Applications of microfluidics for molecular diagnostics

Exploring single-cell RNA sequencing as a decision-making tool in the clinical management of Fuchs' endothelial corneal dystrophy

Single-cell RNA sequencing (scRNA-seq) has enabled the identification of novel gene signatures and cell heterogeneity in numerous tissues and diseases. Here we review the use of this technology for Fuchs' Endothelial Corneal Dystrophy (FECD). FECD is the most common indication for corneal endothelial transplantation worldwide. FECD is challenging to manage because it is genetically heterogenous, can be autosomal dominant or sporadic, and progress at different rates. Single-cell RNA sequencing has enabled the discovery of several FECD subtypes, each with associated gene signatures, and cell heterogeneity. Current FECD treatments are mainly surgical, with various Rho kinase (ROCK) inhibitors used to promote endothelial cell metabolism and proliferation following surgery. A range of emerging therapies for FECD including cell therapies, gene therapies, tissue engineered scaffolds, and pharmaceuticals are in preclinical and clinical trials. Unlike conventional disease management methods based on clinical presentations and family history, targeting FECD using scRNA-seq based precision-medicine has the potential to pinpoint the disease subtypes, mechanisms, stages, severities, and help clinicians in making the best decision for surgeries and the applications of therapeutics. In this review, we first discuss the feasibility and potential of using scRNA-seq in clinical diagnostics for FECD, highlight advances from the latest clinical treatments and emerging therapies for FECD, integrate scRNA-seq results and clinical notes from our FECD patients and discuss the potential of applying alternative therapies to manage these cases clinically.

Nanophotonic waveguide-based sensing of circulating cell-free mitochondrial DNA: implications for personalized medicine

Circulating cell-free mitochondrial DNA (ccf-mtDNA) has emerged as a promising biomarker, with potential implications for disease diagnosis. Changes in mtDNA, such as deletions, mutations or variations in the number of copies, have been associated with mitochondrial disorders, heart diseases, cancer and age-related non-communicable diseases. Previous methods, such as polymerase chain reaction-based approaches, next-generation sequencing and imaging-based techniques, have shown improved accuracy in identifying rare mtDNA variants or mutations, but they have limitations. This article explains the basic principles and benefits of using planar optical waveguide-based detection devices, which represent an advanced approach in the field of sensing.

An integrated microfluidic-based biosensor using a magnetically controlled MNPs-enzyme microreactor to determine cholesterol in serum with fluorometric detection

This work provides a microfluidic-based biosensor to determine total cholesterol in serum based on integrating the reaction/detection zone of a microfluidic chip of a magnetically retained enzyme microreactor (MREµR) coupled with the remote fluorometric detection through a bifurcated fiber-optic bundle (BFOB) connected with a conventional spectrofluorometer. The method is based on developing the enzymatic hydrolysis and oxidation of cholesterol at microscale size using both enzymes (cholesterol esterase (ChE) and cholesterol oxidase (ChOx)) immobilized on magnetic nanoparticles (MNPs). The biocatalyst reactions were followed by monitoring the fluorescence decreasing by the naphtofluorescein (NF) oxidation in the presence of the previous H₂O₂ formed. This microfluidic biosensor supposes the physical integration of a minimal MREµR as a bioactive enzyme area and the focused BFOB connected with the spectrofluorometer detector. The MREµR was formed by a 1 mm length of magnetic retained 2:1 ChE-MNP/ChOx-MNP mixture. The dynamic range of the calibration graph was 0.005-10 mmol L^-1, expressed as total cholesterol concentration with a detection limit of 1.1 µmol L^-1 (r² = 0.9999, s_y/x = 0.03, n = 10, r = 3). The precision expressed as the relative standard deviation (RSD%) was between 1.3 and 2.1%. The microfluidic-based biosensors showed a sampling frequency estimated at 30 h^-1. The method was applied to determine cholesterol in serum samples with recovery values between 94.8 and 102%. The results of the cholesterol determination in serum were also tested by correlation with those obtained using the other two previous methods.

Nano-liter perfusion microfluidic device made entirely by two-photon polymerization for dynamic cell culture with easy cell recovery

Polydimethylsiloxane (PDMS) has been the material of choice for microfluidic applications in cell biology for many years, with recent advances encompassing nano-scaffolds and surface modifications to enhance cell-surface interactions at nano-scale. However, PDMS has not previously been amenable to applications which require complex geometries in three dimensions for cell culture device fabrication in the absence of additional components. Further, PDMS microfluidic devices have limited capacity for cell retrieval following culture without severely compromising cell health. This study presents a designed and entirely 3D-printed microfluidic chip (8.8 mm × 8.2 mm × 3.6 mm) using two-photon polymerization (2PP). The 'nest' chip is composed of ten channels that deliver sub-microliter volume flowrates (to ~ 600 nL/min per channel) to 10 individual retrievable cell sample 'cradles' that interlock with the nest to create the microfluidic device. Computational fluid dynamics modelling predicted medium flow in the device, which was accurately validated by real-time microbead tracking. Functional capability of the device was assessed, and demonstrated the capability to deliver culture medium, dyes, and biological molecules to support cell growth, staining and cell phenotype changes, respectively. Therefore, 2PP 3D-printing provides the precision needed for nanoliter fluidic devices constructed from multiple interlocking parts for cell culture application.

Microfluidic chip and isothermal amplification technologies for the detection of pathogenic nucleic acid

The frequency of outbreaks of newly emerging infectious diseases has increased in recent years. The coronavirus disease 2019 (COVID-19) outbreak in late 2019 has caused a global pandemic, seriously endangering human health and social stability. Rapid detection of infectious disease pathogens is a key prerequisite for the early screening of cases and the reduction in transmission risk. Fluorescence quantitative polymerase chain reaction (qPCR) is currently the most commonly used pathogen detection method, but this method has high requirements in terms of operating staff, instrumentation, venues, and so forth. As a result, its application in the settings such as poorly conditioned communities and grassroots has been limited, and the detection needs of the first-line field cannot be met. The development of point-of-care testing (POCT) technology is of great practical significance for preventing and controlling infectious diseases. Isothermal amplification technology has advantages such as mild reaction conditions and low instrument dependence. It has a promising prospect in the development of POCT, combined with the advantages of high integration and portability of microfluidic chip technology. This study summarized the principles of several representative isothermal amplification techniques, as well as their advantages and disadvantages. Particularly, it reviewed the research progress on microfluidic chip-based recombinase polymerase isothermal amplification technology and highlighted future prospects.

Development of a proof-of-concept microfluidic portable pathogen analysis system for water quality monitoring

Waterborne diseases cause millions of deaths worldwide, especially in developing communities. The monitoring and rapid detection of microbial pathogens in water is critical for public health protection. This study reports the development of a proof-of-concept portable pathogen analysis system (PPAS) that can detect bacteria in water with the potential application in a point-of-sample collection setting. A centrifugal microfluidic platform is adopted to integrate bacterial cell lysis in water samples, nucleic acid extraction, and reagent mixing with a droplet digital loop mediated isothermal amplification assay for bacteria quantification onto a single centrifugal disc (CD). Coupled with a portable "CD Driver" capable of automating the assay steps, the CD functions as a single step bacterial detection "lab" without the need to transfer samples from vial-to-vial as in a traditional laboratory. The prototype system can detect Enterococcus faecalis, a common fecal indicator bacterium, in water samples with a single touch of a start button within 1 h and having total hands-on-time being less than 5 min. An add-on bacterial concentration cup prefilled with absorbent polymer beads was designed to integrate with the pathogen CD to improve the downstream quantification sensitivity. All reagents and amplified products are contained within the single-use disc, reducing the opportunity of cross contamination of other samples by the amplification products. This proof-of-concept PPAS lays the foundation for field testing devices in areas needing more accessible water quality monitoring tools and are at higher risk for being exposed to contaminated waters.

Diagnostic biosensors for coronaviruses and recent developments

Coronaviruses are well known airborne viruses that infect humans, other mammals, and birds. COVID-19 is the disease caused by the last emerging type of corona viruses; SARS-CoV-2 which resulted in the ongoing pandemic. Since its first identification, SARS-CoV-2 has spread globally causing significant morbidity and mortality. Fast and reliable diagnostic methods are crucial to control the virus outbreak. In this chapter, we summarize the traditional methods used to detect corona viruses. Various biosensors used for the detection of the virus antibodies and antigens were briefly discussed. Different biosensing approaches for the detection of corona viruses were presented with special emphasis on the reported biosensors for the detection of SARS-CoV-2. Major advancements in the biosensors area for corona viruses such as the use of cotton, magnetic nanoparticles, graphene, gold nanoparticles, and portable devices are highlighted. The challenges and future perspectives in the biosensors for the detection of corona viruses are discussed.

Nucleic acid amplification-free detection of DNA and RNA at ultralow concentration

The broad spectrum of approaches for nucleic acid amplification-free detection of DNA and RNA at single-digit attomolar (10^-18 M) concentration and lower is reviewed. These low concentrations correspond roughly to the most clinically desirable detection range for pathogen-specific nucleic acid as well as the detection limits of commercially available, nucleic acid amplification tests based primarily on polymerase chain reaction (PCR). The need for more rapid and inexpensive, yet still highly accurate tests, has become evident during the pandemic. It is expected that publication of reports describing improved tests will accelerate soon, and this review covers the wide variety of detection methods based on both optical and electrical measurements that have been conceived over recent years, enabled generally by the advent of nanotechnology.

Integration of FISH and Microfluidics

Suitable molecular methods for a faster microbial identification in food and clinical samples have been explored and optimized during the last decades. However, most molecular methods still rely on time-consuming enrichment steps prior to detection, so that the microbial load can be increased and reach the detection limit of the techniques.In this chapter, we describe an integrated methodology that combines a microfluidic (lab-on-a-chip) platform, designed to concentrate cell suspensions and speed up the identification process in Saccharomyces cerevisiae , and a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) protocol optimized and adapted to microfluidics. Microfluidic devices with different geometries were designed, based on computational fluid dynamics simulations, and subsequently fabricated in polydimethylsiloxane by soft lithography. The microfluidic designs and PNA-FISH procedure described here are easily adaptable for the detection of other microorganisms of similar size.

Automated multiplex nucleic acid tests for rapid detection of SARS-CoV-2, influenza A and B infection with direct reverse-transcription quantitative PCR (dirRT-qPCR) assay in a centrifugal microfluidic platform

The coronavirus disease 2019 (COVID-19) pandemic, caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has posed a threat to public health worldwide. Also, influenza virus has caused a large number of deaths annually. Since co-infection of SARS-CoV-2 and influenza virus, which share similar symptoms, hampers current treatment efficiency, multiple simultaneous detection of these viruses is needed to provide the right treatment for patients. We developed a microfluidic disc-direct RT-qPCR (dirRT-qPCR) assay for rapid multiplex detection of SARS-CoV-2, influenza A and B viral infection in pharyngeal swab samples in an automated manner. Choices of the DNA polymerase, concentrations of dTPs and MgCl2 were characterized to optimize the assay. A detection limit of 2 × 101 copies per reaction was found in all three viral RNAs with as little as 2 μL of swab samples. The accuracy of our assay was evaluated with 2127 clinical swab samples of infection with these three viruses and healthy controls, and it possessed a consistency rate of 100, 99.54 and 99.25% in SARS-CoV-2, influenza A and B detection in comparison to standard RT-qPCR. The reported scheme of our assay is capable of screening other viral infections for up to 16 targets simultaneously. The whole diagnosis could be completed in 1.5 hours after simple sample loading by a non-technical expert. This constitutes an enabling strategy for large-scale point-of-care screening of multiple viral infections, which ultimately lead to a pathway for resolving the critical issue of early diagnosis for the prevention and control of viral outbreaks.

Mixing Optimization in Grooved Serpentine Microchannels

Computational fluid dynamics modeling at Reynolds numbers ranging from 10 to 100 was used to characterize the performance of a new type of micromixer employing a serpentine channel with a grooved surface. The new topology exploits the overlap between the typical Dean flows present in curved channels due to the centrifugal forces experienced by the fluids, and the helical flows induced by slanted groove-ridge patterns with respect to the direction of the flow. The resulting flows are complex, with multiple vortices and saddle points, leading to enhanced mixing across the section of the channel. The optimization of the mixers with respect to the inner radius of curvature (R_in) of the serpentine channel identifies the designs in which the mixing index quality is both high (M > 0.95) and independent of the Reynolds number across all the values investigated.

Amplification-free, sequence-specific 16S rRNA detection at 1 aM

A nucleic acid amplification-free, optics-free platform has been demonstrated for sequence-specific detection of Escherichia coli (E. coli) 16S rRNA at 1 aM (10-18 M) against a 106-fold (1 pM) background of Pseudomonas putida (P. putida) RNA. This work was driven by the need for simple, rapid, and low cost means for species-specific bacterial detection at low concentration. Our simple, conductometric sensing device functioned by detecting blockage of a nanopore fabricated in a sub-micron-thick glass membrane. Upon sequence-specific binding of target 16S rRNA, otherwise charge-neutral, PNA oligonucleotide probe-polystyrene bead conjugates become electrophoretically mobile and are driven to the glass nanopore of lesser diameter, which is blocked, thereby generating a large, sustained and readily observable step decrease in ionic current. No false positive signals were observed with P. putida RNA when this device was configured to detect E. coli 16S rRNA. Also, when a universal PNA probe complementary to the 16S rRNA of both E. coli and P. putida was conjugated to beads, a positive response to rRNA of both bacterial species was observed. Finally, the device readily detected E. coli at 10 CFU mL-1 in a 1 mL sample, also against a million-fold background of viable P. putida. These results suggest that this new device may serve as the basis for small, portable, low power, and low-cost systems for rapid detection of specific bacterial species in clinical samples, food, and water.

Mixing Enhancement in Serpentine Micromixers with a Non-Rectangular Cross-Section

In this numerical study, a new type of serpentine micromixer involving mixing units with a non-rectangular cross-section is investigated. Similar to other serpentine/spiral shaped micromixers, the design exploits the formation of transversal vortices (Dean flows) in pressure-driven systems, associated with the centrifugal forces experienced by the fluid as it is confined to move along curved geometries. In contrast with other previous designs, though, the use of non-rectangular cross-sections that change orientation between mixing units is exploited to control the center of rotation of the transversal flows formed. The associated extensional flows that thus develop between the mixing segments complement the existent rotational flows, leading to a more complex fluid motion. The fluid flow characteristics and associated mixing are determined numerically from computational solutions to Navier⁻Stokes equations and the concentration-diffusion equation. It is found that the performance of the investigated mixers exceeds that of simple serpentine channels with a more consistent behavior at low and high Reynolds numbers. An analysis of the mixing quality using an entropic mixing index indicates that maximum mixing can be achieved at Reynolds numbers as small as 20 in less than four serpentine mixing units.

The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives

The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.

PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli) 16S rRNA at 10 fM, which corresponds to ~100-1000 colony forming units/mL (CFU/mL) depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD) of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids.

Microfluidics-Based PCR for Fusion Transcript Detection

The microfluidic technology allows the production of network of submillimeter-size fluidic channels and reservoirs in a variety of material systems. The microfluidic-based polymerase chain reaction (PCR) allows automated multiplexing of multiple samples and multiple assays simultaneously within a network of microfluidic channels and chambers that are co-ordinated in controlled fashion by the valves. The individual PCR reaction is performed in nanoliter volume, which allows testing on samples with limited DNA and RNA. The microfluidics devices are used in various types of PCR such as digital PCR and single molecular emulsion PCR for genotyping, gene expression, and miRNA expression. In this chapter, the use of a microfluidics-based PCR for simultaneous screening of 14 known fusion transcripts in patients with leukemia is described.

Status and perspective of lab-on-a-chip systems for common diseases: a systematic review from 2003 to 2013

BACKGROUND

Lab-on-a-chip systems (LOCs) are a useful aid for the individualization of therapeutic algorithms at the point-of-care.

MATERIALS & METHODS

We performed a systematic literature review on LOCs for diseases with a global impact for healthcare.

RESULTS

A total of 1007 articles matched the previously specified search criteria, thereof 65 studies could be included in this review. A total of 55 different LOCs were evaluated, most for diagnosis or monitoring of cancer (n = 24). For other diseases we found considerably less analyzed LOCs. The analytical performance of the LOCs was usually very good, 37 (67%) LOCs had a sensitivity higher than 90%.

CONCLUSION

Although LOC systems performance has been positively evaluated in the great majority of studies, the testing was mostly limited to the research laboratory setting rather than real-world scenarios.

Diagnostic lab-on-a-chip systems at the doctor's office: a survey amongst German physicians in routine medical care

AIM & METHOD

We conducted a physician's survey to ask the potential 'users' about needs and options for lab-on-a-chip systems (LOCs) in their office to provide information about the feasibility of the implementation of LOCs into the healthcare system.

RESULTS

From a random sample of 300 questionnaires, 61 were returned. The willingness to use LOCs is very high (91.9%) and only 6.5% mentioned that they would continue to use conventional tests strictly in the future. Reliability is seen as the most important prerequisite for a successful implementation (85%).

CONCLUSION

Generally, physicians are very open-minded and positive regarding the implementation of LOCs in routine care.

Rapid and sensitive detection of canine distemper virus by one-tube reverse transcription-insulated isothermal polymerase chain reaction

Background

Canine distemper virus (CDV) has been associated with outbreaks of canine infectious respiratory disease in shelters and boarding kennel environments. POCKIT^TM Nucleic Acid Analyzer is a field-deployable device capable of generating automatically interpreted insulated isothermal polymerase chain reaction (iiPCR) results from extracted nucleic acid within one hour. In this study, reverse transcription iiPCR (RT-iiPCR) was developed to facilitate point-of-need diagnosis of CDV infection.

Results

Analytical sensitivity (limit of detection 95%) of the established CDV RT-iiPCR was about 11 copies of in vitro transcribed RNA per reaction. CDV RT-iiPCR generated positive signals from CDV, but not Bordetella bronchiseptica, canine parvovirus, canine herpesvirus, canine adenovirus 2, canine influenza virus (subtype H3N8), canine parainfluenza virus, and canine respiratory coronavirus. To evaluate accuracy of the established reaction in canine distemper clinical diagnosis, 110 specimens from dogs, raccoons, and foxes suspected with CDV infection were tested simultaneously by CDV RT-iiPCR and real-time RT-PCR. CDV RT-iiPCR demonstrated excellent sensitivity (100%) and specificity (100%), compared to real-time RT-PCR.

Conclusions

The results indicated an excellent correlation between RT-iiPCR and a reference real time RT-PCR method. Working in a lyophilized format, the established method has great potential to be used for point-of-care diagnosis of canine distemper in animals, especially in resource-limited facilities.

An evaluation of synthetic and natural supravital stains for the cytological examination of dissociated cells in a microfluidic channel

OBJECTIVE

Advances in biotechnology will result in paradigm shifts in both oncology and diagnostics. In pathology, methods such as microfluidics are being explored as delivery tools so that processed cells can serve dual purposes: conventional cytology-based diagnostics and recovery of the same cells for molecular assays. This wet mount-based approach to diagnosis will require staining of these cells by supravital dyes. This study was undertaken to determine the optimal supravital stain for the examination of cells in the wet mount preparations present in microfluidic platforms.

METHODS

Cells were dissociated from portions of tissue similar in size to a traditional core biopsy. These tissue-free cells were separately examined with two synthetic dyes and two natural dyes at varying dilutions.

RESULTS

Different dilutions of the synthetic dyes toluidine blue and methylene blue resulted in varying degrees of staining, whereas different dilutions of the natural dyes resulted in fairly constant intensities of colour. These characteristics affected the visualization of cells in wet mount preparations: optimally titered synthetic dyes gave better nuclear detail and cytoplasmic contrast.

CONCLUSIONS

All four dyes stained the test cells, but to different degrees and intensities. In our assessment, optimally titered synthetic dyes were better suited to the wet mount approach of microfluidics when compared with natural dyes.

Integrated DNA and RNA extraction and purification on an automated microfluidic cassette from bacterial and viral pathogens causing community-acquired lower respiratory tract infections

In this paper, we describe the development of an automated sample preparation procedure for etiological agents of community-acquired lower respiratory tract infections (CA-LRTI). The consecutive assay steps, including sample re-suspension, pre-treatment, lysis, nucleic acid purification, and concentration, were integrated into a microfluidic lab-on-a-chip (LOC) cassette that is operated hands-free by a demonstrator setup, providing fluidic and valve actuation. The performance of the assay was evaluated on viral and Gram-positive and Gram-negative bacterial broth cultures previously sampled using a nasopharyngeal swab. Sample preparation on the microfluidic cassette resulted in higher or similar concentrations of pure bacterial DNA or viral RNA compared to manual benchtop experiments. The miniaturization and integration of the complete sample preparation procedure, to extract purified nucleic acids from real samples of CA-LRTI pathogens to, and above, lab quality and efficiency, represent important steps towards its application in a point-of-care test (POCT) for rapid diagnosis of CA-LRTI.