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Chen M, Li J, Lin Y, Li X, Yu Y, Zhou S, Xu F, Zhang Q, Zhang H, Wang W. Recent research on material-based methods for isolation of extracellular vesicles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3179-3191. [PMID: 38738644 DOI: 10.1039/d4ay00370e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Extracellular vesicles (EVs) are nanoparticles secreted by cells with a closed phospholipid bilayer structure, which can participate in various physiological and pathological processes and have significant clinical value in disease diagnosis, targeted therapy and prognosis assessment. EV isolation methods currently include differential ultracentrifugation, ultrafiltration, size exclusion chromatography, immunoaffinity, polymer co-precipitation and microfluidics. In addition, material-based biochemical or biophysical approaches relying on intrinsic properties of the material or its surface-modified functionalized monomers, demonstrated unique advantages in the efficient isolation of EVs. In order to provide new ideas for the subsequent development of material-based EV isolation methods, this review will focus on the principle, research status and application prospects of material-based EV isolation methods based on different material carriers and functional monomers.
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Affiliation(s)
- Mengxi Chen
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
| | - Jiaxi Li
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
| | - Yujie Lin
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
| | - Xiaowei Li
- School of Pharmacy, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Yantai University, Yantai 264005, PR China
| | - Yuanyuan Yu
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
| | - Shenyue Zhou
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
| | - Fang Xu
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
| | - Qi Zhang
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
| | - Haiyang Zhang
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
| | - Weipeng Wang
- College of Pharmaceutical Sciences, Soochow University, Yunxuan Building #1339 and #2103, Wenjing Road, Suzhou Industrial Park, Suzhou 215123, China.
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2
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Bhadra M, Sachan M. An overview of challenges associated with exosomal miRNA isolation toward liquid biopsy-based ovarian cancer detection. Heliyon 2024; 10:e30328. [PMID: 38707279 PMCID: PMC11068823 DOI: 10.1016/j.heliyon.2024.e30328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024] Open
Abstract
As one of the deadliest gynaecological cancers, ovarian cancer has been on the list. With lesser-known symptoms and lack of an accurate detection method, it is still difficult to catch it early. In terms of both the diagnosis and outlook for cancer, liquid biopsy has come a long way with significant advancements. Exosomes, extracellular components commonly shed by cancerous cells, are nucleic acid-rich particles floating in almost all body fluids and hold enormous promise, leading to minimallyinvasive molecular diagnostics. They have been shown as potential biomarkers in liquid biopsy, being implicated in tumour growth and metastasis. In order to address the drawbacks of ovarian cancer tumor heterogeneity, a liquid biopsy-based approach is being investigated by detecting cell-free nucleic acids, particularly non-coding RNAs, having the advantage of being less invasive and more prominent in nature. microRNAs are known to actively contribute to cancer development and their existence inside exosomes has also been made quite apparent which can be leveraged to diagnose and treat the disease. Extraction of miRNAs and exosomes is an arduous execution, and while other approaches have been investigated, none have produced results that are as encouraging due to limits in time commitment, yield, and, most significantly, damage to the exosomal structure resulting discrepancies in miRNA-based expression profiling for disease diagnosis. We have briefly outlined and reviewed the difficulties with exosome isolation techniques and the need for their standardization. The several widely used procedures and their drawbacks in terms of the exosomal purity they may produce have also been outlined.
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Affiliation(s)
- Mridula Bhadra
- Department of Biotechnology, Motilal Nehru National Institute of Technology-Allahabad, Prayagraj, 211004, Uttar Pradesh, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology-Allahabad, Prayagraj, 211004, Uttar Pradesh, India
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Desai N, Katare P, Makwana V, Salave S, Vora LK, Giri J. Tumor-derived systems as novel biomedical tools-turning the enemy into an ally. Biomater Res 2023; 27:113. [PMID: 37946275 PMCID: PMC10633998 DOI: 10.1186/s40824-023-00445-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/11/2023] [Indexed: 11/12/2023] Open
Abstract
Cancer is a complex illness that presents significant challenges in its understanding and treatment. The classic definition, "a group of diseases characterized by the uncontrolled growth and spread of abnormal cells in the body," fails to convey the intricate interaction between the many entities involved in cancer. Recent advancements in the field of cancer research have shed light on the role played by individual cancer cells and the tumor microenvironment as a whole in tumor development and progression. This breakthrough enables the utilization of the tumor and its components as biological tools, opening new possibilities. This article delves deeply into the concept of "tumor-derived systems", an umbrella term for tools sourced from the tumor that aid in combatting it. It includes cancer cell membrane-coated nanoparticles (for tumor theranostics), extracellular vesicles (for tumor diagnosis/therapy), tumor cell lysates (for cancer vaccine development), and engineered cancer cells/organoids (for cancer research). This review seeks to offer a complete overview of the tumor-derived materials that are utilized in cancer research, as well as their current stages of development and implementation. It is aimed primarily at researchers working at the interface of cancer biology and biomedical engineering, and it provides vital insights into this fast-growing topic.
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Affiliation(s)
- Nimeet Desai
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Pratik Katare
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Vaishali Makwana
- Center for Interdisciplinary Programs, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Sagar Salave
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), Gujarat, India
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK.
| | - Jyotsnendu Giri
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, India.
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Hu M, Brown V, Jackson JM, Wijerathne H, Pathak H, Koestler DC, Nissen E, Hupert ML, Muller R, Godwin AK, Witek MA, Soper SA. Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles' mRNA. Anal Chem 2023; 95:7665-7675. [PMID: 37071799 PMCID: PMC10243595 DOI: 10.1021/acs.analchem.3c00624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Extracellular vesicles (EVs) carry RNA cargo that is believed to be associated with the cell-of-origin and thus have the potential to serve as a minimally invasive liquid biopsy marker for supplying molecular information to guide treatment decisions (i.e., precision medicine). We report the affinity isolation of EV subpopulations with monoclonal antibodies attached to the surface of a microfluidic chip that is made from a plastic to allow for high-scale production. The EV microfluidic affinity purification (EV-MAP) chip was used for the isolation of EVs sourced from two-orthogonal cell types and was demonstrated for its utility in a proof-of-concept application to provide molecular subtyping information for breast cancer patients. The orthogonal selection process better recapitulated the epithelial tumor microenvironment by isolating two subpopulations of EVs: EVEpCAM (epithelial cell adhesion molecule, epithelial origin) and EVFAPα (fibroblast activation protein α, mesenchymal origin). The EV-MAP provided recovery >80% with a specificity of 99 ± 1% based on exosomal mRNA (exo-mRNA) and real time-droplet digital polymerase chain reaction results. When selected from the plasma of healthy donors and breast cancer patients, EVs did not differ in size or total RNA mass for both markers. On average, 0.5 mL of plasma from breast cancer patients yielded ∼2.25 ng of total RNA for both EVEpCAM and EVFAPα, while in the case of cancer-free individuals, it yielded 0.8 and 1.25 ng of total RNA from EVEpCAM and EVFAPα, respectively. To assess the potential of these two EV subpopulations to provide molecular information for prognostication, we performed the PAM50 test (Prosigna) on exo-mRNA harvested from each EV subpopulation. Results suggested that EVEpCAM and EVFAPα exo-mRNA profiling using subsets of the PAM50 genes and a novel algorithm (i.e., exo-PAM50) generated 100% concordance with the tumor tissue.
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Affiliation(s)
- Mengjia Hu
- Department of Cancer Biology, The University of Kansas Medical Center, Cancer Center, Kansas City, Kansas 66160, United States
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Virginia Brown
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Joshua M Jackson
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harshani Wijerathne
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Devin C Koestler
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Department of Biostatistics & Data Science, The University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Emily Nissen
- Department of Biostatistics & Data Science, The University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | | | - Rolf Muller
- BioFluidica, Inc., San Diego, California 92121, United States
| | - Andrew K Godwin
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Malgorzata A Witek
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Steven A Soper
- Department of Cancer Biology, The University of Kansas Medical Center, Cancer Center, Kansas City, Kansas 66160, United States
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- BioFluidica, Inc., San Diego, California 92121, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66045, United States
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5
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Clack K, Soda N, Kasetsirikul S, Mahmudunnabi RG, Nguyen NT, Shiddiky MJA. Toward Personalized Nanomedicine: The Critical Evaluation of Micro and Nanodevices for Cancer Biomarker Analysis in Liquid Biopsy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205856. [PMID: 36631277 DOI: 10.1002/smll.202205856] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Liquid biopsy for the analysis of circulating cancer biomarkers (CBs) is a major advancement toward the early detection of cancer. In comparison to tissue biopsy techniques, liquid biopsy is relatively painless, offering multiple sampling opportunities across easily accessible bodily fluids such as blood, urine, and saliva. Liquid biopsy is also relatively inexpensive and simple, avoiding the requirement for specialized laboratory equipment or trained medical staff. Major advances in the field of liquid biopsy are attributed largely to developments in nanotechnology and microfabrication that enables the creation of highly precise chip-based platforms. These devices can overcome detection limitations of an individual biomarker by detecting multiple markers simultaneously on the same chip, or by featuring integrated and combined target separation techniques. In this review, the major advances in the field of portable and semi-portable micro, nano, and multiplexed platforms for CB detection for the early diagnosis of cancer are highlighted. A comparative discussion is also provided, noting merits and drawbacks of the platforms, especially in terms of portability. Finally, key challenges toward device portability and possible solutions, as well as discussing the future direction of the field are highlighted.
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Affiliation(s)
- Kimberley Clack
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Narshone Soda
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Surasak Kasetsirikul
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Rabbee G Mahmudunnabi
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
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6
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Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection. Int J Mol Sci 2023; 24:ijms24054881. [PMID: 36902312 PMCID: PMC10003255 DOI: 10.3390/ijms24054881] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Despite the diversity of liquid biopsy transcriptomic repertoire, numerous studies often exploit only a single RNA type signature for diagnostic biomarker potential. This frequently results in insufficient sensitivity and specificity necessary to reach diagnostic utility. Combinatorial biomarker approaches may offer a more reliable diagnosis. Here, we investigated the synergistic contributions of circRNA and mRNA signatures derived from blood platelets as biomarkers for lung cancer detection. We developed a comprehensive bioinformatics pipeline permitting an analysis of platelet-circRNA and mRNA derived from non-cancer individuals and lung cancer patients. An optimal selected signature is then used to generate the predictive classification model using machine learning algorithm. Using an individual signature of 21 circRNA and 28 mRNA, the predictive models reached an area under the curve (AUC) of 0.88 and 0.81, respectively. Importantly, combinatorial analysis including both types of RNAs resulted in an 8-target signature (6 mRNA and 2 circRNA), enhancing the differentiation of lung cancer from controls (AUC of 0.92). Additionally, we identified five biomarkers potentially specific for early-stage detection of lung cancer. Our proof-of-concept study presents the first multi-analyte-based approach for the analysis of platelets-derived biomarkers, providing a potential combinatorial diagnostic signature for lung cancer detection.
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7
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Ortega-Sanchez FG, Teresa V, Widmann T, Regiart M, Jerez-Salcedo MT, Fernández-Baldo MA, de Miguel-Perez D. Microfluidic systems in extracellular vesicles single analysis. A systematic review. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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8
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Williams S, Jalal AR, Lewis MP, Davies OG. A survey to evaluate parameters governing the selection and application of extracellular vesicle isolation methods. J Tissue Eng 2023; 14:20417314231155114. [PMID: 36911574 PMCID: PMC9996742 DOI: 10.1177/20417314231155114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/19/2023] [Indexed: 03/11/2023] Open
Abstract
Extracellular vesicles (EVs) continue to gain interest across the scientific community for diagnostic and therapeutic applications. As EV applications diversify, it is essential that researchers are aware of challenges, in particular the compatibility of EV isolation methods with downstream applications and their clinical translation. We report outcomes of the first cross-comparison study looking to determine parameters (EV source, starting volume, operator experience, application and implementation parameters such as cost and scalability) governing the selection of popular EV isolation methods across disciplines. Our findings highlighted an increased clinical focus, with 36% of respondents applying EVs in therapeutics and diagnostics. Data indicated preferential selection of ultracentrifugation for therapeutic applications, precipitation reagents in clinical settings and size exclusion chromatography for diagnostic applications utilising biofluids. Method selection was influenced by operator experience, with increased method diversity when EV research was not the respondents primary focus. Application and implementation criteria were indicated to be major influencers in method selection, with UC and SEC chosen for their abilities to process large and small volumes, respectively. Overall, we identified parameters influencing method selection across the breadth of EV science, providing a valuable overview of practical considerations for the effective translation of research outcomes.
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Affiliation(s)
- Soraya Williams
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Aveen R Jalal
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Mark P Lewis
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Owen G Davies
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
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9
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Advancement and obstacles in microfluidics-based isolation of extracellular vesicles. Anal Bioanal Chem 2023; 415:1265-1285. [PMID: 36284018 PMCID: PMC9928917 DOI: 10.1007/s00216-022-04362-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 11/01/2022]
Abstract
There is a great need for techniques which enable reproducible separation of extracellular vesicles (EVs) from biofluids with high recovery, purity and throughput. The development of new techniques for isolation of EVs from minute sample volumes is instrumental in enabling EV-based biomarker profiling in large biobank cohorts and paves the way to improved diagnostic profiles in precision medicine. Recent advances in microfluidics-based devices offer a toolbox for separating EVs from small sample volumes. Microfluidic devices that have been used in EV isolation utilise different fundamental principles and rely largely on benefits of scaling laws as the biofluid processing is miniaturised to chip level. Here, we review the progress in the practicality and performance of both passive devices (such as mechanical filtering and hydrodynamic focusing) and active devices (using magnetic, electric or acoustic fields). As it stands, many microfluidic devices isolate intact EV populations at higher purities than centrifugation, precipitation or size-exclusion chromatography. However, this comes at a cost. We address challenges (in particular low throughput, clogging risks and ability to process biofluids) and highlight the need for more improvements in microfluidic devices. Finally, we conclude that there is a need to refine and standardise these lab-on-a-chip techniques to meet the growing interest in the diagnostic and therapeutic value of purified EVs.
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10
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Huang C, Jiang Y, Li Y, Zhang H. Droplet Detection and Sorting System in Microfluidics: A Review. MICROMACHINES 2022; 14:mi14010103. [PMID: 36677164 PMCID: PMC9867185 DOI: 10.3390/mi14010103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 05/26/2023]
Abstract
Since being invented, droplet microfluidic technologies have been proven to be perfect tools for high-throughput chemical and biological functional screening applications, and they have been heavily studied and improved through the past two decades. Each droplet can be used as one single bioreactor to compartmentalize a big material or biological population, so millions of droplets can be individually screened based on demand, while the sorting function could extract the droplets of interest to a separate pool from the main droplet library. In this paper, we reviewed droplet detection and active sorting methods that are currently still being widely used for high-through screening applications in microfluidic systems, including the latest updates regarding each technology. We analyze and summarize the merits and drawbacks of each presented technology and conclude, with our perspectives, on future direction of development.
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Affiliation(s)
- Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Yuqian Jiang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuwen Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Han Zhang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
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11
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Meggiolaro A, Moccia V, Brun P, Pierno M, Mistura G, Zappulli V, Ferraro D. Microfluidic Strategies for Extracellular Vesicle Isolation: Towards Clinical Applications. BIOSENSORS 2022; 13:bios13010050. [PMID: 36671885 PMCID: PMC9855931 DOI: 10.3390/bios13010050] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 05/15/2023]
Abstract
Extracellular vesicles (EVs) are double-layered lipid membrane vesicles released by cells. Currently, EVs are attracting a lot of attention in the biological and medical fields due to their role as natural carriers of proteins, lipids, and nucleic acids. Thus, they can transport useful genomic information from their parental cell through body fluids, promoting cell-to-cell communication even between different organs. Due to their functionality as cargo carriers and their protein expression, they can play an important role as possible diagnostic and prognostic biomarkers in various types of diseases, e.g., cancers, neurodegenerative, and autoimmune diseases. Today, given the invaluable importance of EVs, there are some pivotal challenges to overcome in terms of their isolation. Conventional methods have some limitations: they are influenced by the starting sample, might present low throughput and low purity, and sometimes a lack of reproducibility, being operator dependent. During the past few years, several microfluidic approaches have been proposed to address these issues. In this review, we summarize the most important microfluidic-based devices for EV isolation, highlighting their advantages and disadvantages compared to existing technology, as well as the current state of the art from the perspective of the use of these devices in clinical applications.
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Affiliation(s)
- Alessio Meggiolaro
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Valentina Moccia
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Matteo Pierno
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Giampaolo Mistura
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Valentina Zappulli
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy
| | - Davide Ferraro
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
- Correspondence:
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12
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Singh S, Podder PS, Russo M, Henry C, Cinti S. Tailored point-of-care biosensors for liquid biopsy in the field of oncology. LAB ON A CHIP 2022; 23:44-61. [PMID: 36321747 DOI: 10.1039/d2lc00666a] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the field of cancer detection, technologies to analyze tumors using biomarkers circulating in fluids such as blood have developed rapidly based on liquid biopsy. A proactive approach to early cancer detection can lead to more effective treatments with minimal side effects and better long-term patient survival. However, early detection of cancer is hindered by the existing limitations of conventional cancer diagnostic methods. To enable early diagnosis and regular monitoring and improve automation, the development of integrated point-of-care (POC) and biosensors is needed. This is expected to fundamentally change the diagnosis, management, and monitoring of response to treatment of cancer. POC-based techniques will provide a way to avoid complications that occur after invasive tissue biopsy, such as bleeding, infection, and pain. The aim of this study is to provide a comprehensive view of biosensors and their clinical relevance in oncology for the detection of biomarkers with liquid biopsies of proteins, miRNA, ctDNA, exosomes, and cancer cells. The preceding discussion also illustrates the changing landscape of liquid biopsy-based cancer diagnosis through nanomaterials, machine learning, artificial intelligence, wearable devices, and sensors, many of which apply POC design principles. With the advent of sensitive, selective, and timely detection of cancer, we see the field of POC technology for cancer detection and treatment undergoing a positive paradigm shift in the foreseeable future.
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Affiliation(s)
- Sima Singh
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
| | - Pritam Saha Podder
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Matt Russo
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Charles Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
- BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, 80055 Naples, Italy
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13
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Pedraz-Valdunciel C, Giannoukakos S, Giménez-Capitán A, Fortunato D, Filipska M, Bertran-Alamillo J, Bracht JWP, Drozdowskyj A, Valarezo J, Zarovni N, Fernández-Hilario A, Hackenberg M, Aguilar-Hernández A, Molina-Vila MÁ, Rosell R. Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer. Pharmaceutics 2022; 14:2034. [PMID: 36297470 PMCID: PMC9610636 DOI: 10.3390/pharmaceutics14102034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The analysis of liquid biopsies brings new opportunities in the precision oncology field. Under this context, extracellular vesicle circular RNAs (EV-circRNAs) have gained interest as biomarkers for lung cancer (LC) detection. However, standardized and robust protocols need to be developed to boost their potential in the clinical setting. Although nCounter has been used for the analysis of other liquid biopsy substrates and biomarkers, it has never been employed for EV-circRNA analysis of LC patients. METHODS EVs were isolated from early-stage LC patients (n = 36) and controls (n = 30). Different volumes of plasma, together with different number of pre-amplification cycles, were tested to reach the best nCounter outcome. Differential expression analysis of circRNAs was performed, along with the testing of different machine learning (ML) methods for the development of a prognostic signature for LC. RESULTS A combination of 500 μL of plasma input with 10 cycles of pre-amplification was selected for the rest of the study. Eight circRNAs were found upregulated in LC. Further ML analysis selected a 10-circRNA signature able to discriminate LC from controls with AUC ROC of 0.86. CONCLUSIONS This study validates the use of the nCounter platform for multiplexed EV-circRNA expression studies in LC patient samples, allowing the development of prognostic signatures.
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Affiliation(s)
- Carlos Pedraz-Valdunciel
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Department of Biochemistry, Molecular Biology and Biomedicine, Autonomous University of Barcelona, Campus de Bellaterra, 08193 Barcelona, Spain
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | - Stavros Giannoukakos
- Department of Genetics, Facultad de Ciencias, Campus Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
| | - Ana Giménez-Capitán
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | | | - Martyna Filipska
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- B Cell Biology Group, Hospital del Mar Biomedical Research Park (IMIM), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
| | - Jordi Bertran-Alamillo
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | - Jillian W. P. Bracht
- Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Amsterdam UMC location University of Amsterdam, 1105AZ Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, 1105AZ Amsterdam, The Netherlands
| | - Ana Drozdowskyj
- Oncology Institute Dr. Rosell (IOR), Dexeus University Institute, 08028 Barcelona, Spain
| | - Joselyn Valarezo
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | | | - Alberto Fernández-Hilario
- Department of Computer Science and Artificial Intelligence, DaSCI., University of Granada, 18071 Granada, Spain
| | - Michael Hackenberg
- Department of Genetics, Facultad de Ciencias, Campus Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
| | | | | | - Rafael Rosell
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Oncology Institute Dr. Rosell (IOR), Dexeus University Institute, 08028 Barcelona, Spain
- Catalan Institute of Oncology, Campus Can Ruti, 08916 Badalona, Spain
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14
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Sánchez-Herrero E, Serna-Blasco R, Robado de Lope L, González-Rumayor V, Romero A, Provencio M. Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis. Front Oncol 2022; 12:943253. [PMID: 35936733 PMCID: PMC9350013 DOI: 10.3389/fonc.2022.943253] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer cells release nucleic acids, freely or associated with other structures such as vesicles into body fluids, including blood. Among these nucleic acids, circulating tumor DNA (ctDNA) has emerged as a minimally invasive biomarker for tumor molecular profiling. However, certain biological characteristics of ctDNA are still unknown. Here, we provide an overview of the current knowledge about ctDNA biological features, including size and structure as well as the mechanisms of ctDNA shedding and clearance, and the physio-pathological factors that determine ctDNA levels. A better understanding of ctDNA biology is essential for the development of new methods that enable the analysis of ctDNA.
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Affiliation(s)
- Estela Sánchez-Herrero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- +D Department, Atrys Health, Barcelona, Spain
| | - Roberto Serna-Blasco
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | - Lucia Robado de Lope
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | | | - Atocha Romero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
- *Correspondence: Atocha Romero, ; orcid.org/0000-0002-1634-7397
| | - Mariano Provencio
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
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15
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Ferguson S, Yang KS, Weissleder R. Single extracellular vesicle analysis for early cancer detection. Trends Mol Med 2022; 28:681-692. [DOI: 10.1016/j.molmed.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022]
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16
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Ghanam J, Chetty VK, Barthel L, Reinhardt D, Hoyer PF, Thakur BK. DNA in extracellular vesicles: from evolution to its current application in health and disease. Cell Biosci 2022; 12:37. [PMID: 35346363 PMCID: PMC8961894 DOI: 10.1186/s13578-022-00771-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/07/2022] [Indexed: 02/08/2023] Open
Abstract
Extracellular vesicle (EV) secretion is a highly conserved evolutionary trait in all organisms in the three domains of life. The packaging and release of EVs appears to be a bulk-flow process which takes place mainly under extreme conditions. EVs participate in horizontal gene transfer, which supports the survival of prokaryotic and eukaryotic microbes. In higher eukaryotes, almost all cells secrete a heterogeneous population of EVs loaded with various biomolecules. EV secretion is typically higher in cancer microenvironments, promoting tumor progression and metastasis. EVs are now recognized as additional mediators of autocrine and paracrine communication in health and disease. In this context, proteins and RNAs have been studied the most, but extracellular vesicle DNA (EV-DNA) has started to gain in importance in the last few years. In this review, we summarize new findings related to the loading mechanism(s), localization, and post-shedding function of EV-DNA. We also discuss the feasibility of using EV-DNA as a biomarker when performing a liquid biopsy, at the same time emphasizing the lack of data from clinical trials in this regard. Finally, we outline the potential of EV-DNA uptake and its interaction with the host genome as a promising tool for understanding the mechanisms of cancer evolution. Protecting DNA in membrane vesicles seems to be a conserved phenomenon for the horizontal genetic flux between prokaryotes and lower eukaryotes. Capturing and analyzing this vesicular DNA enables quick and non-invasive monitoring of natural ecosystems. Cancer-derived extracellular vesicles containing DNA open up novel directions in cell-to-cell communication and therefore disease monitoring. Complex and fluctuating conditions of the tumor microenvironment, mimicking natural ecosystems, could favor EV-DNA release, mediating tumor multi-clonal evolution and providing survival benefits.
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Affiliation(s)
- Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Venkatesh Kumar Chetty
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Lennart Barthel
- Department of Neurosurgery and Spine Surgery, Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany.,Institute of Medical Psychology and Behavioral Immunobiology, Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Peter-Friedrich Hoyer
- Department of Pediatrics II, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany.
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17
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Teixeira A, Carneiro A, Piairo P, Xavier M, Ainla A, Lopes C, Sousa-Silva M, Dias A, Martins AS, Rodrigues C, Pereira R, Pires LR, Abalde-Cela S, Diéguez L. Advances in Microfluidics for the Implementation of Liquid Biopsy in Clinical Routine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1379:553-590. [DOI: 10.1007/978-3-031-04039-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Aleotti V, Catoni C, Poggiana C, Rosato A, Facchinetti A, Scaini MC. Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy. Cancers (Basel) 2021; 13:6217. [PMID: 34944843 PMCID: PMC8699653 DOI: 10.3390/cancers13246217] [Citation(s) in RCA: 9] [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: 11/15/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 01/19/2023] Open
Abstract
Malignant melanoma is the most serious, life-threatening form of all dermatologic diseases, with a poor prognosis in the presence of metastases and advanced disease. Despite recent advances in targeted therapy and immunotherapy, there is still a critical need for a better understanding of the fundamental mechanisms behind melanoma progression and resistance onset. Recent advances in genome-wide methylation methods have revealed that aberrant changes in the pattern of DNA methylation play an important role in many aspects of cancer progression, including cell proliferation and migration, evasion of cell death, invasion, and metastasization. The purpose of the current review was to gather evidence regarding the usefulness of DNA methylation tracking in liquid biopsy as a potential biomarker in melanoma. We investigated the key genes and signal transduction pathways that have been found to be altered epigenetically in melanoma. We then highlighted the circulating tumor components present in blood, including circulating melanoma cells (CMC), circulating tumor DNA (ctDNA), and tumor-derived extracellular vesicles (EVs), as a valuable source for identifying relevant aberrations in DNA methylation. Finally, we focused on DNA methylation signatures as a marker for tracking response to therapy and resistance, thus facilitating personalized medicine and decision-making in the treatment of melanoma patients.
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Affiliation(s)
- Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
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19
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Hur JY, Lee KY. Characteristics and Clinical Application of Extracellular Vesicle-Derived DNA. Cancers (Basel) 2021; 13:3827. [PMID: 34359729 PMCID: PMC8345206 DOI: 10.3390/cancers13153827] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.
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Affiliation(s)
- Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pathology, Konkuk University Medical Center, Seoul 05030, Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul 05030, Korea
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20
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Malhotra S, Amin ZM, Dobhal G, Cottam S, Nann T, Goreham RV. Novel devices for isolation and detection of bacterial and mammalian extracellular vesicles. Mikrochim Acta 2021; 188:139. [PMID: 33772384 DOI: 10.1007/s00604-021-04790-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/15/2021] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles are spherical nanoparticles inherently released by almost all cell types. They acquire the cell's membrane and cytoplasmic characteristics offering abundant identical units that can be captured to recognize the cell of origin. The abundance of vital cell information and multifunctional roles in cellular processes has rendered them attention, particularly as promising biomarkers for disease diagnosis and use in potential drug delivery systems. This review provides insights into standard approaches towards cultivation and isolation of mammalian and bacterial extracellular vesicles. We assess gaps in conventional separation and detection technologies while also tracking developments in ongoing research. The review focuses on highlighting alternative state-of-the-art microfluidic devices that offer avenues for fast, cost-effective, precision-oriented capture and sensing of extracellular vesicles. Combining different detection technologies on an integrated "lab-on-a-chip" system has the prospective to provide customizable opportunities for clinical use of extracellular vesicles in disease diagnostics and therapeutic applications.
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Affiliation(s)
- Shiana Malhotra
- School of Mathematical and Physical Sciences, University of Newcastle, Callaghan, 2308, Australia
| | - Zarinah M Amin
- School of Mathematical and Physical Sciences, University of Newcastle, Callaghan, 2308, Australia
| | - Garima Dobhal
- School of Mathematical and Physical Sciences, University of Newcastle, Callaghan, 2308, Australia
| | - Sophie Cottam
- School of Mathematical and Physical Sciences, University of Newcastle, Callaghan, 2308, Australia
| | - Thomas Nann
- School of Mathematical and Physical Sciences, University of Newcastle, Callaghan, 2308, Australia
| | - Renee V Goreham
- School of Mathematical and Physical Sciences, University of Newcastle, Callaghan, 2308, Australia.
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21
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Bracht JWP, Gimenez-Capitan A, Huang CY, Potie N, Pedraz-Valdunciel C, Warren S, Rosell R, Molina-Vila MA. Analysis of extracellular vesicle mRNA derived from plasma using the nCounter platform. Sci Rep 2021; 11:3712. [PMID: 33580122 PMCID: PMC7881020 DOI: 10.1038/s41598-021-83132-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/29/2021] [Indexed: 12/24/2022] Open
Abstract
Extracellular vesicles (EVs) are double-layered phospholipid membrane vesicles that are released by most cells and can mediate intercellular communication through their RNA cargo. In this study, we tested if the NanoString nCounter platform can be used for the analysis of EV-mRNA. We developed and optimized a methodology for EV enrichment, EV-RNA extraction and nCounter analysis. Then, we demonstrated the validity of our workflow by analyzing EV-RNA profiles from the plasma of 19 cancer patients and 10 controls and developing a gene signature to differentiate cancer versus control samples. TRI reagent outperformed automated RNA extraction and, although lower plasma input is feasible, 500 μL provided highest total counts and number of transcripts detected. A 10-cycle pre-amplification followed by DNase treatment yielded reproducible mRNA target detection. However, appropriate probe design to prevent genomic DNA binding is preferred. A gene signature, created using a bioinformatic algorithm, was able to distinguish between control and cancer EV-mRNA profiles with an area under the ROC curve of 0.99. Hence, the nCounter platform can be used to detect mRNA targets and develop gene signatures from plasma-derived EVs.
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Affiliation(s)
- Jillian W P Bracht
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Sabino Arana 5-19, 08028, Barcelona, Spain.
- Department of Biochemistry, Molecular Biology and Biomedicine, Universitat Autónoma de Barcelona (UAB), 08193, Cerdanyola, Spain.
| | - Ana Gimenez-Capitan
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Sabino Arana 5-19, 08028, Barcelona, Spain
| | | | - Nicolas Potie
- Department of Genetics, Faculty of Science, University of Granada, 18071, Granada, Spain
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigacion Biomedica, PTS, Avda. del Conocimiento s/n, 18100, Granada, Spain
| | - Carlos Pedraz-Valdunciel
- Department of Biochemistry, Molecular Biology and Biomedicine, Universitat Autónoma de Barcelona (UAB), 08193, Cerdanyola, Spain
- Germans Trias i Pujol Health Sciences Institute and Hospital (IGTP), Badalona, Barcelona, Spain
| | | | - Rafael Rosell
- Germans Trias i Pujol Health Sciences Institute and Hospital (IGTP), Badalona, Barcelona, Spain
| | - Miguel A Molina-Vila
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Sabino Arana 5-19, 08028, Barcelona, Spain.
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22
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Amintas S, Vendrely V, Dupin C, Buscail L, Laurent C, Bournet B, Merlio JP, Bedel A, Moreau-Gaudry F, Boutin J, Dabernat S, Buscail E. Next-Generation Cancer Biomarkers: Extracellular Vesicle DNA as a Circulating Surrogate of Tumor DNA. Front Cell Dev Biol 2021; 8:622048. [PMID: 33604335 PMCID: PMC7884755 DOI: 10.3389/fcell.2020.622048] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) are produced by healthy tissues and tumor cells and are released in various bodily fluids, including blood. They are limited by bilayer phospholipidic membranes, and they carry a rich content in biomolecules. Their release cleanses the cells of their waste or serves as functional local and distant cell-cell communication and molecular exchange particles. This rich and heterogeneous content has been given intense attention in cancer physiopathology because EVs support cancer control and progression. Because of their specific active cargo, they are being evaluated as carriers of liquid biopsy biomarkers. Compared to soluble circulating biomarkers, their complexity might provide rich information on tumor and metastases status. Thanks to the acquired genomic changes commonly observed in oncogenic processes, double-stranded DNA (dsDNA) in EVs might be the latest most promising biomarker of tumor presence and complexity. This review will focus on the recent knowledge on the DNA inclusion in vesicles, the technical aspects of EV-DNA detection and quantification, and the use of EV-DNA as a clinical biomarker.
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Affiliation(s)
- Samuel Amintas
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- U1035 Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
| | - Véronique Vendrely
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- U1035 Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
| | - Charles Dupin
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- U1035 Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
| | - Louis Buscail
- Centre Hospitalier Universitaire (CHU) de Toulouse, Toulouse, France
- INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France
| | - Christophe Laurent
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- U1035 Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
| | - Barbara Bournet
- Centre Hospitalier Universitaire (CHU) de Toulouse, Toulouse, France
| | - Jean-Philippe Merlio
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
- INSERM U1053, Bordeaux, France
| | - Aurélie Bedel
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- U1035 Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
| | - François Moreau-Gaudry
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- U1035 Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
| | - Julian Boutin
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- U1035 Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
| | - Sandrine Dabernat
- Département des Sciences Biologiques et Médicales, Université de Bordeaux, Bordeaux, France
- U1035 Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux, France
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Bordeaux, France
| | - Etienne Buscail
- Centre Hospitalier Universitaire (CHU) de Toulouse, Toulouse, France
- INSERM, UMR-1220, IRSD, University of Toulouse III, Toulouse, France
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23
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Zhang B, Zhao M, Lu Q. Extracellular Vesicles in Rheumatoid Arthritis and Systemic Lupus Erythematosus: Functions and Applications. Front Immunol 2021; 11:575712. [PMID: 33519800 PMCID: PMC7841259 DOI: 10.3389/fimmu.2020.575712] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022] Open
Abstract
In the last two decades, extracellular vesicles (EVs) have aroused wide interest among researchers in basic and clinical research. EVs, small membrane vesicles are released by almost all kinds of cells into the extracellular environment. According to many recent studies, EVs participate in immunomodulation and play an important role in the pathogenesis of autoimmune diseases. In addition, EVs have great potential in the diagnosis and therapy of autoimmune diseases. Here, we reviewed the latest research advances on the functions and mechanisms of EVs and their roles in the pathogenesis, diagnosis, and treatment of rheumatoid arthritis and systemic lupus erythematosus.
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Affiliation(s)
- Bo Zhang
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China.,Clinical Immunology Research Center, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences (2019RU027), Changsha, China
| | - Ming Zhao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China.,Clinical Immunology Research Center, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences (2019RU027), Changsha, China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China.,Clinical Immunology Research Center, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences (2019RU027), Changsha, China
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24
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Recent Advances in Extracellular Vesicles as Drug Delivery Systems and Their Potential in Precision Medicine. Pharmaceutics 2020; 12:pharmaceutics12111006. [PMID: 33105857 PMCID: PMC7690579 DOI: 10.3390/pharmaceutics12111006] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are membrane-bilayered nanoparticles released by most cell types. Recently, an enormous number of studies have been published on the potential of EVs as carriers of therapeutic agents. In contrast to systems such as liposomes, EVs exhibit less immunogenicity and higher engineering potential. Here, we review the most relevant publications addressing the potential and use of EVs as a drug delivery system (DDS). The information is divided based on the key steps for designing an EV-mediated delivery strategy. We discuss possible sources and isolation methods of EVs. We address the administration routes that have been tested in vivo and the tissue distribution observed. We describe the current knowledge on EV clearance, a significant challenge towards enhancing bioavailability. Also, EV-engineering approaches are described as alternatives to improve tissue and cell-specificity. Finally, a summary of the ongoing clinical trials is performed. Although the application of EVs in the clinical practice is still at an early stage, a high number of studies in animals support their potential as DDS. Thus, better treatment options could be designed to precisely increase target specificity and therapeutic efficacy while reducing off-target effects and toxicity according to the individual requirements of each patient.
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Malkin EZ, Bratman SV. Bioactive DNA from extracellular vesicles and particles. Cell Death Dis 2020; 11:584. [PMID: 32719324 PMCID: PMC7385258 DOI: 10.1038/s41419-020-02803-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) and particles (EPs) have recently emerged as active carriers of molecular biomarkers and mediators of intercellular communication. While most investigations have focused exclusively on the protein, lipid and RNA constituents of these extracellular entities, EV/EP DNA remains poorly understood, despite DNA being found in association with virtually all EV/EP populations. The functional potential of EV/EP DNA has been proposed in a number of pathological states, including malignancies and autoimmune diseases. Moreover, the effectiveness of cell-free DNA as the biomarker of choice in emerging liquid biopsy applications highlights the role that EV/EP DNA may play as a novel disease biomarker. In this review, we provide a comprehensive overview of EV/EP DNA studies conducted to date, with a particular focus on the roles of EV/EP DNA as a functional mediator and molecular biomarker in various pathologic states. We also review what is currently known about the origins, structure, localisation and distribution of EV/EP DNA, highlighting current controversies as well as opportunities for future investigation.
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Affiliation(s)
- Ethan Z Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, Toronto, ON, Canada.
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MicroRNAs from Liquid Biopsy Derived Extracellular Vesicles: Recent Advances in Detection and Characterization Methods. Cancers (Basel) 2020; 12:cancers12082009. [PMID: 32707943 PMCID: PMC7465219 DOI: 10.3390/cancers12082009] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Liquid biopsies have become a convenient tool in cancer diagnostics, real-time disease monitoring, and evaluation of residual disease. Yet, the information still encrypted in the variety of tumor-derived molecules identified in biofluids has proven difficult to decipher due to the technological limitations imposed by their biological nature. Such is the case of extracellular vesicle (EV) encapsulated ncRNAs, which have gained traction in recent years as biomarkers. Due to their resilience towards degrading factors they may act as suitable disease indicators. This review addresses the less described issues in this context. We present an overview of less investigated biofluids that can be used for EV isolation in addition to different isolation approaches to overcome the technical challenges these specimens harbor. Furthermore, we summarize the latest technological advances providing improvement to ncRNA detection and analysis. Thereby, this review summarizes the current state-of-the-art methodologies regarding EV and EV derived miRNA analysis and how they compare to current approaches.
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