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Lee KCM, Chung BMF, Siu DMD, Ho SCK, Ng DKH, Tsia KK. Dispersion-free inertial focusing (DIF) for high-yield polydisperse micro-particle filtration and analysis. LAB ON A CHIP 2024; 24:4182-4197. [PMID: 39101363 DOI: 10.1039/d4lc00275j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Inertial focusing excels at the precise spatial ordering and separation of microparticles by size within fluid flows. However, this advantage, resulting from its inherent size-dependent dispersion, could turn into a drawback that challenges applications requiring consistent and uniform positioning of polydisperse particles, such as microfiltration and flow cytometry. To overcome this fundamental challenge, we introduce Dispersion-Free Inertial Focusing (DIF). This new method minimizes particle size-dependent dispersion while maintaining the high throughput and precision of standard inertial focusing, even in a highly polydisperse scenario. We demonstrate a rule-of-thumb principle to reinvent an inertial focusing system and achieve an efficient focusing of particles ranging from 6 to 30 μm in diameter onto a single plane with less than 3 μm variance and over 95% focusing efficiency at highly scalable throughput (2.4-30 mL h-1) - a stark contrast to existing technologies that struggle with polydispersity. We demonstrated that DIF could be applied in a broad range of applications, particularly enabling high-yield continuous microparticle filtration and large-scale high-resolution single-cell morphological analysis of heterogeneous cell populations. This new technique is also readily compatible with the existing inertial microfluidic design and thus could unleash more diverse systems and applications.
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Affiliation(s)
- Kelvin C M Lee
- The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Bob M F Chung
- The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Dickson M D Siu
- The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Sam C K Ho
- The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong.
| | - Daniel K H Ng
- The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong.
| | - Kevin K Tsia
- The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
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2
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Shaker F, Razi S, Rezaei N. Circulating miRNA and circulating tumor DNA application as liquid biopsy markers in gastric cancer. Clin Biochem 2024; 129:110767. [PMID: 38705444 DOI: 10.1016/j.clinbiochem.2024.110767] [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: 02/05/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Liquid biopsy has been investigated as a novel method to overcome the numerous challenges in gastric cancer (GC) management. This non-invasive, feasible, and easy-to-repeat method has been shown to be cost-effective and capable of increasing diagnostic sensitivity and prognostic assessment. Additionally, it is potentially accurate to aid decision-making and personalized treatment planning. MicroRNA (miRNA) and circulating tumor DNA (ctDNA) markers can enhance GC management in various aspects, including diagnosis (mainly earlier diagnosis and the ability to perform population-based screening), prognosis (more precise stratification of prognosis), and treatment (including more accurate prediction of treatment response and earlier detection of resistance to the treatment). Concerning the treatment-related application, miRNAs' mimics and antagonists (by using two main strategies of restoring tumor suppressor miRNAs and inhibiting oncogene miRNAs) have been shown to be effective therapeutic agents. However, these need to be further validated in clinical trials. Furthermore, novel delivery systems, such as lipid-based vectors, polymeric-based vectors, and exosome-based delivery, have been developed to enhance the performance of these agents. Moreover, this paper explores the current detection and measuring methods for these markers. These approaches are categorized into direct methods (e.g., Chem-NAT, HTG EdgeSeq, and Multiplex Circulating Fireplex) and indirect methods (e.g., Reverse transcription-quantitative polymerase chain reaction (RT-qPCR), qPCR, microarray, and NGS) for miRNA detection. For ctDNA measurement, main core technologies like NGS, digital PCR, real-time PCR, and mass spectrometry are suggested.
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Affiliation(s)
- Farhad Shaker
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Sepideh Razi
- Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden.
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3
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Zole E, Sathyanarayanan G, Regenberg B, Kutter JP. Microfluidic isolation of extrachromosomal circular DNA through selective digestion of plasmids and linear DNA using immobilized nucleases. LAB ON A CHIP 2024; 24:3101-3111. [PMID: 38752699 DOI: 10.1039/d3lc01028g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Extrachromosomal circular DNA (eccDNA) refers to small circular DNA molecules that are distinct from chromosomal DNA and play diverse roles in various biological processes. They are also explored as potential biomarkers for disease diagnosis and precision medicine. However, isolating eccDNA from tissues and plasma is challenging due to low abundance and the presence of interfering linear DNA, requiring time-consuming processes and expert handling. Our study addresses this by utilizing a microfluidic chip tailored for eccDNA isolation, leveraging microfluidic principles for enzymatic removal of non-circular DNA. Our approach involves integrating restriction enzymes into the microfluidic chip, enabling selective digestion of mitochondrial and linear DNA fragments while preserving eccDNA integrity. This integration is facilitated by an in situ photo-polymerized emulsion inside microchannels, creating a porous monolithic structure suitable for immobilizing restriction and exonuclease enzymes (restriction enzyme MssI and exonuclease ExoV). Evaluation using control DNA mixtures and plasma samples with artificially introduced eccDNA demonstrated that our microfluidic chips reduce linear DNA by over 99%, performing comparable to conventional off-chip methods but with substantially faster digestion times, allowing for a remarkable 76-fold acceleration in overall sample preparation time. This technological advancement holds great promise for enhancing the isolation and analysis of eccDNA from tissue and plasma and the potential for increasing the speed of other molecular methods with multiple enzymatic steps.
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Affiliation(s)
- Egija Zole
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Birgitte Regenberg
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jörg P Kutter
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark.
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4
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Dong Y, Chen B, Cai G, Xu F, Li L, Cheng X, Shi X, Peng B, Mi S. Integrated nucleic acid purification technology based on amino-modified centrifugal microfluidic chip. Biotechnol J 2024; 19:e2300113. [PMID: 38050772 DOI: 10.1002/biot.202300113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Nucleic acid detection is an important tool for clinical diagnosis. The purification of the sample is the most time-consuming step in the nucleic acid testing process and will affect the results of the assay. Here, we developed a surface modification-based nucleic acid purification method and designed an accompanying set of centrifugation equipment and chips to integrate the steps of nucleic acid purification on a single platform. The results of experiments with HeLa cells and HPV type 16 as samples showed that the mentioned method had good nucleic acid purification capability and the accompanying equipment greatly simplified the operation of the experimenters in the whole process. Overall, our equipment can improve the efficiency of nucleic acid purification and is suitable for application in larger-scale clinical assays.
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Affiliation(s)
- Yongkang Dong
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Bailiang Chen
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Gangpei Cai
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Fei Xu
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Linzhi Li
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaoqi Cheng
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaolu Shi
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Bo Peng
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Shengli Mi
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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5
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Haghjooy Javanmard S, Rafiee L, Bahri Najafi M, Khorsandi D, Hasan A, Vaseghi G, Makvandi P. Microfluidic-based technologies in cancer liquid biopsy: Unveiling the role of horizontal gene transfer (HGT) materials. ENVIRONMENTAL RESEARCH 2023; 238:117083. [PMID: 37690629 DOI: 10.1016/j.envres.2023.117083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
Liquid biopsy includes the isolating and analysis of non-solid biological samples enables us to find new ways for molecular profiling, prognostic assessment, and better therapeutic decision-making in cancer patients. Despite the conventional theory of tumor development, a non-vertical transmission of DNA has been reported among cancer cells and between cancer and normal cells. The phenomenon referred to as horizontal gene transfer (HGT) has the ability to amplify the advancement of tumors by disseminating genes that encode molecules conferring benefits to the survival or metastasis of cancer cells. Currently, common liquid biopsy approaches include the analysis of extracellular vesicles (EVs) and tumor-free DNA (tfDNA) derived from primary tumors and their metastatic sites, which are well-known HGT mediators in cancer cells. Current technological and molecular advances expedited the high-throughput and high-sensitive HGT materials analyses by using new technologies, such as microfluidics in liquid biopsies. This review delves into the convergence of microfluidic-based technologies and the investigation of Horizontal Gene Transfer (HGT) materials in cancer liquid biopsy. The integration of microfluidics offers unprecedented advantages such as high sensitivity, rapid analysis, and the ability to analyze rare cell populations. These attributes are instrumental in detecting and characterizing CTCs, circulating nucleic acids, and EVs, which are carriers of genetic cargo that could potentially undergo HGT. The phenomenon of HGT in cancer has raised intriguing questions about its role in driving genomic diversity and acquired drug resistance. By leveraging microfluidic platforms, researchers have been able to capture and analyze individual cells or genetic material with enhanced precision, shedding light on the potential transfer of genetic material between cancer cells and surrounding stromal cells. Furthermore, the application of microfluidics in single-cell sequencing has enabled the elucidation of the genetic changes associated with HGT events, providing insights into the evolution of tumor genomes. This review also discusses the challenges and opportunities in studying HGT materials using microfluidic-based technologies. In conclusion, microfluidic-based technologies have significantly advanced the field of cancer liquid biopsy, enabling the sensitive and accurate detection of HGT materials. As the understanding of HGT's role in tumor evolution and therapy resistance continues to evolve, the synergistic integration of microfluidics and HGT research promises to provide valuable insights into cancer biology, with potential implications for precision oncology and therapeutic strategies.
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Affiliation(s)
- Shaghayegh Haghjooy Javanmard
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Laleh Rafiee
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majed Bahri Najafi
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Danial Khorsandi
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA, 90024, United States
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center, Qatar University, Doha 2713, Qatar.
| | - Golnaz Vaseghi
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China.
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Islam MS, Gopalan V, Lam AK, Shiddiky MJA. Current advances in detecting genetic and epigenetic biomarkers of colorectal cancer. Biosens Bioelectron 2023; 239:115611. [PMID: 37619478 DOI: 10.1016/j.bios.2023.115611] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Colorectal carcinoma (CRC) is the third most common cancer in terms of diagnosis and the second in terms of mortality. Recent studies have shown that various proteins, extracellular vesicles (i.e., exosomes), specific genetic variants, gene transcripts, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and altered epigenetic patterns, can be used to detect, and assess the prognosis of CRC. Over the last decade, a plethora of conventional methodologies (e.g., polymerase chain reaction [PCR], direct sequencing, enzyme-linked immunosorbent assay [ELISA], microarray, in situ hybridization) as well as advanced analytical methodologies (e.g., microfluidics, electrochemical biosensors, surface-enhanced Raman spectroscopy [SERS]) have been developed for analyzing genetic and epigenetic biomarkers using both optical and non-optical tools. Despite these methodologies, no gold standard detection method has yet been implemented that can analyze CRC with high specificity and sensitivity in an inexpensive, simple, and time-efficient manner. Moreover, until now, no study has critically reviewed the advantages and limitations of these methodologies. Here, an overview of the most used genetic and epigenetic biomarkers for CRC and their detection methods are discussed. Furthermore, a summary of the major biological, technical, and clinical challenges and advantages/limitations of existing techniques is also presented.
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Affiliation(s)
- Md Sajedul Islam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia.
| | - Alfred K Lam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia; Pathology Queensland, Gold Coast University Hospital, Southport, QLD, 4215, Australia
| | - Muhammad J A Shiddiky
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
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7
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Guo Y, Zhang X, Zhang H, Liu Y, Shi J, Meng H, Chen X, Lan Q, Zhu B. Application of microfluidic technologies in forensic analysis. Electrophoresis 2023; 44:1725-1743. [PMID: 37857551 DOI: 10.1002/elps.202200268] [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: 11/07/2022] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 10/21/2023]
Abstract
The application of microfluidic technology in forensic medicine has steadily expanded over the last two decades due to the favorable features of low cost, rapidity, high throughput, user-friendliness, contamination-free, and minimum sample and reagent consumption. In this context, bibliometric methods were adopted to visualize the literature information contained in the Science Citation Index Expanded from 1989 to 2022, focusing on the co-occurrence analysis of forensic and microfluidic topics. A deep interpretation of the literature was conducted based on co-occurrence results, in which microfluidic technologies and their applications in forensic medicine, particularly forensic genetics, were elaborated. The purpose of this review is to provide an impartial evaluation of the utilization of microfluidic technology in forensic medicine. Additionally, the challenges and future trends of implementing microfluidic technology in forensic genetics are also addressed.
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Affiliation(s)
- Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, P. R. China
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yaoshun Liu
- Ankang Hospital of Traditional Chinese Medicine, Ankang, Shaanxi, P. R. China
| | - Jianfeng Shi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Xin Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
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Yaghoubi Naei V, Bordhan P, Mirakhorli F, Khorrami M, Shrestha J, Nazari H, Kulasinghe A, Ebrahimi Warkiani M. Advances in novel strategies for isolation, characterization, and analysis of CTCs and ctDNA. Ther Adv Med Oncol 2023; 15:17588359231192401. [PMID: 37692363 PMCID: PMC10486235 DOI: 10.1177/17588359231192401] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Over the past decade, the detection and analysis of liquid biopsy biomarkers such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have advanced significantly. They have received recognition for their clinical usefulness in detecting cancer at an early stage, monitoring disease, and evaluating treatment response. The emergence of liquid biopsy has been a helpful development, as it offers a minimally invasive, rapid, real-time monitoring, and possible alternative to traditional tissue biopsies. In resource-limited settings, the ideal platform for liquid biopsy should not only extract more CTCs or ctDNA from a minimal sample volume but also accurately represent the molecular heterogeneity of the patient's disease. This review covers novel strategies and advancements in CTC and ctDNA-based liquid biopsy platforms, including microfluidic applications and comprehensive analysis of molecular complexity. We discuss these systems' operational principles and performance efficiencies, as well as future opportunities and challenges for their implementation in clinical settings. In addition, we emphasize the importance of integrated platforms that incorporate machine learning and artificial intelligence in accurate liquid biopsy detection systems, which can greatly improve cancer management and enable precision diagnostics.
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Affiliation(s)
- Vahid Yaghoubi Naei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Science, Institute for Biomedical Materials & Devices, University of Technology Sydney, Australia
| | - Fatemeh Mirakhorli
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Arutha Kulasinghe
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, 1, Broadway, Ultimo New South Wales 2007, Australia
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Alexandre L, Araya-Farias M, Nguyen ML, Naoumi N, Gropplero G, Gizeli E, Malaquin L, Descroix S. High-throughput extraction on a dynamic solid phase for low-abundance biomarker isolation from biological samples. MICROSYSTEMS & NANOENGINEERING 2023; 9:109. [PMID: 37680311 PMCID: PMC10480215 DOI: 10.1038/s41378-023-00582-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/25/2023] [Accepted: 07/13/2023] [Indexed: 09/09/2023]
Abstract
Liquid biopsy, in particular circulating tumor DNA (ctDNA) analysis, has paved the way for a new noninvasive approach to cancer diagnosis, treatment selection and follow-up. As a crucial step in the analysis, the extraction of the genetic material from a complex matrix needs to meet specific requirements such as high specificity and low loss of target. Here, we developed a new generation of microfluidic fluidized beds (FBs) that enable the efficient extraction and preconcentration of specific ctDNA sequences from human serum with flow rates up to 15 µL/min. We first demonstrated that implementation of a vibration system inducing flow rate fluctuations combined with a mixture of different bead sizes significantly enhanced bead homogeneity, thereby increasing capture efficiency. Taking advantage of this new generation of high-throughput magnetic FBs, we then developed a new method to selectively capture a double-stranded (dsDNA) BRAF mutated DNA sequence in complex matrices such as patient serum. Finally, as proof of concept, ligation chain reaction (LCR) assays were performed to specifically amplify a mutated BRAF sequence, allowing the detection of concentrations as low as 6 × 104 copies/µL of the mutated DNA sequence in serum.
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Affiliation(s)
- Lucile Alexandre
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes (IPGG), Sorbonne University, Paris, France
| | - Monica Araya-Farias
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes (IPGG), Sorbonne University, Paris, France
- Present Address: Frédéric Joliot Institute for Life Sciences, Pharmacology and Immunoanalysis Unit, Immunoanalysis Studies and Research Laboratory, Alternative Energies and Atomic Energy Commission (CEA), Gif-sur-Yvette, France
| | - Manh-Louis Nguyen
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes (IPGG), Sorbonne University, Paris, France
| | - Nikoletta Naoumi
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology (IMBB) - FORTH, Heraklion, Greece
| | - Giacomo Gropplero
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes (IPGG), Sorbonne University, Paris, France
| | - Electra Gizeli
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology (IMBB) - FORTH, Heraklion, Greece
| | - Laurent Malaquin
- Laboratoire d’analyse et d’architecture des systèmes (LAAS) CNRS, Elia Group, Toulouse, France
| | - Stéphanie Descroix
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes (IPGG), Sorbonne University, Paris, France
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10
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Biglari N, Soltani-Zangbar MS, Mohammadian J, Mehdizadeh A, Abbasi K. ctDNA as a novel and promising approach for cancer diagnosis: a focus on hepatocellular carcinoma. EXCLI JOURNAL 2023; 22:752-780. [PMID: 37720239 PMCID: PMC10502204 DOI: 10.17179/excli2023-6277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 09/19/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent forms of cancer worldwide. Therefore, it is essential to diagnose and treat HCC patients promptly. As a novel discovery, circulating tumor DNA (ctDNA) can be used to analyze the tumor type and the cancer location. Additionally, ctDNA assists the cancer stage determination, which enables medical professionals to provide patients with the most appropriate treatment. This review will discuss the HCC-related mutated genes diagnosed by ctDNA. In addition, we will introduce the different and the most appropriate ctDNA diagnosis approaches based on the facilities.
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Affiliation(s)
- Negin Biglari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad Sadegh Soltani-Zangbar
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jamal Mohammadian
- School of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Mehdizadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khadijeh Abbasi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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11
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Cai P, Yang B, Zhao J, Ye P, Yang D. Detection of KRAS mutation using plasma samples in non-small-cell lung cancer: a systematic review and meta-analysis. Front Oncol 2023; 13:1207892. [PMID: 37483491 PMCID: PMC10357383 DOI: 10.3389/fonc.2023.1207892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Background The aim of this study was to investigate the diagnostic accuracy of KRAS mutation detection using plasma sample of patients with non-small cell lung cancer (NSCLC). Methods Databases of Pubmed, Embase, Cochrane Library, and Web of Science were searched for studies detecting KRAS mutation in paired tissue and plasma samples of patients with NSCLC. Data were extracted from each eligible study and analyzed using MetaDiSc and STATA. Results After database searching and screening of the studies with pre-defined criteria, 43 eligible studies were identified and relevant data were extracted. After pooling the accuracy data from 3341 patients, the pooled sensitivity, specificity and diagnostic odds ratio were 71%, 94%, and 59.28, respectively. Area under curve of summary receiver operating characteristic curve was 0.8883. Subgroup analysis revealed that next-generation sequencing outperformed PCR-based techniques in detecting KRAS mutation using plasma sample of patients with NSCLC, with sensitivity, specificity, and diagnostic odds ratio of 73%, 94%, and 82.60, respectively. Conclusion Compared to paired tumor tissue sample, plasma sample showed overall good performance in detecting KRAS mutation in patients with NSCLC, which could serve as good surrogate when tissue samples are not available.
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Affiliation(s)
- Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Bofan Yang
- School of Clinical Medicine, Chengdu University, Chengdu, China
| | - Jiahui Zhao
- School of Clinical Medicine, Chengdu University, Chengdu, China
| | - Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Dongmei Yang
- Clinical Laboratory & Clinical Research and Translational Center, Second People’s Hospital of Yibin City-West China Yibin Hospital, Sichuan University, Yibin, China
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12
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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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13
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Lab-on-a-chip systems for cancer biomarker diagnosis. J Pharm Biomed Anal 2023; 226:115266. [PMID: 36706542 DOI: 10.1016/j.jpba.2023.115266] [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: 11/22/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
Lab-on-a-chip (LOC) or micro total analysis system is one of the microfluidic technologies defined as the adaptation, miniaturization, integration, and automation of analytical laboratory procedures into a single instrument or "chip". In this article, we review developments over the past five years in the application of LOC biosensors for the detection of different types of cancer. Microfluidics encompasses chemistry and biotechnology skills and has revolutionized healthcare diagnosis. Superior to traditional cell culture or animal models, microfluidic technology has made it possible to reconstruct functional units of organs on chips to study human diseases such as cancer. LOCs have found numerous biomedical applications over the past five years, including integrated bioassays, cell analysis, metabolomics, drug discovery and delivery systems, tissue and organ physiology and disease modeling, and personalized medicine. This review provides an overview of the latest developments in microfluidic-based cancer research, with pros, cons, and prospects.
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14
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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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15
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Gharib G, Bütün İ, Muganlı Z, Kozalak G, Namlı İ, Sarraf SS, Ahmadi VE, Toyran E, van Wijnen AJ, Koşar A. Biomedical Applications of Microfluidic Devices: A Review. BIOSENSORS 2022; 12:1023. [PMID: 36421141 PMCID: PMC9688231 DOI: 10.3390/bios12111023] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/30/2022] [Accepted: 11/08/2022] [Indexed: 05/26/2023]
Abstract
Both passive and active microfluidic chips are used in many biomedical and chemical applications to support fluid mixing, particle manipulations, and signal detection. Passive microfluidic devices are geometry-dependent, and their uses are rather limited. Active microfluidic devices include sensors or detectors that transduce chemical, biological, and physical changes into electrical or optical signals. Also, they are transduction devices that detect biological and chemical changes in biomedical applications, and they are highly versatile microfluidic tools for disease diagnosis and organ modeling. This review provides a comprehensive overview of the significant advances that have been made in the development of microfluidics devices. We will discuss the function of microfluidic devices as micromixers or as sorters of cells and substances (e.g., microfiltration, flow or displacement, and trapping). Microfluidic devices are fabricated using a range of techniques, including molding, etching, three-dimensional printing, and nanofabrication. Their broad utility lies in the detection of diagnostic biomarkers and organ-on-chip approaches that permit disease modeling in cancer, as well as uses in neurological, cardiovascular, hepatic, and pulmonary diseases. Biosensor applications allow for point-of-care testing, using assays based on enzymes, nanozymes, antibodies, or nucleic acids (DNA or RNA). An anticipated development in the field includes the optimization of techniques for the fabrication of microfluidic devices using biocompatible materials. These developments will increase biomedical versatility, reduce diagnostic costs, and accelerate diagnosis time of microfluidics technology.
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Affiliation(s)
- Ghazaleh Gharib
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - İsmail Bütün
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Zülâl Muganlı
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Gül Kozalak
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - İlayda Namlı
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | | | | | - Erçil Toyran
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Andre J. van Wijnen
- Department of Biochemistry, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Ali Koşar
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
- Turkish Academy of Sciences (TÜBA), Çankaya, Ankara 06700, Turkey
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16
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Recent advances in integrated microfluidics for liquid biopsies and future directions. Biosens Bioelectron 2022; 217:114715. [PMID: 36174359 DOI: 10.1016/j.bios.2022.114715] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022]
Abstract
Liquid biopsies have piqued the interest of researchers as a new tumor diagnosis technique due to their unique benefits of non-invasiveness, sensitivity, and convenience. Recent advances in microfluidic technology have integrated separation, purification, and detection, allowing for high-throughput, high-sensitivity, and high-controllability detection of specific biomarkers in liquid biopsies. With the increasing demand for tumor detection and individualized treatment, new challenges are emerging for the ever-improving microfluidic technology. The state-of-the-art microfluidic design and fabrications have been reviewed in this manuscript, and how this technology can be applied to liquid biopsies from the point of view of the detection process. The primary discussion objectives are circulating tumor cells (CTCs), exosomes, and circulating nucleic acid (ctDNA). Furthermore, the challenges and future direction of microfluidic technology in detecting liquid biomarkers have been discussed.
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17
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Chavez‐Pineda OG, Rodriguez‐Moncayo R, Cedillo‐Alcantar DF, Guevara‐Pantoja PE, Amador‐Hernandez JU, Garcia‐Cordero JL. Microfluidic systems for the analysis of blood‐derived molecular biomarkers. Electrophoresis 2022; 43:1667-1700. [DOI: 10.1002/elps.202200067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Oriana G. Chavez‐Pineda
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Roberto Rodriguez‐Moncayo
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Diana F. Cedillo‐Alcantar
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Pablo E. Guevara‐Pantoja
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Josue U. Amador‐Hernandez
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Jose L. Garcia‐Cordero
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
- Roche Institute for Translational Bioengineering (ITB) Roche Pharma Research and Early Development, Roche Innovation Center Basel Basel Switzerland
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18
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Hapsianto BN, Kojima N, Kurita R, Yamagata H, Fujita H, Fujii T, Kim SH. Direct Capture and Amplification of Small Fragmented DNAs Using Nitrogen-Mustard-Coated Microbeads. Anal Chem 2022; 94:7594-7600. [PMID: 35578745 DOI: 10.1021/acs.analchem.2c00531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Circulating cell-free DNA (cfDNA) has been implicated as an important biomarker and has been intensively studied for "liquid biopsy" applications in cancer diagnostics. Owing to its small fragment size and its low concentration in circulation, cfDNA extraction and purification from serum samples are complicated, and the extraction yield affects the precision of subsequent molecular diagnostic tests. Here, we report a novel approach using nitrogen-mustard-coated DNA capture beads (NMD beads) that covalently capture DNA and allow direct subsequent polymerase chain reaction (PCR) amplification from the NMD bead without elusion. The complex DNA extraction and purification processes are not required. To illustrate the diagnostic use of the NMD beads, we detected short DNA fragments (142 bp) that were spiked into fetal bovine serum (as a model serum sample). The spiked DNAs were captured directly from serum samples and detected using real-time PCR at concentrations as low as 10 fg/mL. We anticipate that this DNA capture bead technique has the potential to simplify the preanalytical processes required for cfDNA detection, which could significantly expand the diagnostic applications of liquid biopsy.
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Affiliation(s)
- Benediktus N Hapsianto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan
| | - Naoshi Kojima
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Ryoji Kurita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Hitoshi Yamagata
- Advanced Research Laboratory (ARL), Canon Medical Systems Corporation, 1385 Shimoishigami, Otawara 324-8550, Tochigi, Japan
| | - Hiroyuki Fujita
- Advanced Research Laboratory (ARL), Canon Medical Systems Corporation, 1385 Shimoishigami, Otawara 324-8550, Tochigi, Japan
| | - Teruo Fujii
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Soo Hyeon Kim
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
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19
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Recent advances for cancer detection and treatment by microfluidic technology, review and update. Biol Proced Online 2022; 24:5. [PMID: 35484481 PMCID: PMC9052508 DOI: 10.1186/s12575-022-00166-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022] Open
Abstract
Numerous cancer-associated deaths are owing to a lack of effective diagnostic and therapeutic approaches. Microfluidic systems for analyzing a low volume of samples offer a precise, quick, and user-friendly technique for cancer diagnosis and treatment. Microfluidic devices can detect many cancer-diagnostic factors from biological fluids and also generate appropriate nanoparticles for drug delivery. Thus, microfluidics may be valuable in the cancer field due to its high sensitivity, high throughput, and low cost. In the present article, we aim to review recent achievements in the application of microfluidic systems for the diagnosis and treatment of various cancers. Although microfluidic platforms are not yet used in the clinic, they are expected to become the main technology for cancer diagnosis and treatment. Microfluidic systems are proving to be more sensitive and accurate for the detection of cancer biomarkers and therapeutic strategies than common assays. Microfluidic lab-on-a-chip platforms have shown remarkable potential in the designing of novel procedures for cancer detection, therapy, and disease follow-up as well as the development of new drug delivery systems for cancer treatment.
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20
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Cheng YH, Wang CH, Hsu KF, Lee GB. Integrated Microfluidic System for Cell-Free DNA Extraction from Plasma for Mutant Gene Detection and Quantification. Anal Chem 2022; 94:4311-4318. [PMID: 35235296 DOI: 10.1021/acs.analchem.1c04988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ovarian cancer (OvCa) is among the most severe gynecologic cancers, yet individuals may be asymptomatic during its early stages. Routine, early screening for genetic abnormalities associated with OvCa could improve prognoses, and this can be achieved by detecting mutant genes in cell-free DNA (cfDNA). Herein, we developed an integrated microfluidic chip (IMC) that could extract cfDNA from plasma and automatically detect and quantify mutations in the OvCa biomarker BRCA1. The cfDNA extraction module relied on a vortex-type micromixer to mix cfDNA with magnetic beads surface-coated with cfDNA probes and could isolate 76% of molecules from a 200 μL plasma sample in 45 min. The cfDNA quantification module, which comprised a micropump that evenly distributed 4.5 μL of purified cfDNA into the on-chip, allele-specific quantitative polymerase chain reaction (qPCR) zones, was capable of quantifying mutant genes within 90 min. By automating the cfDNA extraction and qPCR processes, this IMC could be used for clinical screening for OvCa-associated mutations.
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Affiliation(s)
- Yu-Hung Cheng
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Keng-Fu Hsu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu 30013, Taiwan
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21
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Schneider L, Usherwood T, Tripathi A. A microfluidic platform for high-purity cell free DNA extraction from plasma for non-invasive prenatal testing. Prenat Diagn 2022; 42:240-253. [PMID: 35032044 DOI: 10.1002/pd.6092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Increase the yield and purity of cell-free DNA (cfDNA) extracted from plasma for non-invasive prenatal testing (NIPT) as inefficiencies in this extraction and purification can dramatically affect the sensitivity and specificity of the test. METHODS This work integrates cfDNA extraction from plasma with a microfluidic chip platform by combining magnetic bead-based extraction and electroosmotic flow on the microfluidic chip. Various wash buffers and voltage conditions were simulated using COMSOL Multiphysics Modeling and tested experimentally. RESULTS When performing the first wash step of this assay on the microfluidic chip with 300 V applied across the channel there was a six-fold increase in the A260 /A230 ratio showing a significant improvement (p value 0.0005) in the purity of the extracted sample all while maintaining a yield of 68.19%. These values are critical as a high yield results in more sample to analyze and an increase in A260 /A230 ratio corresponds to a decrease in salt contaminants such as guanidinium thiocyanate which can interfere with downstream processes during DNA library preparation and potentially hinder the NIPT screening results. CONCLUSIONS This technique has the potential to improve NIPT outcomes and other clinically relevant workflows that use cfDNA as an analyte such as cancer detection.
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Affiliation(s)
- Lindsay Schneider
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| | - Thomas Usherwood
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
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22
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Abouali H, Hosseini SA, Purcell E, Nagrath S, Poudineh M. Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers. Cancers (Basel) 2022; 14:288. [PMID: 35053452 PMCID: PMC8774172 DOI: 10.3390/cancers14020288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
During cancer progression, tumors shed different biomarkers into the bloodstream, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). The analysis of these biomarkers in the blood, known as 'liquid biopsy' (LB), is a promising approach for early cancer detection and treatment monitoring, and more recently, as a means for cancer therapy. Previous reviews have discussed the role of CTCs and ctDNA in cancer progression; however, ctDNA and EVs are rapidly evolving with technological advancements and computational analysis and are the subject of enormous recent studies in cancer biomarkers. In this review, first, we introduce these cell-released cancer biomarkers and briefly discuss their clinical significance in cancer diagnosis and treatment monitoring. Second, we present conventional and novel approaches for the isolation, profiling, and characterization of these markers. We then investigate the mathematical and in silico models that are developed to investigate the function of ctDNA and EVs in cancer progression. We convey our views on what is needed to pave the way to translate the emerging technologies and models into the clinic and make the case that optimized next-generation techniques and models are needed to precisely evaluate the clinical relevance of these LB markers.
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Affiliation(s)
- Hesam Abouali
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Seied Ali Hosseini
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Emma Purcell
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
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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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24
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Žvirblytė J, Mažutis L. Microfluidics for Cancer Biomarker Discovery, Research, and Clinical Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1379:499-524. [DOI: 10.1007/978-3-031-04039-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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25
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Alidoust M, Baharfar M, Manouchehri M, Yamini Y, Tajik M, Seidi S. Emergence of microfluidic devices in sample extraction; an overview of diverse methodologies, principals, and recent advancements. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Kim CJ, Dong L, Amend SR, Cho YK, Pienta KJ. The role of liquid biopsies in prostate cancer management. LAB ON A CHIP 2021; 21:3263-3288. [PMID: 34346466 DOI: 10.1039/d1lc00485a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Liquid biopsy has emerged as a complement to invasive tissue biopsy to guide cancer diagnosis and treatment. The common liquid biopsy biomarkers are circulating tumor cells (CTCs), extracellular vesicles (EVs), and circulating tumor DNA (ctDNA). Each biomarker provides specific information based on its intrinsic characteristics. Prostate cancer is the second most common cancer in males worldwide. In men with low-grade localized prostate cancer, the disease can often be managed by active surveillance. For men who require treatment, the 5-year survival rate of localized prostate cancer is the highest among all cancer types, but the metastatic disease remains incurable. Metastatic prostate cancer invariably progresses to involve multiple bone sites and develops into a castration-resistant disease that leads to cancer death. The need to appropriately diagnose and guide the serial treatment of men with prostate cancer has led to the implementation of many studies to apply liquid biopsies to prostate cancer management. This review describes recent advancements in isolation and detection technology and the strength and weaknesses of the three circulating biomarkers. The clinical studies based on liquid biopsy results are summarized to depict the future perspective in the role of liquid biopsy on prostate cancer management.
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Affiliation(s)
- Chi-Ju Kim
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Campos CDM, Childers K, Gamage SST, Wijerathne H, Zhao Z, Soper SA. Analytical Technologies for Liquid Biopsy of Subcellular Materials. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:207-229. [PMID: 33974805 PMCID: PMC8601690 DOI: 10.1146/annurev-anchem-091520-093931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Liquid biopsy markers, which can be secured from a simple blood draw or other biological samples, are used to manage a variety of diseases and even monitor for bacterial or viral infections. Although there are several different types of liquid biopsy markers, the subcellular ones, including cell-free DNA, microRNA, extracellular vesicles, and viral particles, are evolving in terms of their utility. A challenge with liquid biopsy markers is that they must be enriched from the biological sample prior to analysis because they are a vast minority in a mixed population, and potential interferences may be present in the sample matrix that can inhibit profiling the molecular cargo from the subcellular marker. In this article, we discuss existing and developing analytical enrichment platforms used to isolate subcellular liquid biopsy markers, and discuss their figures of merit such as recovery, throughput, and purity.
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Affiliation(s)
- Camila D M Campos
- Life Science Department, Imec, 3001 Leuven, Belgium
- Department of Electrical Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Katie Childers
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
| | - Sachindra S T Gamage
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Harshani Wijerathne
- Department of Mechanical Engineering, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Zheng Zhao
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
| | - Steven A Soper
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, Kansas 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
- Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
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Chen L, Cabot JM, Paull B. Thread-based isotachophoresis for DNA extraction and purification from biological samples. LAB ON A CHIP 2021; 21:2565-2573. [PMID: 34002759 DOI: 10.1039/d1lc00179e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A rapid, low-cost, and disposable microfluidic thread-based isotachophoresis method was developed for the purification and preconcentration of nucleic acids from biological samples, prior to their extraction and successful analysis using quantitative polymerase chain reaction (qPCR). This approach extracts and concentrates protein-free DNA from the terminating electrolyte buffer, via a continuous sampling approach, resulting in significant focussing of the extracted DNA upon a 6 cm length nylon thread. The platform was optimised using the preconcentration of a fluorescent dye, showing a 600-fold concentration capacity within <5 min. The system was then applied to the one-step extraction of lambda DNA - an E. coli bacteriophage - spiked into whole blood, exhibiting the exclusion of PCR inhibitors. The extraction efficiency from the thread material following concentration was consistent, between 94.4-113.9%. The determination of lambda DNA in whole blood was achieved within a linear range of 1.0-1 × 105 fg μL-1 (20-2 × 106 copies per μL). This technique demonstrates great potential for the development of thread-based affordable analytical and diagnostic devices based upon DNA and RNA isolation.
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Affiliation(s)
- Liang Chen
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Sciences, University of Tasmania, Private Bag 75, Hobart 7001, Australia and ARC Centre of Excellence for Electromaterials Sciences (ACES), School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Joan M Cabot
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Sciences, University of Tasmania, Private Bag 75, Hobart 7001, Australia and ARC Centre of Excellence for Electromaterials Sciences (ACES), School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia and Diagnostic Devices Unit, Leitat Technology Center, Innovació 2, Terrassa, Barcelona 08225, Spain.
| | - Brett Paull
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Sciences, University of Tasmania, Private Bag 75, Hobart 7001, Australia and ARC Centre of Excellence for Electromaterials Sciences (ACES), School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
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Pahattuge TN, Freed IM, Hupert ML, Vaidyanathan S, Childers K, Witek MA, Weerakoon-Ratnayake K, Park D, Kasi A, Al-Kasspooles MF, Murphy MC, Soper SA. System Modularity Chip for Analysis of Rare Targets (SMART-Chip): Liquid Biopsy Samples. ACS Sens 2021; 6:1831-1839. [PMID: 33938745 DOI: 10.1021/acssensors.0c02728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Liquid biopsies are becoming popular for managing a variety of diseases due to the minimally invasive nature of their acquisition, thus potentially providing better outcomes for patients. Circulating tumor cells (CTCs) are among the many different biomarkers secured from a liquid biopsy, and a number of efficient platforms for their isolation and enrichment from blood have been reported. However, many of these platforms require manual sample handling, which can generate difficulties when translating CTC assays into the clinic due to potential sample loss, contamination, and the need for highly specialized operators. We report a system modularity chip for the analysis of rare targets (SMART-Chip) composed of three task-specific modules that can fully automate processing of CTCs. The modules were used for affinity selection of the CTCs from peripheral blood with subsequent photorelease, simultaneous counting, and viability determinations of the CTCs and staining/imaging of the CTCs for immunophenotyping. The modules were interconnected to a fluidic motherboard populated with valves, interconnects, pneumatic control channels, and a fluidic network. The SMART-Chip components were made from thermoplastics via microreplication, which lowers the cost of production making it amenable to clinical implementation. The utility of the SMART-Chip was demonstrated by processing blood samples secured from colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC) patients. We were able to affinity-select EpCAM expressing CTCs with high purity (0-3 white blood cells/mL of blood), enumerate the selected cells, determine their viability, and immunophenotype the cells. The assay could be completed in <4 h, while manual processing required >8 h.
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Affiliation(s)
- Thilanga N. Pahattuge
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ian M. Freed
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
| | - Mateusz L. Hupert
- BioFluidica, Inc., 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Swarnagowri Vaidyanathan
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
- Department of BioEngineering, University of Kansas, 1530 West 15th Street, Lawrence, Kansas 66045, United States
| | - Katie Childers
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
- Department of BioEngineering, University of Kansas, 1530 West 15th Street, Lawrence, Kansas 66045, United States
| | - Malgorzata A. Witek
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
| | - Kumuditha Weerakoon-Ratnayake
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
| | - Daniel Park
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Mechanical & Industrial Engineering, Louisiana State University, 3261 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Anup Kasi
- Department of Medical Oncology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Mazin F Al-Kasspooles
- Department of Medical Oncology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Michael C. Murphy
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Mechanical & Industrial Engineering, Louisiana State University, 3261 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Steven A. Soper
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
- Center of BioModular Multi-scale Systems for Precision Medicine, University of Kansas, Lawrence, Kansas 66045, United States
- BioFluidica, Inc., 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
- Department of BioEngineering, University of Kansas, 1530 West 15th Street, Lawrence, Kansas 66045, United States
- Department of Mechanical Engineering, University of Kansas, 3138 Learned Hall, 1530 West 15th Street, Lawrence, Kansas 66045, United States
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Park J, Woo S, Kim J, Lee H, Yoo YE, Hong S. Rapid and simple single-chamber nucleic acid detection system prepared through nature-inspired surface engineering. Am J Cancer Res 2021; 11:6735-6745. [PMID: 34093850 PMCID: PMC8171086 DOI: 10.7150/thno.57153] [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: 12/14/2020] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Nucleic acid (NA)-based diagnostics enable a rapid response to various diseases, but current techniques often require multiple labor-intensive steps, which is a major obstacle to successful translation to a clinical setting. Methods: We report on a surface-engineered single-chamber device for NA extraction and in situ amplification without sample transfer. Our system has two reaction sites: a NA extraction chamber whose surface is patterned with micropillars and a reaction chamber filled with reagents for in situ polymerase-based NA amplification. These two sites are integrated in a single microfluidic device; we applied plastic injection molding for cost-effective, mass-production of the designed device. The micropillars were chemically activated via a nature-inspired silica coating to possess a specific affinity to NA. Results: As a proof-of-concept, a colorimetric pH indicator was coupled to the on-chip analysis of NA for the rapid and convenient detection of pathogens. The NA enrichment efficiency was dependent on the lysate incubation time, as diffusion controls the NA contact with the engineered surface. We could detect down to 1×103 CFU by the naked eye within one hour of the total assay time. Conclusion: We anticipate that the surface engineering technique for NA enrichment could be easily integrated as a part of various types of microfluidic chips for rapid and convenient nucleic acid-based diagnostics.
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Obino D, Vassalli M, Franceschi A, Alessandrini A, Facci P, Viti F. An Overview on Microfluidic Systems for Nucleic Acids Extraction from Human Raw Samples. SENSORS 2021; 21:s21093058. [PMID: 33925730 PMCID: PMC8125272 DOI: 10.3390/s21093058] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 02/08/2023]
Abstract
Nucleic acid (NA) extraction is a basic step for genetic analysis, from scientific research to diagnostic and forensic applications. It aims at preparing samples for its application with biomolecular technologies such as isothermal and non-isothermal amplification, hybridization, electrophoresis, Sanger sequencing and next-generation sequencing. Multiple steps are involved in NA collection from raw samples, including cell separation from the rest of the specimen, cell lysis, NA isolation and release. Typically, this process needs molecular biology facilities, specialized instrumentation and labor-intensive operations. Microfluidic devices have been developed to analyze NA samples with high efficacy and sensitivity. In this context, the integration within the chip of the sample preparation phase is crucial to leverage the promise of portable, fast, user-friendly and economic point-of-care solutions. This review presents an overview of existing lab-on-a-chip (LOC) solutions designed to provide automated NA extraction from human raw biological fluids, such as whole blood, excreta (urine and feces), saliva. It mainly focuses on LOC implementation aspects, aiming to describe a detailed panorama of strategies implemented for different human raw sample preparations.
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Affiliation(s)
- Daniele Obino
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
| | - Massimo Vassalli
- Centre for the Cellular Microenvironment, James Watt School of Engineering, University of Glasgow, James Watt South Building, Glasgow G128LT, UK;
| | | | - Andrea Alessandrini
- Nanoscience Institute, National Research Council, 41125 Modena, Italy;
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Paolo Facci
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
- Correspondence:
| | - Federica Viti
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
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Carvalho Â, Ferreira G, Seixas D, Guimarães-Teixeira C, Henrique R, Monteiro FJ, Jerónimo C. Emerging Lab-on-a-Chip Approaches for Liquid Biopsy in Lung Cancer: Status in CTCs and ctDNA Research and Clinical Validation. Cancers (Basel) 2021; 13:cancers13092101. [PMID: 33925308 PMCID: PMC8123575 DOI: 10.3390/cancers13092101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/16/2021] [Accepted: 04/25/2021] [Indexed: 01/31/2023] Open
Abstract
Simple Summary Lung cancer (LCa) remains the leading cause of cancer-related mortality worldwide, with late diagnosis and limited therapeutic approaches still constraining patient’s outcome. In recent years, liquid biopsies have significantly improved the disease characterization and brought new insights into LCa diagnosis and management. The integration of microfluidic devices in liquid biopsies have shown promising results regarding circulating biomarkers isolation and analysis and these tools are expected to establish automatized and standardized results for liquid biopsies in the near future. Herein, we review the status of lab-on-a-chip approaches for liquid biopsies in LCa and highlight their current applications for circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) research and clinical validation studies. Abstract Despite the intensive efforts dedicated to cancer diagnosis and treatment, lung cancer (LCa) remains the leading cause of cancer-related mortality, worldwide. The poor survival rate among lung cancer patients commonly results from diagnosis at late-stage, limitations in characterizing tumor heterogeneity and the lack of non-invasive tools for detection of residual disease and early recurrence. Henceforth, research on liquid biopsies has been increasingly devoted to overcoming these major limitations and improving management of LCa patients. Liquid biopsy is an emerging field that has evolved significantly in recent years due its minimally invasive nature and potential to assess various disease biomarkers. Several strategies for characterization of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have been developed. With the aim of standardizing diagnostic and follow-up practices, microfluidic devices have been introduced to improve biomarkers isolation efficiency and specificity. Nonetheless, implementation of lab-on-a-chip platforms in clinical practice may face some challenges, considering its recent application to liquid biopsies. In this review, recent advances and strategies for the use of liquid biopsies in LCa management are discussed, focusing on high-throughput microfluidic devices applied for CTCs and ctDNA isolation and detection, current clinical validation studies and potential clinical utility.
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Affiliation(s)
- Ângela Carvalho
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (G.F.); (D.S.); (F.J.M.)
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.G.-T.); (R.H.); (C.J.)
- Correspondence: ; Tel.: +351-226-074-900
| | - Gabriela Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (G.F.); (D.S.); (F.J.M.)
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.G.-T.); (R.H.); (C.J.)
| | - Duarte Seixas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (G.F.); (D.S.); (F.J.M.)
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.G.-T.); (R.H.); (C.J.)
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Catarina Guimarães-Teixeira
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.G.-T.); (R.H.); (C.J.)
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Rui Henrique
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.G.-T.); (R.H.); (C.J.)
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Fernando J. Monteiro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (G.F.); (D.S.); (F.J.M.)
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.G.-T.); (R.H.); (C.J.)
- Faculdade de Engenharia, Departamento de Engenharia Metalúrgica e Materiais, Universidade do Porto, Rua Dr Roberto Frias, s/n, 4200-465 Porto, Portugal
| | - Carmen Jerónimo
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.G.-T.); (R.H.); (C.J.)
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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Athapattu US, Amarasekara CA, Immel JR, Bloom S, Barany F, Nagel AC, Soper SA. Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing. Nucleic Acids Res 2021; 49:e41. [PMID: 33511416 PMCID: PMC8053086 DOI: 10.1093/nar/gkab001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 01/29/2023] Open
Abstract
Modifications in RNA are numerous (∼170) and in higher numbers compared to DNA (∼5) making the ability to sequence an RNA molecule to identify these modifications highly tenuous using next generation sequencing (NGS). The ability to immobilize an exoribonuclease enzyme, such as XRN1, to a solid support while maintaining its activity and capability to cleave both the canonical and modified ribonucleotides from an intact RNA molecule can be a viable approach for single-molecule RNA sequencing. In this study, we report an enzymatic reactor consisting of covalently attached XRN1 to a solid support as the groundwork for a novel RNA exosequencing technique. The covalent attachment of XRN1 to a plastic solid support was achieved using EDC/NHS coupling chemistry. Studies showed that the solid-phase digestion efficiency of model RNAs was 87.6 ± 2.8%, while the XRN1 solution-phase digestion for the same model was 78.3 ± 4.4%. The ability of immobilized XRN1 to digest methylated RNA containing m6A and m5C ribonucleotides was also demonstrated. The processivity and clipping rate of immobilized XRN1 secured using single-molecule fluorescence measurements of a single RNA transcript demonstrated a clipping rate of 26 ± 5 nt s-1 and a processivity of >10.5 kb at 25°C.
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Affiliation(s)
| | | | - Jacob R Immel
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | | | | | - Steven A Soper
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
- Sunflower Genomics, Inc., Lawrence, KS 66047, USA
- Department of Mechanical Engineering and Bioengineering, University of Kansas, Lawrence, KS 66045, USA
- Department of Cancer Biology and KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Pisapia P, Costa JL, Pepe F, Russo G, Gragnano G, Russo A, Iaccarino A, de Miguel-Perez D, Serrano MJ, Denninghoff V, Quagliata L, Rolfo C, Malapelle U. Next generation sequencing for liquid biopsy based testing in non-small cell lung cancer in 2021. Crit Rev Oncol Hematol 2021; 161:103311. [PMID: 33781866 DOI: 10.1016/j.critrevonc.2021.103311] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide, with non-small cell lung cancer (NSCLC) representing its most commonly diagnosed sub-type. Despite the significant improvements in lung cancer biomarkers knowledge, accompanied by substantial technological advances in molecular tumor profiling, a considerable fraction (up to 30 %) of advanced NSCLC patient presents with major testing challenges or tissue unavailability for molecular analysis. In this context, liquid biopsy is on the rise, currently gaining considerable interest within the molecular pathology and oncology community. Molecular profiling of liquid biopsy specimens using next generation molecular biology methodologies is a rapidly evolving field with promising applications not exclusively limited to advanced stages but also more recently expanding to early stages cancer patients. Here, we offer an overview of some of the most consolidated and emerging applications of next generation sequencing technologies for liquid biopsy testing in NSCLC.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - José Luis Costa
- Medical Affairs Clinical NGS and Oncology Division Life Sciences Solutions, Thermo Fisher Scientific, Zug, Switzerland
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Diego de Miguel-Perez
- Liquid Biopsy and Metastasis Research Group, GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government PTS, Granada, Spain; Thoracic Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Maria Josè Serrano
- Liquid Biopsy and Metastasis Research Group, GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government PTS, Granada, Spain
| | - Valeria Denninghoff
- University of Buenos Aires - National Council for Scientific and Technical Research (CONICET), Buenos Aires, Argentina
| | - Luca Quagliata
- Medical Affairs Clinical NGS and Oncology Division Life Sciences Solutions, Thermo Fisher Scientific, Zug, Switzerland
| | - Christian Rolfo
- Thoracic Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
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Wang L, Pumera M. Recent advances of 3D printing in analytical chemistry: Focus on microfluidic, separation, and extraction devices. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116151] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Guo QR, Zhang LL, Liu JF, Li Z, Li JJ, Zhou WM, Wang H, Li JQ, Liu DY, Yu XY, Zhang JY. Multifunctional microfluidic chip for cancer diagnosis and treatment. Nanotheranostics 2021; 5:73-89. [PMID: 33391976 PMCID: PMC7738943 DOI: 10.7150/ntno.49614] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
Microfluidic chip is not a chip in the traditional sense. It is technologies that control fluids at the micro level. As a burgeoning biochip, microfluidic chips integrate multiple disciplines, including physiology, pathology, cell biology, biophysics, engineering mechanics, mechanical design, materials science, and so on. The application of microfluidic chip has shown tremendous promise in the field of cancer therapy in the past three decades. Various types of cell and tissue cultures, including 2D cell culture, 3D cell culture and tissue organoid culture could be performed on microfluidic chips. Patient-derived cancer cells and tissues can be cultured on microfluidic chips in a visible, controllable, and high-throughput manner, which greatly advances the process of personalized medicine. Moreover, the functionality of microfluidic chip is greatly expanding due to the customizable nature. In this review, we introduce its application in developing cancer preclinical models, detecting cancer biomarkers, screening anti-cancer drugs, exploring tumor heterogeneity and producing nano-drugs. We highlight the functions and recent development of microfluidic chip to provide references for advancing cancer diagnosis and treatment.
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Affiliation(s)
- Qiao-Ru Guo
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, P.R.China
| | - Ling-Ling Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, P.R.China
| | - Ji-Fang Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, P.R.China
| | - Zhen Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, P.R.China
| | - Jia-Jun Li
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, P.R.China
| | - Wen-Min Zhou
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, P.R.China
| | - Hui Wang
- Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R.China
| | - Jing-Quan Li
- The First Affiliated Hospital, Hainan Medical University, Haikou, P.R.China
| | - Da-Yu Liu
- Department of Laboratory Medicine, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, P.R.China
| | - Xi-Yong Yu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, P.R.China
| | - Jian-Ye Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, P.R.China.,The First Affiliated Hospital, Hainan Medical University, Haikou, P.R.China
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McCarthy Riley BF, Ward CL, Linz TH. Influence of microfabrication on digital PCR performance in bead-based microwell array assays. Anal Bioanal Chem 2020; 412:6917-6926. [PMID: 32772126 DOI: 10.1007/s00216-020-02822-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 11/25/2022]
Abstract
Digital PCR (dPCR) is a highly sensitive analytical technique used to quantify DNA targets. Detection sensitivity can be further enhanced by capturing target sequences onto beads for preconcentration and sample cleanup prior to analysis in microfluidic microwell arrays. However, robust digital analysis requires individual beads to be interrogated within individual wells. Fabricating microwells with dimensions ≤ 3 μm is challenging, and the high surface area-to-volume ratio of the wells leaves PCR susceptible to inhibition stemming from materials used during device processing. This report describes the development of a microfabrication procedure to create ultralow-volume wells (100 fL) for bead-based dPCR and characterize the effects of microprocessing materials on assay performance. Standard microfabrication protocols used for creating microelectronics resulted in devices with nanoscopic debris originating from photoresists used during processing. A model dPCR assay was developed to characterize the effects of this debris, which revealed variable PCR inhibition. Debris within microwells attenuated digital and analog assay signals to a greater extent than debris on the device surface. Spatial heterogeneity of debris across devices was quantified to characterize regional PCR inhibition and intra- and inter-device variability. Ultimately, a fabrication procedure was developed to create pristine microfluidic arrays using dual processes to remove positive resist and forgoing use of negative resist entirely, which enabled robust amplification with digital signals matching theoretical predictions. Results from this work catalog the unique performance artifacts from device microfabrication and provide a guide for future studies seeking to conduct robust, high-sensitivity bead-based dPCR assays. Graphical abstract.
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Affiliation(s)
| | - Cassandra L Ward
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA
| | - Thomas H Linz
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA.
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40
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Zhao X, Park DSW, Soper SA, Murphy MC. Microfluidic gasketless interconnects sealed by superhydrophobic surfaces. JOURNAL OF MICROELECTROMECHANICAL SYSTEMS : A JOINT IEEE AND ASME PUBLICATION ON MICROSTRUCTURES, MICROACTUATORS, MICROSENSORS, AND MICROSYSTEMS 2020; 29:894-899. [PMID: 33746475 PMCID: PMC7978084 DOI: 10.1109/jmems.2020.3000325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Existing methods for sealing chip-to-chip (or module-to-motherboard) microfluidic interconnects commonly use additional interconnect components (O-rings, gaskets, and tubing), and manual handling expertise for assembly. Novel gasketless superhydrophobic fluidic interconnects (GSFIs) sealed by transparent superhydrophobic surfaces, forming liquid bridges between the fluidic ports for fluidic passages were demonstrated. Two test platforms were designed, fabricated, and evaluated, a multi-port chip system (ten interconnects) and a modules-on-a-motherboard system (four interconnects). System assembly in less than 3 sec was done by embedded magnets and pin-in-V-groove structures. Flow tests with deionized (DI) water, ethanol/water mixture, and plasma confirmed no leakage through the gasketless interconnects up to a maximum flow rate of 100 μL/min for the multi-port chip system. The modules-on-a-motherboard system showed no leakage of water at a flow rate of 20 μL/min and a pressure drop of 3.71 psi. Characterization of the leakage pressure as a function of the surface tension of the sample liquid in the multi-port chip system revealed that lower surface tension of the liquid led to lower static water contact angles on the superhydrophobic-coated substrate and lower leakage pressures. The high-density, rapidly assembled, gasketless interconnect technology will open up new avenues for chip-to-chip fluid transport in complex microfluidic modular systems.
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Affiliation(s)
- Xiaoxiao Zhao
- Center for BioModular Multiscale Systems for Precision Medicine, Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Daniel S-W Park
- Center for BioModular Multiscale Systems for Precision Medicine, Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Steven A Soper
- Center for BioModular Multiscale Systems for Precision Medicine Departments of Chemistry and Mechanical Engineering, University of Kansas, Lawrence, KS, 66045, USA
| | - Michael C Murphy
- Center for BioModular Multiscale Systems for Precision Medicine, Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
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41
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Bickham AV, Pang C, George BQ, Topham DJ, Nielsen JB, Nordin GP, Woolley AT. 3D Printed Microfluidic Devices for Solid-Phase Extraction and On-Chip Fluorescent Labeling of Preterm Birth Risk Biomarkers. Anal Chem 2020; 92:12322-12329. [PMID: 32829631 DOI: 10.1021/acs.analchem.0c01970] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Solid-phase extraction (SPE) is a general preconcentration method for sample preparation that can be performed on a variety of specimens. The miniaturization of SPE within a 3D printed microfluidic device further allows for fast and simple extraction of analytes while also enabling integration of SPE with other sample preparation and separation methods. Here, we present the development and application of a reversed-phase lauryl methacrylate-based monolith, formed in 3D printed microfluidic devices, which can selectively retain peptides and proteins. The effectiveness of these SPE monoliths and 3D printed microfluidic devices was tested using a panel of nine preterm birth biomarkers of varying hydrophobicities and ranging in mass from 2 to 470 kDa. The biomarkers were selectively retained, fluorescently labeled, and eluted separately from the excess fluorescent label in 3D printed microfluidic systems. These are the first results demonstrating microfluidic analysis processes on a complete panel of preterm birth biomarkers, an important step toward developing a miniaturized, fully integrated analysis system.
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Affiliation(s)
- Anna V Bickham
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - Benjamin Q George
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - David J Topham
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - Jacob B Nielsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - Gregory P Nordin
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, Utah 84602 United States
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
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42
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Kye HG, Ahrberg CD, Park BS, Lee JM, Chung BG. Separation, Purification, and Detection of cfDNA in a Microfluidic Device. BIOCHIP JOURNAL 2020. [DOI: 10.1007/s13206-020-4208-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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43
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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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44
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Lee H, Park C, Na W, Park KH, Shin S. Precision cell-free DNA extraction for liquid biopsy by integrated microfluidics. NPJ Precis Oncol 2020; 4:3. [PMID: 32133418 PMCID: PMC7039987 DOI: 10.1038/s41698-019-0107-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/20/2019] [Indexed: 01/05/2023] Open
Abstract
Cell-free DNA (cfDNA) has been implicated as an important biomarker in cancer management. Thus, efficient techniques for cfDNA extraction are necessary for precision medicine. We developed a centrifugation-free cfDNA extraction microfluidic chip capable of extracting cfDNA from plasma samples through microfluidic circuits within 15 min under vacuum pressure using an immiscible solvent. The microfluidic chip had excellent performance that was comparable to the most widely used commercial product (QIAamp kit) in terms of extraction efficiency, purity, and quality of DNA samples. The microfluidic chip was validated for the continuous monitoring of HER-2 type breast cancer and was able to successfully detect a point mutation in phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA) during severe liver metastasis. The chip effectively eliminates the repetitive centrifugation processes and dramatically shortened the sample preparation time. The proposed platform could facilitate the development of a sample-to-answer system for use in liquid biopsy of cancers.
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Affiliation(s)
- Hoyoon Lee
- 1School of Mechanical Engineering, Korea University, Seoul, 02841 Republic of Korea
| | - Chanhee Park
- 1School of Mechanical Engineering, Korea University, Seoul, 02841 Republic of Korea
| | - Wonhwi Na
- 2Nano-Biofluigonstic Research Center, Korea University, Seoul, 02841 Republic of Korea
| | - Kyong Hwa Park
- 3Division of Oncology/Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul, 02841 Republic of Korea
| | - Sehyun Shin
- 1School of Mechanical Engineering, Korea University, Seoul, 02841 Republic of Korea.,2Nano-Biofluigonstic Research Center, Korea University, Seoul, 02841 Republic of Korea
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45
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Chen Y, Gong T, Yu C, Qian X, Wang X. Microfluidic Flow-through SPME Chip for Online Separation and MS Detection of Multiple Analyses in Complex Matrix. MICROMACHINES 2020; 11:mi11020120. [PMID: 31973161 PMCID: PMC7073986 DOI: 10.3390/mi11020120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 12/04/2022]
Abstract
Simplifying tedious sample preparation procedures to improve analysis efficiency is a major challenge in contemporary analytical chemistry. Solid phase microextraction (SPME), a technology developed for rapid sample pretreatment, has flexibility in design, geometry, and calibration strategies, which makes it a useful tool in a variety of fields, especially environmental and life sciences. Therefore, it is important to study the coupling between the microfluidic electrospray ionization (ESI) chip integrated with the solid phase microextraction (SPME) module and the electrospray mass spectrometer (MS). In our previous work, we designed a solid phase microextraction (SPME) module on a microfluidic chip through geometric design. However, automation and calibration methods for the extraction process remain unresolved in the SPME on-chip domain, which will lead to faster and more accurate results. This paper discusses the necessity to design a micromixer structure that can produce different elution conditions on the microfluidic chip. By calculating the channel resistances, the microfluidic chip’s integrated module with the micromixer, SPME, and ESI emitters optimize the geometry structure. We propose the annular channel for SPME to perform the resistances balance of the entire chip. Finally, for SPME on a single chip, this work provides a quantitation calibration method to describe the distribution of the analytes between the sample and the extraction phase before reaching the adsorption equilibrium.
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Affiliation(s)
- Yujun Chen
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (Y.C.); (T.G.); (X.W.)
| | - Tao Gong
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (Y.C.); (T.G.); (X.W.)
| | - Cilong Yu
- College of Mechatronics and Control Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Xiang Qian
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (Y.C.); (T.G.); (X.W.)
- Correspondence: ; Tel.: +86-755-2603-6755
| | - Xiaohao Wang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (Y.C.); (T.G.); (X.W.)
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46
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Nielsen JB, Hanson RL, Almughamsi HM, Pang C, Fish TR, Woolley AT. Microfluidics: Innovations in Materials and Their Fabrication and Functionalization. Anal Chem 2020; 92:150-168. [PMID: 31721565 PMCID: PMC7034066 DOI: 10.1021/acs.analchem.9b04986] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jacob B. Nielsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700, USA
| | - Robert L. Hanson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700, USA
| | - Haifa M. Almughamsi
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700, USA
| | - Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700, USA
| | - Taylor R. Fish
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700, USA
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700, USA
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47
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Geng Z, Gu Y, Li S, Lin B, Liu P. A Fully Integrated In Vitro Diagnostic Microsystem for Pathogen Detection Developed Using a "3D Extensible" Microfluidic Design Paradigm. MICROMACHINES 2019; 10:E873. [PMID: 31842384 PMCID: PMC6953088 DOI: 10.3390/mi10120873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/04/2019] [Accepted: 12/10/2019] [Indexed: 01/09/2023]
Abstract
Microfluidics is facing critical challenges in the quest of miniaturizing, integrating, and automating in vitro diagnostics, including the increasing complexity of assays, the gap between the macroscale world and the microscale devices, and the diverse throughput demands in various clinical settings. Here, a "3D extensible" microfluidic design paradigm that consists of a set of basic structures and unit operations was developed for constructing any application-specific assay. Four basic structures-check valve (in), check valve (out), double-check valve (in and out), and on-off valve-were designed to mimic basic acts in biochemical assays. By combining these structures linearly, a series of unit operations can be readily formed. We then proposed a "3D extensible" architecture to fulfill the needs of the function integration, the adaptive "world-to-chip" interface, and the adjustable throughput in the X, Y, and Z directions, respectively. To verify this design paradigm, we developed a fully integrated loop-mediated isothermal amplification microsystem that can directly accept swab samples and detect Chlamydia trachomatis automatically with a sensitivity one order higher than that of the conventional kit. This demonstration validated the feasibility of using this paradigm to develop integrated and automated microsystems in a less risky and more consistent manner.
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Affiliation(s)
- Zhi Geng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Z.G.); (Y.G.); (S.L.); (B.L.)
| | - Yin Gu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Z.G.); (Y.G.); (S.L.); (B.L.)
- FengteBio Corporation, Beijing 100079, China
| | - Shanglin Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Z.G.); (Y.G.); (S.L.); (B.L.)
- FengteBio Corporation, Beijing 100079, China
| | - Baobao Lin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Z.G.); (Y.G.); (S.L.); (B.L.)
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Z.G.); (Y.G.); (S.L.); (B.L.)
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48
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Zhang C, Sun G, Senapati S, Chang HC. A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification. LAB ON A CHIP 2019; 19:3853-3861. [PMID: 31621762 PMCID: PMC6982425 DOI: 10.1039/c9lc00818g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca2+) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm-1) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.
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Affiliation(s)
- Chenguang Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gongchen Sun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA and Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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49
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Soda N, Rehm BHA, Sonar P, Nguyen NT, Shiddiky MJA. Advanced liquid biopsy technologies for circulating biomarker detection. J Mater Chem B 2019; 7:6670-6704. [PMID: 31646316 DOI: 10.1039/c9tb01490j] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid biopsy is a new diagnostic concept that provides important information for monitoring and identifying tumor genomes in body fluid samples. Detection of tumor origin biomolecules like circulating tumor cells (CTCs), circulating tumor specific nucleic acids (circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), microRNAs (miRNAs), long non-coding RNAs (lnRNAs)), exosomes, autoantibodies in blood, saliva, stool, urine, etc. enables cancer screening, early stage diagnosis and evaluation of therapy response through minimally invasive means. From reliance on painful and hazardous tissue biopsies or imaging depending on sophisticated equipment, cancer management schemes are witnessing a rapid evolution towards minimally invasive yet highly sensitive liquid biopsy-based tools. Clinical application of liquid biopsy is already paving the way for precision theranostics and personalized medicine. This is achieved especially by enabling repeated sampling, which in turn provides a more comprehensive molecular profile of tumors. On the other hand, integration with novel miniaturized platforms, engineered nanomaterials, as well as electrochemical detection has led to the development of low-cost and simple platforms suited for point-of-care applications. Herein, we provide a comprehensive overview of the biogenesis, significance and potential role of four widely known biomarkers (CTCs, ctDNA, miRNA and exosomes) in cancer diagnostics and therapeutics. Furthermore, we provide a detailed discussion of the inherent biological and technical challenges associated with currently available methods and the possible pathways to overcome these challenges. The recent advances in the application of a wide range of nanomaterials in detecting these biomarkers are also highlighted.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia
| | - Prashant Sonar
- School of Chemistry, Physics and Mechanical Engineering, Molecular Design and Synthesis, Queensland University of Technology (QUT), Brisbane, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
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50
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Xu Z, Qiao Y, Tu J. Microfluidic Technologies for cfDNA Isolation and Analysis. MICROMACHINES 2019; 10:mi10100672. [PMID: 31623361 PMCID: PMC6843514 DOI: 10.3390/mi10100672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/27/2019] [Accepted: 09/29/2019] [Indexed: 12/18/2022]
Abstract
Cell-free DNA (cfDNA), which promotes precision oncology, has received extensive concern because of its abilities to inform genomic mutations, tumor burden and drug resistance. The absolute quantification of cfDNA concentration has been proved as an independent prognostic biomarker of overall survival. However, the properties of low abundance and high fragmentation hinder the isolation and further analysis of cfDNA. Microfluidic technologies and lab-on-a-chip (LOC) devices provide an opportunity to deal with cfDNA sample at a micrometer scale, which reduces required sample volume and makes rapid isolation possible. Microfluidic platform also allow for high degree of automation and high-throughput screening without liquid transfer, where rapid and precise examination and quantification could be performed at the same time. Microfluidic technologies applied in cfDNA isolation and analysis are limited and remains to be further explored. This paper reviewed the existing and potential applications of microfluidic technologies in collection and enrichment of cfDNA, quantification, mutation detection and sequencing library construction, followed by discussion of future perspectives.
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Affiliation(s)
- Zheyun Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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