A reusable microfluidic device provides continuous measurement capability and improves the detection limit of digital biology

Digital detection of proteins

This paper reviews methods for detecting proteins based on molecular digitization, i.e., the isolation and detection of single protein molecules or singulated ensembles of protein molecules. The single molecule resolution of these methods has resulted in significant improvements in the sensitivity of immunoassays beyond what was possible using traditional "analog" methods: the sensitivity of some digital immunoassays approach those of methods for measuring nucleic acids, such as the polymerase chain reaction (PCR). The greater sensitivity of digital protein detection has resulted in immuno-diagnostics with high potential societal impact, e.g., the early diagnosis and therapeutic intervention of Alzheimer's Disease. In this review, we will first provide the motivation for developing digital protein detection methods given the limitations in the sensitivity of analog methods. We will describe the paradigm shift catalyzed by single molecule detection, and will describe in detail one digital approach - which we call digital bead assays (DBA) - based on the capture and labeling of proteins on beads, identifying "on" and "off" beads, and quantification using Poisson statistics. DBA based on the single molecule array (Simoa) technology have sensitivities down to attomolar concentrations, equating to ∼10 proteins in a 200 μL sample. We will describe the concept behind DBA, the different single molecule labels used, the ways of analyzing beads (imaging of arrays and flow), the binding reagents and substrates used, and integration of these technologies into fully automated and miniaturized systems. We provide an overview of emerging approaches to digital protein detection, including those based on digital detection of nucleic acids labels, single nanoparticle detection, measurements using nanopores, and methods that exploit the kinetics of single molecule binding. We outline the initial impact of digital protein detection on clinical measurements, highlighting the importance of customized assay development and translational clinical research. We highlight the use of DBA in the measurement of neurological protein biomarkers in blood, and how these higher sensitivity methods are changing the diagnosis and treatment of neurological diseases. We conclude by summarizing the status of digital protein detection and suggest how the lab-on-a-chip community might drive future innovations in this field.

Recent Advances in Digital Biosensing Technology

Digital biosensing assays demonstrate remarkable advantages over conventional biosensing systems because of their ability to achieve single-molecule detection and absolute quantification. Unlike traditional low-abundance biomarking screening, digital-based biosensing systems reduce sample volumes significantly to the fL-nL level, which vastly reduces overall reagent consumption, improves reaction time and throughput, and enables high sensitivity and single target detection. This review presents the current technology for compartmentalizing reactions and their applications in detecting proteins and nucleic acids. We also analyze existing challenges and future opportunities associated with digital biosensing and research opportunities for developing integrated digital biosensing systems.

An overview of proteomic methods for the study of 'cytokine storms'

Introduction: The cytokine storm is a form of excessive systemic inflammatory reaction triggered by a myriad of factors that may lead to multi-organ failure, and finally to death. The cytokine storm can occur in a number of infectious and noninfectious diseases including COVID-19, sepsis, ebola, avian influenza, and graft versus host disease, or during the severe inflammatory response syndrome.Area covered: This review mainly focuses on the most common and well-known methods of protein studies (PAGE, SDS-PAGE, and high- performance liquid chromatography). It also discusses other modern technologies in proteomics like mass spectrometry, soft ionization techniques, cytometric bead assays, and the next generation of microarrays that have been used to get an in-depth understanding of the pathomechanisms involved during the cytokine storm.Expert opinion: Overactivation of leukocytes drives the production and secretion of inflammatory cytokines fueling the cytokine storm. These events lead to a systemic hyper-inflammation, circulatory collapse and shock, and finally to multiorgan failure. Therefore, monitoring the patient's systemic cytokine levels with proteomic technologies that are redundant, economical, and require minimal sample volume for real-time assessment might help in a better clinical evaluation and management of critically ill patients.

A digital protein microarray for COVID-19 cytokine storm monitoring

Despite widespread concern regarding cytokine storms leading to severe morbidity in COVID-19, rapid cytokine assays are not routinely available for monitoring critically ill patients. We report the clinical application of a digital protein microarray platform for rapid multiplex quantification of cytokines from critically ill COVID-19 patients admitted to the intensive care unit (ICU) at the University of Michigan Hospital. The platform comprises two low-cost modules: (i) a semi-automated fluidic dispensing/mixing module that can be operated inside a biosafety cabinet to minimize the exposure of the technician to the virus infection and (ii) a 12-12-15 inch compact fluorescence optical scanner for the potential near-bedside readout. The platform enabled daily cytokine analysis in clinical practice with high sensitivity (<0.4 pg mL-1), inter-assay repeatability (∼10% CV), and rapid operation providing feedback on the progress of therapy within 4 hours. This test allowed us to perform serial monitoring of two critically ill patients with respiratory failure and to support immunomodulatory therapy using the selective cytopheretic device (SCD). We also observed clear interleukin-6 (IL-6) elevations after receiving tocilizumab (IL-6 inhibitor) while significant cytokine profile variability exists across all critically ill COVID-19 patients and to discover a weak correlation between IL-6 to clinical biomarkers, such as ferritin and C-reactive protein (CRP). Our data revealed large subject-to-subject variability in patients' response to COVID-19, reaffirming the need for a personalized strategy guided by rapid cytokine assays.

A Digital Protein Microarray for COVID-19 Cytokine Storm Monitoring

Despite widespread concern for cytokine storms leading to severe morbidity in COVID-19, rapid cytokine assays are not routinely available for monitoring critically ill patients. We report the clinical application of a machine learning-based digital protein microarray platform for rapid multiplex quantification of cytokines from critically ill COVID-19 patients admitted to the intensive care unit (ICU) at the University of Michigan Hospital. The platform comprises two low-cost modules: (i) a semi-automated fluidic dispensing/mixing module that can be operated inside a biosafety cabinet to minimize the exposure of technician to the virus infection and (ii) a 12-12-15 inch compact fluorescence optical scanner for the potential near-bedside readout. The platform enabled daily cytokine analysis in clinical practice with high sensitivity (<0.4pg/mL), inter-assay repeatability (~10% CV), and near-real-time operation with a 10 min assay incubation. A cytokine profiling test with the platform allowed us to observe clear interleukin-6 (IL-6) elevations after receiving tocilizumab (IL-6 inhibitor) while significant cytokine profile variability exists across all critically ill COVID-19 patients and to discover a weak correlation between IL-6 to clinical biomarkers, such as Ferritin and CRP. Our data revealed large subject-to-subject variability in a patient's response to anti-inflammatory treatment for COVID-19, reaffirming the need for a personalized strategy guided by rapid cytokine assays.

Mobile imaging platform for digital influenza virus counting

Droplet-based digital bioassays enable highly sensitive and quantitative analysis of biomolecules, and are thought to be suitable for point-of-care diagnosis. However, digital bioassays generally require fluorescence microscopy for detection, which is too large for point-of-care testing. Here, we developed a simple smartphone-based mobile imaging platform for digital bioassays. The size of the mobile imaging platform was 23 × 10 × 7 cm (length × width × height). With this platform, a digital enzyme assay of bovine alkaline phosphatase was successfully completed. Digital influenza virus counting-based on a fluorogenic assay for neuraminidase activity of the virus-was also demonstrated. Distinct fluorescence spots derived from single virus particles were observed with the mobile imaging platform. The number of detected fluorescence spots showed good linearity against the virus titer, suggesting that high sensitivity and quantification were achieved, although the imaging with the mobile platform detected 60% of influenza virus particles that were identified with conventional fluorescence microscopy. The lower detection efficiency is due to its relatively lower signal-to-noise ratio than that found with conventional microscopes, and unavoidable intrinsic heterogeneity of neuraminidase activity among virus particles. Digital influenza virus counting with the mobile imaging platform still showed 100 times greater sensitivity than that with a commercial rapid influenza test kit. Virus detection of clinical samples was also successfully demonstrated, suggesting the potential to realize a highly sensitive point-of-care system for influenza virus detection with smartphones.

Antibody-free digital influenza virus counting based on neuraminidase activity

There is large demand for a quantitative method for rapid and ultra-sensitive detection of the influenza virus. Here, we established a digital influenza virus counting (DIViC) method that can detect a single virion without antibody. In the assay, a virion is stochastically entrapped inside a femtoliter reactor array device for the fluorogenic assay of neuraminidase, and incubated for minutes. By analyzing 600,000 reactors, the practical limit of detection reached the order of 103 (PFU)/mL, only 10-times less sensitive than RT-PCR and more than 1000-times sensitive than commercial rapid test kits (RIDTs). Interestingly, neuraminidase activity differed among virions. The coefficient of variance was 30-40%, evidently broader than that of alkaline phosphatase measured as a model enzyme for comparison, suggesting the heterogeneity in size and integrity among influenza virus particles. Sensitivity to oseltamivir also differed between virions. We also tested DIViC using clinical gargle samples that imposes less burden for sampling while with less virus titre. The comparison with RIDTs showed that DIViC was largely superior to RIDTs in the sensitivity with the clinical samples although a few false-positive signals were observed in some clinical samples that remains as a technical challenge.

Multiplexed detection of cancer biomarkers using a microfluidic platform integrating single bead trapping and acoustic mixing techniques

It is critical to reliably and rapidly detect multiple disease biomarkers in tiny liquid samples with high sensitivity to meet the growing demand for point-of-care diagnostics. This paper reports a microfluidic platform integrating magnetic-based single bead trapping in conjunction with acoustic micromixing for simultaneous detection of multiple cancer biomarkers within minutes. Individual beads retained by permalloy (NiFe81/19) microarray were used to capture biomarkers and facilitate the fluorescence identification. A numerical study indicates that the magnetic force keeping a bead in the trap is proportional to the thickness of the permalloy array and the external magnetic field strength, while inversely proportional to the size of the trap. The acoustic microstreaming activated by a piezo transducer was applied to generate fast-switching flow patterns to minimize the diffusion length scales. The flow at various driving frequencies was experimentally tested to achieve the optimal mixing effect. The flow field of the microstreaming was subsequently described by a mathematical model to understand the flow further. Finally, the prostate-specific antigen (PSA) and carcinoembryonic antigen (CEA) were employed as model analytes to demonstrate the capability of the platform for rapid biomarker detection. With the aid of acoustic micromixing, the detection can be finished in 20 minutes. The respective limit of detection of PSA and CEA is 0.028 ng mL-1 (0.8 pM) and 3.1 ng mL-1 (17 pM), which is respectively 1/142 and 1/3 of the cutoff value of PSA and CEA. Our results indicate this platform has great potential for the rapid detection of multiple biomarkers in future point-of-care diagnostics.

High-throughput single-molecule bioassay using micro-reactor arrays with a concentration gradient of target molecules

Micro-reactor arrays enable highly sensitive and quantitative bioassays at a single-molecule level. Accordingly, they are widely used for sensitive "digital" bioassays, e.g., digital PCR and digital ELISA. Despite high integration, individual reactors in digital bioassays are filled with a uniform reaction solution, thus limiting the ability to simultaneously conduct multiple bioassays under different conditions using integrated reactors in parallel, resulting in the loss of potential throughput. We developed micro-reactor arrays with a concentration gradient of target molecules, in which individual reactors sealed with a lipid-bilayer membrane contained a precise amount of target molecules. Using the arrays, we successfully demonstrated multiple single-molecule bioassays in parallel using alkaline phosphatase or α-hemolysin, key components in various biomedical sensors. This new platform extends the versatility of micro-reactor arrays and could enable further analytical and pharmacological applications.

Biocompatible Magnetic Nanocomposite Microcapsules as Microfluidic One-way Diffusion Blocking Valves with Ultra-low Opening Pressure

A one-of-a-kind biocompatible magnetic nanocomposite microcapsule is developed as an in-line passive valve that can be integrated with micropumps and microfluidics. The magnetic nanocomposites act as the core for building a valve that utilizes the magnetic force attraction for sealing the microfluidic channels. The nanocomposites, molded with commercial microtubings, are prepared by incorporating Fe3O4 nanoparticles into polyethylene-glycol (PEG). Parylene-C provides a flexible, biocompatible shell and moisture barrier for the microcapsule that enables deformation and sealing to the microfluidic channel wall. The highly customizable valve design offers easy scalability, and simplicity for integration into microfluidic systems. The presented magnetically-responsive microcapsule demonstrates reliable performance as a passive one-way valve that exhibits unique features and capabilities including effective flow-rectification with steady flows, extremely low leakage flows from backpressures at a rate of 4.7 nL/min kPa-1, successfully block 99.96% of the diffusion, and extremely low inlet flow opening pressure of 2.1 kPa.

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.

Heterotypic 3D tumor culture in a reusable platform using pneumatic microfluidics

The construction of a micro-platform capable of microscale control for continuous, dynamic, and high-throughput biomimetic tumor manipulation and analysis plays a significant role in biological and clinical research. Here, we introduce a pneumatic microstructure-based microfluidic platform for versatile three-dimensional (3D) tumor cultures. The manipulative potential of pneumatic microstructures in a fabrication-optimized microfluidic device can be stimulated to achieve ultra-repetitive (tens of thousands of times) and persistent (over several months) microfluidic control. We demonstrated that the microfluidic platform is reusable (dozens of times) for stable, reproducible, and high-throughput generation of tumors with uniform size. Various heterotypic and homotypic 3D tumor arrays can be produced successfully in the device based on robust pneumatic control. On-chip monitoring and analysis of tumor phenotypes and responses to different culture conditions and chemotherapies were also achieved in real-time in the microfluidic platform. The results indicate that fibroblasts cocultured with tumor cells positively promote the phenotypical appearance of heterotypic tumors. This microfluidic advancement offers a new methodological approach for the development of high-performance and non-disposable 3D culture systems and for tissue-mimicking cancer research. We believe that it could be valuable for various tumor-related research fields such as oncology, pharmacology, tissue engineering, and bioimaging.