Fully automated, on-site isolation of cfDNA from whole blood for cancer therapy monitoring

Multiple on-line active valves based centrifugal microfluidics for dynamic solid-phase enrichment and purification of viral nucleic acid

Point of care testing (POCT) of nucleic acids holds significant importance in the realm of infectious disease prevention and control, as well as the advancement of personalized precision medicine. Nevertheless, conventional nucleic acid testing methods continue to face challenges such as prolonged detection times and dependence on extensive specialized equipment and personnel, rendering them unsuitable for point of care applications. Here, we proposed an innovative active centrifugal microfluidic system (ACMS) for automatic nucleic acid extraction, encompassing modules for active valve control and magnetic control. An on-chip centrifugal puncture valve (PV) was devised based on the elastic tolerance differences between silicone membranes and tinfoils to release pre-embedded liquid reagents on demand. Furthermore, we have utilized the returnable valve (RV) technology to accurately control the retention and release of liquids, leveraging the high elastic tolerance of the silicone membrane. By incorporating an online controllable magnetic valve, we have achieved controlled and rapid aggregation and dispersion of magnetic beads. The final chip encapsulates multiple reagents and magnetic beads necessary for nucleic acid extraction. Upon sample addition and loading into the instrument, automated on-chip sample loading and nucleic acid extraction, purification, and collection can be accomplished within 30 minutes, halving the overall operation time and even increasing the efficiency of pseudovirus extraction by three orders of magnitude. Consequently, real-time fluorescence quantitative PCR amplification has successfully detected multiple targets of the SARS-CoV-2 virus (with an impressive detection limit as low as 10 copies per μL), along with targeted sequencing analysis yielding a conformity rate of 99%.

Cell-free fetal DNA (cffDNA) extraction from whole blood by using a fully automatic centrifugal microfluidic device based on displacement of magnetic silica beads

The purpose of this research was to design a fully automated centrifugal microfluidic system (Lab-on-a-Disk) for isolating cell free fetal DNAs (cffDNAs) from whole blood. To achieve this goal, magnetic silica beads were used, such that after attaching cffDNA to them, they were transferred between chambers by using external fixed magnets. All the standards and required steps for cffDNA extraction including plasma separation, adding proteinase K, lysis buffer, binding buffer, washing buffer, and elution buffer were considered in this designed disk. To evaluate the function of the disk, the collected samples were tested from several aspects. First, the purity of extracted plasma from whole blood was investigated which included hemoglobin test, hemocytometer, etc. This disk could extract 1.3 mL pure plasma from 3 mL blood with 45% hematocrit. The results of the extracted plasma showed 99% purity. Finally, the cffDNAs were examined by using a male fetal gender identification kit and real-time PCR machine. The results indicated the correct function of the disk in extracting cffDNAs in samples of 10 Landa from cycle 34 onwards. Compared to the clinical method, the disk not only was able to extract cffDNA in 20 min but also it led to less buffer consumption since the disk only required 1 mL plasma for extraction of cffDNAs.

Room temperature roll-to-roll additive manufacturing of polydimethylsiloxane-based centrifugal microfluidic device for on-site isolation of ribonucleic acid from whole blood

Polymer-based lab-on-a-disc (LoaD) devices for isolating ribonucleic acid (RNA) from whole blood samples have gained considerable attention for accurate biomedical analysis and point-of-care diagnostics. However, the mass production of these devices remains challenging in manufacturing cost and sustainability, primarily due to the utilization of a laser cutter or router computer numerical control (CNC) machine for engraving and cutting plastics in the conventional prototyping process. Herein, we reported the first energy-efficient room-temperature printing-imprinting integrated roll-to-roll manufacturing platform for mass production of a polydimethylsiloxane (PDMS)-based LoaD to on-site isolate ribonucleic acid (RNA) from undiluted blood samples. We significantly reduced energy consumption and eliminated thermal expansion variations between the mold, substrate, and resists by accelerating the PDMS curing time to less than 10 min at room temperature without using heat or ultraviolet radiation. The additive manufacturing technology was applied to fabricate a multi-depth flexible polymer mold that integrated macro (2 mm) and micro-sized (500 μm) features, which overcomes the economic and environmental challenges of conventional molding techniques. Our integrated R2R platform was enabled to print adhesion-promoting films at the first printing unit and continuously in-line imprint with a high replication accuracy (99%) for high-volume manufacturing of a new centrifugal microfluidic chip with an enhancement of mixing performance by integrating an efficient mixing chamber and serpentine micromixer. This research paved the way for scalable green manufacturing of large-volume polymer-based microfluidic devices, often required in real-world sample-driven analytical systems for clinical bioanalysis.

On-Line Dual-Active Valves Based Centrifugal Microfluidic Chip for Fully Automated Point-of-Care Immunoassay

There remains an unmet need for a fully integrated microfluidic platform that can automatically perform multistep and multireagent immunoassays. Here, we proposed a novel online dual-active valve-based centrifugal microfluidic chip, termed DAVM, for fully automatic point-of-care immunoassay. Practically, the puncture valve, one of the dual active valves, is capable of achieving precise, on-demand, sequential release of prestored reagents, while the other valve-reversible active valve enables controlled retention and drainage of the reaction solutions. Thereby, our technology mitigates the challenges of hydrophilic/hydrophobic modifications and unstable valve control performance commonly observed in passive valve controls. As a proof of concept, the indirect enzymatic immunoblotting technique was employed on DAVM for fully automated immunological analysis of eight targets, yielding outcomes within an hour. Furthermore, we conducted a comparative analysis of 28 clinical samples with autoimmune diseases. According to 224 clinical data, the sample testing concordance rate between DAVM and the traditional instrument was 82%, with a target compliance rate of 97%. Therefore, our DAVM system has powerful potential for fully automated immunoassays.

Lab-on-a-chip systems for cancer biomarker diagnosis

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.

Liquid Biopsies, Novel Approaches and Future Directions

Cancer is among the leading causes of death worldwide. Early diagnosis and prognosis are vital to improve patients' outcomes. The gold standard of tumor characterization leading to tumor diagnosis and prognosis is tissue biopsy. Amongst the constraints of tissue biopsy collection is the sampling frequency and the incomplete representation of the entire tumor bulk. Liquid biopsy approaches, including the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs), as well as certain protein signatures that are released in the circulation from primary tumors and their metastatic sites, present a promising and more potent candidate for patient diagnosis and follow up monitoring. The minimally invasive nature of liquid biopsies, allowing frequent collection, can be used in the monitoring of therapy response in real time, allowing the development of novel approaches in the therapeutic management of cancer patients. In this review we will describe recent advances in the field of liquid biopsy markers focusing on their advantages and disadvantages.

Nanobead handling on a centrifugal microfluidic LabDisk for automated extraction of cell-free circulating DNA with high recovery rates

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.

Magnetophoresis in Centrifugal Microfluidics at Continuous Rotation for Nucleic Acid Extraction

Centrifugal microfluidics enables fully automated molecular diagnostics at the point-of-need. However, the integration of solid-phase nucleic acid extraction remains a challenge. Under this scope, we developed the magnetophoresis under continuous rotation for magnetic bead-based nucleic acid extraction. Four stationary permanent magnets are arranged above a cartridge, creating a magnetic field that enables the beads to be transported between the chambers of the extraction module under continuous rotation. The centrifugal force is maintained to avoid uncontrolled spreading of liquids. We concluded that below a frequency of 5 Hz, magnetic beads move radially inwards. In support of magnetophoresis, bead inertia and passive geometrical design features allow to control the azimuthal bead movement between chambers. We then demonstrated ferrimagnetic bead transfer in liquids with broad range of surface tension and density values. Furthermore, we extracted nucleic acids from lysed Anopheles gambiae mosquitoes reaching comparable results of eluate purity (LabDisk: A260/A280 = 1.6 ± 0.04; Reference: 1.8 ± 0.17), and RT-PCR of extracted RNA (LabDisk: Ct = 17.9 ± 1.6; Reference: Ct = 19.3 ± 1.7). Conclusively, magnetophoresis at continuous rotation enables easy cartridge integration and nucleic acid extraction at the point-of-need with high yield and purity.

Biomedical Applications of Microfluidic Devices: A Review

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.

Rapid and Efficient Extraction of Cell-Free DNA Using Homobifunctional Crosslinkers

Since its discovery in circulating blood seven decades ago, cell-free DNA (cfDNA) has become a highly focused subject in cancer management using liquid biopsy. Despite its clinical utility, the extraction of cfDNA from blood has many technical difficulties, including a low efficiency of recovery and long processing times. We introduced a magnetic bead-based cfDNA extraction method using homobifunctional crosslinkers, including dimethyl suberimidate dihydrochloride (DMS). Owing to its bifunctional nature, DMS can bind to DNA through either covalent or electrostatic bonding. By adopting amine-conjugated magnetic beads, DMS–DNA complexes can be rapidly isolated from blood plasma. Using standard washing and eluting processes, we successfully extracted cfDNA from plasma within 10 min. This method yielded a 56% higher extraction efficiency than that of a commercial product (QIAamp kit). Furthermore, the instant binding mechanism of amine coupling between the microbeads and DMS–DNA complexes significantly reduced the processing time. These results highlight the potential of this magnetic bead-based homobifunctional crosslinker platform for extraction of cfDNA from blood plasma.

Design and fabrication of a low-cost wireless camera imaging system for centrifugal microfluidics

Centrifugal microfluidic devices offer a robust method for low-volume fluid handling by combining low-cost instrumentation with highly integrated automation. Crucial to the efficacy of Lab-on-a-Disc (LoaD) device operation is the selection of robust valving technology, the design of on-disc fluidic structures, and accurate control of disc spin-speeds (centrifugal force) during operation. The design and refinement of fluidic and valving structures is often guided by inspecting disc operation using high-speed camera systems. This approach involves synchronising image acquisition with disc rotation to visualise liquid flow through a series of images often presented in a video format. Depending on the decisions taken, such systems can cost from €4,000 upwards. This paper outlines the development of a low-cost centrifugal test-stand with an integrated imaging system using a generic wireless camera to record videos directly to a smartphone device. This imaging system can be fabricated using only 3D printers and a low-cost CNC milling machine from widely available materials for approximately €350. High-fidelity imaging of the entire disc for flow visualisation and the recording of real-time colour intensity measurements are facilitated by this standalone device. A vibration analysis study has been performed to determine the rotational velocity range at which the system can be safely operated. Furthermore, the efficacy of the imaging system has been demonstrated by performing real-time colour intensity measurements of dyed water dilutions.

Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers

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.

Fully automated light transmission aggregometry on a disc for platelet function tests

Platelet function tests, a group of assays that measure the ability of platelets to aggregate and promote clotting in a sample of blood, are performed in various medical fields to assess inherited platelet function disorders and monitor antiplatelet therapies. Light transmission aggregometry (LTA) is considered the gold standard for platelet function assessment. However, the lack of a standardized protocol is a major drawback when applied at the point of care. Moreover, it is a time-consuming and labor-intensive assay that requires a large volume of blood. Here, we describe the design, fabrication, and operation of a centrifugal microfluidic disc that can perform a fully automated LTA assay from a small volume of a whole blood sample (<1 mL), achieving highly reproducible results (3.2% coefficient of variation) within a short period (<25 min). The assays performed with this device yield more precise and accurate results than traditional LTA because of the automation of the reaction steps, minimal human operation, robust detection strategy via the distinctive structure of the microfluidic chamber, and quick analysis that minimizes the adverse effects of platelet instability.

An automated centrifugal microfluidic assay for whole blood fractionation and isolation of multiple cell populations using an aqueous two-phase system

Fractionating whole blood and separating its constituent components one from another is an essential step in many clinical applications. Currently blood sample handling and fractionation processes remain a predominantly manual task that require well-trained operators to produce reliable and reproducible results. Herein, we demonstrate an advanced on-chip whole human blood fractionation and cell isolation process combining (i) an aqueous two-phase system (ATPS) to create complex separation layers with (ii) a centrifugal microfluidic platform (PowerBlade) with active pneumatic pumping to control and automate the assay. We use a polyethylene glycol (PEG) and dextran (DEX) mixture as the two-phase density gradient media and our automated centrifugal microfluidic platform to fractionate blood samples. Different densities of precisely tuned PEG-DEX solutions were tested to match each of the cell types typically targeted during blood fractionation applications. By employing specially designed microfluidic devices, we demonstrate the automation of the following steps: loading of a whole blood sample on-chip, layering of the blood on the ATPS solution, blood fractionation, precise radial repositioning of the fractionated layers, and finally extraction of multiple, selected fractionated components. Fractionation of up to six distinct layers is shown: platelet-rich plasma, buffy coat, PEG, DEX with neutrophils, red blood cells (RBCs) and high density gradient media (HDGM). Furthermore, through controlled dispensing of HDGM to the fractionation chamber, we show that each of the fractionated layers can be repositioned radially, on-the-fly, without disturbing the interfaces, allowing precise transfer of target fractions and cell types into external vials via a chip-to-world interface. Cell counting analysis and cell viability studies showed equivalence to traditional, manual methods. An overall cell viability greater than 90% of extracted cells demonstrates that the proposed approach is suitable for cell isolation applications. This proof-of-principle demonstration highlights the utility of the proposed system for automated whole blood fractionation and isolation for blood cell applications. We anticipate that the proposed approach will be a useful tool for many clinical applications such as standard cell isolation procedures and other bioanalytical assays (e.g., circulating tumor cells, and cell and gene therapy).

Lab-on-a-Disc for Point-of-Care Infection Diagnostics

Reliable, inexpensive, and rapid diagnostic tools are essential to control and prevent the spread of infectious diseases. Many commercial kits for coronavirus disease 2019 (COVID-19) diagnostics have played a crucial role in the fight against the COVID-19 pandemic. Most current standard in vitro diagnostic (IVD) protocols for infectious diseases are sensitive but time-consuming and require sophisticated laboratory equipment and specially trained personnel. Recent advances in biosensor technology suggest the potential to deliver point-of-care (POC) diagnostics that are affordable and provide accurate results in a short time. The ideal "sample-in-answer-out" type fully integrated POC infection diagnostic platforms are expected to be autonomous or easy-to-operate, equipment-free or infrastructure-independent, and high-throughput or easy to upscale. In this Account, we detail the recent progress made by our group and others in the development of centrifugal microfluidic devices or lab-on-a-disc (LOAD) systems. Unlike conventional pump-based fluid actuation, the centrifugal force generated by spinning the disc induces liquid pumping and no external fluidic interconnects are required. This allows a total fluidic network required for multiple steps of biological assays to be integrated on a disc, enabling fully automated POC diagnostics. Various applications have been demonstrated, including liquid biopsy for personalized cancer management, food applications, and environmental monitoring; here, we focus on IVD for infectious disease. First, we introduce various on-disc unit operation technologies, including reagent storage, sedimentation, filtration, valving, decanting, aliquoting, mixing, separation, serial dilution, washing, and calibration. Such centrifugal microfluidic technologies have already proved promising for micro-total-analysis systems for automated IVD ranging from molecular detection of pathogens to multiplexed enzyme-linked immunosorbent assays (ELISAs) that use raw samples such as whole blood or saliva. Some recent examples of LOAD systems for molecular diagnostics in which some or all steps of the assays are integrated on a disc, including pathogen enrichment, nucleic acid extraction, amplification, and detection, are discussed in detail. We then introduce fully automated ELISA systems with enhanced sensitivity. Furthermore, we demonstrate a toy-inspired fidget spinner that enables electricity-free and rapid analysis of pathogens from undiluted urine samples of patients with urinary tract infection symptoms and a phenotypic antimicrobial susceptibility test for an extreme POC diagnostics application. Considering the urgent need for cost-effective and reliable POC infection diagnostic tools, especially in the current pandemic crisis, the current limitations and future directions of fast and broad adaptation in real-world settings are also discussed. With proper attention to key challenges and leverage with recent advances in bio-sensing technologies, molecular biology, nanomaterials, analytical chemistry, miniaturization, system integration, and data management, LOAD systems hold the potential to deliver POC infection diagnostic tools with unprecedented performance regarding time, accuracy, and cost. We hope the new insight and promise of LOAD systems for POC infection diagnostics presented in this Account can spark new ideas and inspire further research and development to create better healthcare systems for current and future pandemics.

The role of liquid biopsies in prostate cancer management

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.

Analytical Technologies for Liquid Biopsy of Subcellular Materials

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.

Emerging Lab-on-a-Chip Approaches for Liquid Biopsy in Lung Cancer: Status in CTCs and ctDNA Research and Clinical Validation

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.

Siphon-Controlled Automation on a Lab-on-a-Disc Using Event-Triggered Dissolvable Film Valves

Within microfluidic technologies, the centrifugal microfluidic “Lab-on-a-Disc” (LoaD) platform offers great potential for use at the PoC and in low-resource settings due to its robustness and the ability to port and miniaturize ‘wet bench’ laboratory protocols. We present the combination of ‘event-triggered dissolvable film valves’ with a centrifugo-pneumatic siphon structure to enable control and timing, through changes in disc spin-speed, of the release and incubations of eight samples/reagents/wash buffers. Based on these microfluidic techniques, we integrated and automated a chemiluminescent immunoassay for detection of the CVD risk factor marker C-reactive protein displaying a limit of detection (LOD) of 44.87 ng mL⁻¹ and limit of quantitation (LoQ) of 135.87 ng mL⁻¹.

A centrifugal microfluidic cross-flow filtration platform to separate serum from whole blood for the detection of amphiphilic biomarkers

The separation of biomarkers from blood is straightforward in most molecular biology laboratories. However, separation in resource-limited settings, allowing for the successful removal of biomarkers for diagnostic applications, is not always possible. The situation is further complicated by the need to separate hydrophobic signatures such as lipids from blood. Herein, we present a microfluidic device capable of centrifugal separation of serum from blood at the point of need with a system that is compatible with biomarkers that are both hydrophilic and hydrophobic. The cross-flow filtration device separates serum from blood as efficiently as traditional methods and retains amphiphilic biomarkers in serum for detection.

Selective extraction of low-abundance BRAF V600E mutation from plasma, urine, and sputum using ion-tagged oligonucleotides and magnetic ionic liquids

Sequence-specific DNA extractions have the potential to improve the detection of low-abundance mutations from complex matrices, making them ideal for circulating tumor DNA analysis during the early stages of cancer. Ion-tagged oligonucleotides (ITOs) are oligonucleotides modified with an allylimidazolium salt via thiolene click chemistry. The allylimidazolium-based tag allows the ITO-DNA duplex to be selectively captured by a hydrophobic magnetic ionic liquid (MIL). In this study, the selectivity of the ITO-MIL method was examined by extracting low abundance of the BRAF V600E mutation-a common single-nucleotide polymorphism associated with several different cancers-from diluted human plasma, artificial urine, and diluted artificial sputum. Quantitative polymerase chain reaction (qPCR) was not able to distinguish a 9% BRAF V600E standard (50 fg·μL^-1 BRAF V600E, 500 fg·μL^-1 wild-type BRAF) from the 100% wild-type BRAF (50 fg·μL^-1) standard. However, introducing the ITO-MIL extraction prior to qPCR allowed for samples consisting of 0.1% BRAF V600E (50 fg·μL^-1 V600E BRAF, 50,000 fg·μL^-1 wild-type BRAF) to be distinguished from the 100% wild-type BRAF standard. Ion-tagged oligonucleotides (ITOs) are combined with magnetic ionic liquids (MILs) to extract low-abundance BRAF V600E mutation from diluted human plasma, artificial urine, and diluted artificial sputum. The ITO-MIL extraction prior to qPCR allowed for samples consisting of 0.1% BRAF V600E to be distinguished from the 100% wild-type BRAF standard.

Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.

Reciprocating flow-assisted nucleic acid purification using a finger-actuated microfluidic device

Molecular diagnostics can provide a powerful diagnostic tool since it can detect pathogens with high sensitivity, but complicated sample preparation procedures limit its widespread use as an on-site detection tool that relies on the skilled person and external equipment. To resolve these limitations, we report a solid-phase nucleic acid purification using a finger-actuated microfluidic device, which can control a set amount of flow regardless of differences in end-users. To increase the recovery rate, a finger-actuated reciprocator was newly developed and integrated into the microfluidic device that can efficiently react with silica microbeads and reagents. After verifying the finger-actuated microfluidic reciprocator, the effect of the reciprocating flow on the recovery rate was assessed to purify the standard DNA of the hepatitis B virus (HBV). The recovery rate was increased up to ∼50% and 955 to 955 000 IU mL^-1 of HBV standard DNA was successfully purified and detected by a real-time polymerase chain reaction. Furthermore, the proposed microfluidic device was exploited to purify the HBV DNA from the patient's blood plasma samples.

Nanotechnology Strategies for the Analysis of Circulating Tumor DNA: A Review

Circulating tumor DNA (ctDNA) describes the fragmented DNA released from tumor cells into the blood. The ctDNA may have the same genetic changes as the primary tumor. Currently, ctDNA has become a popular biomarker for diagnosis, treatment, real-time clinical response monitoring, and prognosis, for solid tumors. Detection of ctDNA is minimally invasive, and repeat sampling can easily be performed. However, due to its low quality and short DNA fragment length, ctDNA detection still faces challenges and requires highly sensitive analytical techniques. Recently, liquid biopsies for the analysis of circulating tumor cells (CTCs) and circulating tumor-derived exosomes have been studied, and nanotechnology techniques have rapidly developed. Compared to traditional analytical methods, these nanotechnology-based platforms have the advantages of sensitivity, multiplex detection, simplicity, miniaturization, and automation, which support their potential use in clinical practice. This review aims to discuss the recent nanotechnological strategies for ctDNA analysis and the design of reliable techniques for ctDNA detection and to identify the potential clinical applications.

Fully automated platelet isolation on a centrifugal microfluidic device for molecular diagnostics

Platelets play crucial roles in hemostasis and immunity. Over the last decades, clinical evidence has revealed the significance of platelets as complementary biomarkers for the detection and treatment of various diseases, including cancer. Due to a lack of well standardized convenient isolation methods for platelets, pre-analytical factors such as complex handling procedures negatively impact the quality of the platelet samples, including overactivation, low purity, and poor reproducibility. This may lead to biased interpretation of various downstream analyses, such as proteomic and genomic analyses. Herein, we describe a fully automated lab-on-a-disc-based method of platelet isolation from a small volume of blood (<1 mL). This method provides higher yields (>4 folds) and purity (>99%) and lower platelet activation than the conventional method. Moreover, it was also superior in the detection of platelet-related RNAs CD41, PF4, and P2Y12 due to lower contamination with white blood cells.

Precision cell-free DNA extraction for liquid biopsy by integrated microfluidics

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.

Direct electrophoretic microRNA preparation from clinical samples using nanofilter membrane

A method to directly collect negatively charged nucleic acids, such as DNA and RNA, in the biosamples simply by applying an electric field in between the sample and collection buffer separated by the nanofilter membrane is proposed. The nanofilter membrane was made of low-stress silicon nitride with a thickness of 100 nm, and multiple pores were perforated in a highly arranged pattern using nanoimprint technology with a pore size of 200 nm and a pore density of 7.22 × 108/cm2. The electrophoretic transport of hsa-mir-93-5p across the membrane was confirmed in pure microRNA (miRNA) mimic solution using quantitative reverse transcription-polymerase chain reactions (qRT-PCR). Consistency of the collected miRNA quantity, stability of the system during the experiment, and yield and purity of the prepared sample were discussed in detail to validate the effectiveness of the electrical protocol. Finally, in order to check the applicability of this method to clinical samples, liquid biopsy process was demonstrated by evaluating the miRNA levels in sera of hepatocellular carcinoma patients and healthy controls. This efficient system proposed a simple, physical idea in preparation of nucleic acid from biosamples, and demonstrated its compatibility to biological downstream applications such as qRT-PCR as the conventional nucleic acid extraction protocols.

Wash-free non-spectroscopic optical immunoassay by controlling retroreflective microparticle movement in a microfluidic chip

Here, we proposed a retroreflective optical immunoassay platform by introducing the intrinsic sedimentation characteristics of a micro-retroreflector, namely retroreflective Janus particles (RJPs), wherein the sediment-based passive movement of RJPs minimised the random errors due to human involvement and resulted in a simple procedure that does not require the washing step, to follow the concept of point-of-care testing. The transparent sensing interface and the sedimentation property of RJPs were combined to develop a practical retroreflective immunoassay platform. For the sensing surface, transparent silanized poly(methyl methacrylate) was applied to the inverted focusing method. In the retroreflection phenomenon, as the incident light returns to its source by the retroreflector, efficient design of the retroreflective optical path between the light source and retroreflector can be crucial in signal registration. While preparing the RJP-bound transparent substrate on the microfluidic channel, the signal could be achieved more efficiently by directly focusing on the sensing interface, and not via the fluidic channels. To integrate this to build an immunoassay protocol, the sedimentation property of RJPs was employed for microfluidic chip inversion-based particle movement control, which was utilised for both luring and separating RJPs on the sensing surface, resulting in a wash-free immunoassay without any human involvement. To ensure accurate analysis, a time-lapse imaging-based image processing was conducted to eliminate the non-specific signals. To validate the applicability of the proposed immunoassay platform, quantification of acute cardiac infarction marker creatine kinase-MB was performed.

A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification

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.

Dual-neodymium magnet-based microfluidic separation device

Microfluidic-based separation methods have been highlighted for a number of biological applications, such as single cell analysis, disease diagnostics, and therapeutics. Although a number of previous studies have been carried out to minimize the physical damage and chemical deformations of the sample during the separation process, it still remains a challenge. In this paper, we developed a microfluidic device with dual-neodymium magnet-based negative magnetophoresis for the separation of the microparticles and cells. The poly(ethylene oxide) (PEO) was added to the solution to increase the viscoelasticity of the medium which could assist the sorting of the microparticles in the microfluidic device even at low flow rates, while minimizing damage to the cells and microparticles. Following this method, it was possible to separate 10 and 16 μm microparticles with high efficiency of 99 ± 0.1%, and 97 ± 0.8%, respectively. We also demonstrated the separation of glioblastoma cancer cells and neural stem cells (NSCs) in the microfluidic device.

Extraction of nucleic acids from blood: unveiling the potential of active pneumatic pumping in centrifugal microfluidics for integration and automation of sample preparation processes

This paper describes the development of an on-chip nucleic acid (NA) extraction assay from whole blood using a centrifugal microfluidic platform that allows for pneumatic actuation of liquids during rotation. The combination of pneumatic and centrifugal forces makes it possible to perform fluidic operations without the need for integrating active control elements on the microfluidic cartridge. The cartridge is fabricated from thermoplastic polymers (e.g., Zeonor 1060R) and features a simple design that is compatible with injection molding. In addition, the cartridge is interfaced with two external vials for off-chip storage of the blood sample and retrieval of the eluted NA solution, respectively. On-chip capture of NAs is performed using an embedded solid-phase extraction matrix composed of commercial glass microfiber filters (Whatman GF/D and GF/F). The yield of the automated, on-chip extraction protocol, determined by measuring absorbance at 260 nm, is comparable to some of the best manually operated kits (e.g., Qiagen QIAamp DNA Mini Kit) while providing low assay-to-assay variability due to the high level of control provided by the platform for each processing step. The A260/A280 and A260/A230 ratios of the absorbance spectra also reveal that protein contamination of the sample is negligible. The capability of the pneumatic platform to circulate air flux through the microfluidic conduit was used to dry leftover ethanol residues retained in the capture matrix during washing. This method, applied in combination with localized heating, proved effective for reducing ethanol contamination in eluted samples from ∼12% to 1% (v/v).

Circulating cell-free nucleic acids as biomarkers in colorectal cancer screening and diagnosis - an update

Introduction: Screening methods for one of the most frequently diagnosed malignancy, colorectal cancer (CRC), have limitations. Circulating cell-free nucleic acids (cfNA) hold clinical relevance as screening, prognostic and therapy monitoring markers. Area covered: In this review, we summarize potential CRC-specific cfNA biomarkers, the recently developed sample preparation techniques, their applications, and pitfalls. Expert opinion: Automated extraction of cfDNA is highly reproducible, however, cfDNA yield is less compared to manual isolation. Quantitative and highly sensitive detection techniques (e.g. digital PCR, NGS) can be applied to analyze genetic and epigenetic changes. Detection of DNA mutations or methylation in cfDNA and related altered levels of mRNA, miRNA, and lncRNA may improve early cancer recognition, based on specific, CRC-related patterns. Detection of cfDNA mutations (e.g. TP53, KRAS, APC) has limited diagnostic sensitivity (40-60%), however, methylated DNA including SEPT9, SFRP1, SDC2 can be applied with higher sensitivity (up to 90%) for CRC. Circulating miRNAs (e.g. miR-21, miR-92, miR-141) provide comparably high sensitivity for CRC as the circulating tumor cell mRNA markers (e.g. EGFR, CK19, CK20, CEA). Automation of cfNA isolation coupled with quantitative analysis of CRC-related, highly sensitive biomarkers may enhance CRC screening and early detection in the future.

Fully Automated, Label-Free Isolation of Extracellular Vesicles from Whole Blood for Cancer Diagnosis and Monitoring

Extracellular vesicles (EVs) that circulate in body fluids possess significant potential for disease diagnosis. Their use in clinical settings, however, has been limited owing to lack of simple and robust isolation methods. To rectify this problem, a centrifugal device for automatic, fast, and efficient isolation of EVs from whole-blood, called Exodisc-B is presented in this paper.

Methods: The device comprises a built-in chamber to facilitate plasma separation and two nanoporous filters—one for removing larger particles and the other for enriching EVs. The performance of the device in comparison to ultracentrifugation (UC) was evaluated by analyzing the yield, purity, protein and RNA content of the isolated EVs. Additionally, the EV protein marker expressions were measured by ELISA and statistically analyzed to differentiate prostate cancer patients from healthy donors.

Results: Compared with the UC technique, the proposed device is capable of isolating at least an order of magnitude higher number of EVs with about 30-fold higher mRNA count within 40 min. Sandwich ELISA of EV-specific membrane proteins—CD9-CD81—confirmed that Exodisc-B can isolate EVs from a volume of whole blood as low as 30 µL with a capture efficiency exceeding 75%. The device also facilitates temporal monitoring of tumor progression within live mouse xenograft models over a period of 13 weeks while using minimal volumes of weekly collected blood samples. Further, in ELISA analyses of multiple cancer-related proteins, such as prostate-specific antigen (PSA), prostate-specific membrane antigen (PSMA), epithelial cell adhesion molecule (EpCAM), epidermal growth factor receptor 1 (EGFR1), and heat shock protein 90 (HSP90), extracted from EVs isolated from human plasma, 43 patients were differentiated from 30 healthy donors.

Conclusion: The results demonstrated the ability of Exodisc-B to provide a rapid, sensitive, and point-of-care-type method for extracting intact EVs from small volumes of clinical blood samples for disease diagnosis and monitoring.

On-chip isolation and enrichment of circulating cell-free DNA using microfluidic device

Circulating cell-free DNA (cfDNA), containing cancer-specific DNAs derived from tumor cells, plays an important role in real-time monitoring of disease progression. Due to the abnormal growth of cancer and the promotion of cancer cell apoptosis by chemotherapy, the higher cfDNA concentration than healthy individuals is closely correlated with the diagnosis and treatment of cancer. Also, the mutation detection in tumor cell-derived cfDNA can be used to predict tumor progression. Human blood contains many blood cells (red blood cells, white blood cells, and platelets), proteins, extracellular vesicles, and so on. These blood components act as the inhibitors when the cfDNA is analyzed using polymerase chain reaction. So, analysis of cfDNA using whole blood directly may affect the sensitivity of the analysis or result in false-negative. The conventional methods of cfDNA isolation, such as silica absorption and polymer-mediated enrichment, are labor-intensive and time-consuming processes that can also lead to the loss of cfDNA in cumbersome procedures. Here, we designed an integrated microfluidic chip capable of on-chip cfDNA extracting to reduce sample loss and processing time. Our proposed device minimizes the number of experimental steps from 5 to 1, the total processing time from 42 to 19 min, and the required volume of washing reagents from 2 to 0.4 ml for cfDNA enrichment compared to the conventional method.

Liquid Biopsies in Cancer Diagnosis, Monitoring, and Prognosis

Liquid biopsies, comprising the noninvasive analysis of circulating tumor-derived material (the 'tumor circulome'), represent an innovative tool in precision oncology to overcome current limitations associated with tissue biopsies. Within the tumor circulome, circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) are the only components the clinical application of which is approved by the US Food and Drug Administration (FDA). Extracellular vesicles (EVs), circulating tumor RNA (ctRNA), and tumor-educated platelets (TEPs) are relatively new tumor circulome constituents with promising potential at each stage of cancer management. Here, we discuss the clinical applications of each element of the tumor circulome and the prevailing factors that currently limit their implementation in clinical practice. We also detail the most recent technological developments in the field, which demonstrate potential in improving the clinical value of liquid biopsies.

Rapid isolation of cfDNA from large-volume whole blood on a centrifugal microfluidic chip based on immiscible phase filtration

The C-IFAST device enabled the rapid isolation of cfDNA, from 4 ml whole blood to 50 μl elution, within 15 min.

Microfluidic-based solid phase extraction of cell free DNA

Cell-free DNA (cfDNA) is a liquid biopsy marker that can carry signatures (i.e., mutations) associated with certain pathological conditions. Therefore, the extraction of cfDNA from a variety of clinical samples can be an effective and minimally invasive source of markers for disease detection and subsequent management. In the oncological diseases, circulating tumor DNA (ctDNA), a cfDNA sub-class, can carry clinically actionable mutations and coupled with next generation sequencing or other mutation detection methods provide a venue for effective in vitro diagnostics. However, cfDNA mutational analyses require high quality inputs. This necessitates extraction platforms that provide high recovery over the entire ctDNA size range (50 → 150 bp) with minimal interferences (i.e., co-extraction of genomic DNA), and high reproducibility with a simple workflow. Herein, we present a novel microfluidic solid-phase extraction device (μSPE) consisting of a plastic chip that is activated with UV/O3 to generate surface-confined carboxylic acid functionalities for the μSPE of cfDNA. The μSPE uses an immobilization buffer (IB) consisting of polyethylene glycol and salts that induce cfDNA condensation onto the activated plastic microfluidic surface. The μSPE consists of an array of micropillars to increase extraction bed load (scalable to loads >700 ng of cfDNA) and can be produced at low-cost using replication-based techniques. The entire μSPE can be fabricated in a single molding step negating the need for adding additional extraction supports to the device simplifying production and keeping device and assay cost low. The μSPE allowed for recoveries >90% of model cfDNA fragments across a range of sizes (100-700 bp) and even the ability to extract efficiently short cfDNA fragments (50 bp, >70%). In addition, the composition of the IB allowed for reducing the interference of co-extracted genomic DNA. We demonstrated the clinical utility of the μSPE by quantifying the levels of cfDNA in healthy donors and patients with non-small-cell lung and colorectal cancers. μSPE extracted cfDNA from plasma samples was also subjected to a ligase detection reaction (LDR) for determining the presence of mutations in the KRAS gene for colorectal and non-small cell lung cancer patients.