, Paris, France
| | - Nicolas Robillard
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Microbiologie (Unité de virologie), Hôpital Européen Georges Pompidou, Paris, France
| | - Valérie Taly
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), F-75015 Paris, France
| | - Anne-Sophie L'Honneur
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Information sciences to support medicine Paris, France
| | - Flore Rozenberg
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Information sciences to support medicine Paris, France
| | - Pierre Laurent-Puig
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), F-75015 Paris, France.,Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Virologie, Hôpital Cochin, Paris, France
| | - Laurent Bélec
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Microbiologie (Unité de virologie), Hôpital Européen Georges Pompidou, Paris, France.,Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, AP-HP CUP, Paris, France
| | - Jérôme Hadjadj
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Biochimie, Hôpital Européen Georges Pompidou, Paris, France.,Imagine Institute, laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163
| | - Benjamin Terrier
- Imagine Institute, laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163.,Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, AP-HP CUP, Paris, France
| | - Hélène Péré
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Microbiologie (Unité de virologie), Hôpital Européen Georges Pompidou, Paris, France.,PARCC, Université de Paris, INSERM U970, Paris, France
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Plasma-based early screening and monitoring of EGFR mutations in NSCLC patients by a 3-color digital PCR assay. Br J Cancer 2020; 123:1437-1444. [PMID: 32782293 PMCID: PMC7592053 DOI: 10.1038/s41416-020-1024-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/30/2022] Open
Abstract
Background Noninvasive plasma-based detection of EGFR mutations using digital PCR promises a fast, sensitive and reliable approach to predicting the efficiency of EGFR-TKI. However, the low throughput and high cost of digital PCR restricts its clinical application. Methods We designed a digital PCR assay, which can simultaneously detect 39 mutations of exons 18–21 of the EGFR gene. To assess overall performance, retrospective FFPE tissues from 30 NSCLC patients and plasma from 33 NSCLC patients were collected and analysed. Results The LoD of the EGFR mutations was as low as 0.308 copies/μL, and the linear correlation between the detected and expected values at different concentrations (0.01–10%) was low as well. Compared to ARMS-PCR in FFPE, the accuracy values of the dEGFR39 assay in plasma from 33 patients was 87.88% (29/33, 95% CI 72.67–95.18%). While monitoring the 33 patients, the EGFR mutation load as assessed by dEGFR39 was associated with the objective response to treatment. Thirteen samples from eight patients were identified by dEGFR39 to harbour the T790M mutation over time; of these patients, only nine (69%) were detected using SuperARMS. Conclusion Our results indicate that dEGFR39 assay is reliable, sensitive and cost-efficient. This method is beneficial for profiling EGFR mutations for precision therapy and prognosis after TKI treatment, especially in patients with insufficient tissue biopsy samples.
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Laurito S, Branham MT, Campoy E, Real S, Cueto J, Urrutia G, Gago F, Tello O, Glatstein T, De la Iglesia P, Atanesyan L, Savola S, Roqué M. Working together for the family: determination of HER oncogene co-amplifications in breast cancer. Oncotarget 2020; 11:2774-2792. [PMID: 32733648 PMCID: PMC7367656 DOI: 10.18632/oncotarget.27671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/20/2020] [Indexed: 11/25/2022] Open
Abstract
HER2 is a well-studied tyrosine kinase (TK) membrane receptor which functions as a therapeutic target in invasive ductal breast carcinomas (IDC). The standard of care for the treatment of HER2-positive breast is the antibody trastuzumab. Despite specific treatment unfortunately, 20% of primary and 70% of metastatic HER2 tumors develop resistance. HER2 belongs to a gene family, with four members (HER1-4) and these members could be involved in resistance to anti-HER2 therapies. In this study we designed a probemix to detect the amplification of the four HER oncogenes in a single reaction. In addition, we developed a protocol based on the combination of MLPA with ddPCR to detect the tumor proportion of co-amplified HERs. On 111 IDC, the HER2 MLPA results were validated by FISH (Adjusted r 2 = 0,91, p < 0,0001), CISH (Adjusted r 2 = 0,938, p < 0,0001) and IHC (Adjusted r 2 = 0,31, p < 0,0001). HER1-4 MLPA results were validated by RT-qPCR assays (Spearman Rank test p < 0,05). Of the 111 samples, 26% presented at least one HER amplified, of which 23% showed co-amplifications with other HERs. The percentage of cells with HER2 co-amplified varied among the tumors (from 2-72,6%). Independent in-silico findings show that the outcome of HER2+ patients is conditioned by the status of HER3 and HER4. Our results encourage further studies to investigate the relationship with patient's response to single or combined treatment. The approach could serve as proof of principle for other tumors in which the HER oncogenes are involved.
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Affiliation(s)
- Sergio Laurito
- Institute of Histology and Embryology, National Council of Research, Consejo Nacional de Investigaciones Científicas y Técnicas, Mendoza, Argentina.,Universidad Nacional de Cuyo, Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
| | - María Teresita Branham
- Institute of Histology and Embryology, National Council of Research, Consejo Nacional de Investigaciones Científicas y Técnicas, Mendoza, Argentina
| | - Emanuel Campoy
- Institute of Histology and Embryology, National Council of Research, Consejo Nacional de Investigaciones Científicas y Técnicas, Mendoza, Argentina.,Universidad Nacional de Cuyo, Facultad de Ciencias Médicas, Mendoza, Argentina
| | - Sebastián Real
- Institute of Histology and Embryology, National Council of Research, Consejo Nacional de Investigaciones Científicas y Técnicas, Mendoza, Argentina.,Universidad Nacional de Cuyo, Facultad de Ciencias Médicas, Mendoza, Argentina
| | - Juan Cueto
- Universidad Nacional de Cuyo, Facultad de Ciencias Médicas, Mendoza, Argentina
| | - Guillermo Urrutia
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Olga Tello
- Instituto Gineco-Mamario, Mendoza, Argentina
| | | | | | - Lilit Atanesyan
- MRC-Holland BV, Department of Oncogenetics, Amsterdam, The Netherlands
| | - Suvi Savola
- MRC-Holland BV, Department of Oncogenetics, Amsterdam, The Netherlands
| | - Maria Roqué
- Institute of Histology and Embryology, National Council of Research, Consejo Nacional de Investigaciones Científicas y Técnicas, Mendoza, Argentina.,Universidad Nacional de Cuyo, Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
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Coombs CC, Dickherber T, Crompton BD. Chasing ctDNA in Patients With Sarcoma. Am Soc Clin Oncol Educ Book 2020; 40:e351-e360. [PMID: 32598183 DOI: 10.1200/edbk_280749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Liquid biopsies are new technologies that allow cancer profiling of tumor fragments found in body fluids, such as peripheral blood, collected noninvasively from patients with malignancies. These assays are increasingly valuable in clinical oncology practice as prognostic biomarkers, as guides for therapy selection, for treatment monitoring, and for early detection of disease progression and relapse. However, application of these assays to rare cancers, such as pediatric and adult sarcomas, have lagged. In this article, we review the technical challenges of applying liquid biopsy technologies to sarcomas, provide an update on progress in the field, describe common pitfalls in interpreting liquid biopsy data, and discuss the intersection of sarcoma clinical care and commercial assays emerging on the horizon.
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Affiliation(s)
| | | | - Brian D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
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Chen CK, Liao J, Li MS, Khoo BL. Urine biopsy technologies: Cancer and beyond. Theranostics 2020; 10:7872-7888. [PMID: 32685026 PMCID: PMC7359094 DOI: 10.7150/thno.44634] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/02/2020] [Indexed: 12/18/2022] Open
Abstract
Since the discovery of circulating tumor cells in 1869, technological advances in the study of biomarkers from liquid biopsy have made it possible to diagnose disease in a less invasive way. Although blood-based liquid biopsy has been used extensively for the detection of solid tumors and immune diseases, the potential of urine-based liquid biopsy has not been fully explored. Advancements in technologies for the harvesting and analysis of biomarkers are providing new opportunities for the characterization of other disease types. Liquid biopsy markers such as exfoliated bladder cancer cells, cell-free DNA (cfDNA), and exosomes have the potential to change the nature of disease management and care, as they allow a cost-effective and convenient mode of patient monitoring throughout treatment. In this review, we addressed the advancement of research in the field of disease detection for the key liquid biopsy markers such as cancer cells, cfDNA, and exosomes, with an emphasis on urine-based liquid biopsy. First, we highlighted key technologies that were widely available and used extensively for clinical urine sample analysis. Next, we presented recent technological developments in cell and genetic research, with implications for the detection of other types of diseases, besides cancer. We then concluded with some discussions on these areas, emphasizing the role of microfluidics and artificial intelligence in advancing point-of-care applications. We believe that the benefits of urine biopsy provide diagnostic development potential, which will pave opportunities for new ways to guide treatment selections and facilitate precision disease therapies.
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Affiliation(s)
| | | | | | - Bee Luan Khoo
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
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Geng Z, Li S, Zhu L, Cheng Z, Jin M, Liu B, Guo Y, Liu P. “Sample-to-Answer” Detection of Rare ctDNA Mutation from 2 mL Plasma with a Fully Integrated DNA Extraction and Digital Droplet PCR Microdevice for Liquid Biopsy. Anal Chem 2020; 92:7240-7248. [DOI: 10.1021/acs.analchem.0c00818] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zhi Geng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shanglin Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lingxiang Zhu
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, China
| | - Zhen Cheng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Min Jin
- FengteBio Corporation, Beijing 100079, China
| | - Baoxia Liu
- TargetingOne Corporation, Beijing 100190, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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