Ultrafast Microfluidic Immunoassays Towards Real-time Intervention of Cytokine Storms

Biomarker-guided precision medicine holds great promise to provide personalized therapy with a good understanding of the molecular or cellular data of an individual patient. However, implementing this approach in critical care uniquely faces enormous challenges as it requires obtaining “real-time” data with high sensitivity, reliability, and multiplex capacity near the patient’s bedside in the quickly evolving illness. Current immunodiagnostic platforms generally compromise assay sensitivity and specificity for speed or face significantly increased complexity and cost for highly multiplexed detection with low sample volume. This thesis introduces two novel ultrafast immunoassay platforms: one is a machine learning-based digital molecular counting assay, and the other is a label-free nano-plasmonic sensor integrated with an electrokinetic mixer. Both of them incorporate microfluidic approaches to pave the way for near-real-time interventions of cytokine storms. In the first part of the thesis, we present an innovative concept and the theoretical study that enables ultrafast measurement of multiple protein biomarkers (<1 min assay incubation) with comparable sensitivity to the gold standard ELISA method. The approach, which we term “pre-equilibrium digital enzyme-linked immunosorbent assay” (PEdELISA) incorporates the single-molecular counting of proteins at the early, pre-equilibrium state to achieve the combination of high speed and sensitivity. We experimentally demonstrated the assay’s application in near-real-time monitoring of patients receiving chimeric antigen receptor (CAR) T-cell therapy and for longitudinal serum cytokine measurements in a mouse sepsis model. In the second part, we report the further development of a machine learning-based PEdELISA microarray data analysis approach with a significantly extended multiplex capacity using the spatial-spectral microfluidic encoding technique. This unique approach, together with a convolutional neural network-based image analysis algorithm, remarkably reduced errors faced by the highly multiplexed digital immunoassay at low analyte concentrations. As a result, we demonstrated the longitudinal data collection of 14 serum cytokines in human patients receiving CAR-T cell therapy at concentrations < 10pg/mL with a sample volume < 10 µL and 5-min assay incubation. In the third part, we demonstrate 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. The platform comprises two low-cost modules: (i) a semi-automated fluidic dispensing module that can be operated inside a biosafety cabinet to minimize the exposure of technician to the virus infection and (ii) a compact fluorescence optical scanner for the potential near-bedside readout. The automated system has achieved high interassay precision (~10% CV) with high sensitivity (<0.4pg/mL). Our data revealed large subject-to-subject variability in patient responses to anti-inflammatory treatment for COVID-19, reaffirming the need for a personalized strategy guided by rapid cytokine assays. Lastly, an AC electroosmosis-enhanced localized surface plasmon resonance (ACE-LSPR) biosensing device was presented for rapid analysis of cytokine IL-1β among sepsis patients. The ACE-LSPR device is constructed using both bottom-up and top-down sensor fabrication methods, allowing the seamless integration of antibody-conjugated gold nanorod (AuNR) biosensor arrays with microelectrodes on the same microfluidic platform. Applying an AC voltage to microelectrodes while scanning the scattering light intensity variation of the AuNR biosensors results in significantly enhanced biosensing performance. The technologies developed have enabled new capabilities with broad application to advance precision medicine of life-threatening acute illnesses in critical care, which potentially will allow the clinical team to make individualized treatment decisions based on a set of time-resolved biomarker signatures.PHDMechanical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/163129/1/yujing_1.pd

Programmable graphene-based microfluidic sensor for DNA detection

This study presents the development of a lab-on-a-chip (LoC) by integrating a graphene field-effect transistor (FET) chip with a programmable microfluidic device for DNA detection. The real-time biochemical events on the graphene FET chip were monitored through Dirac voltage shift data from the portable graphene curve reader with changes dependent on the fluidic flow into the sensing interface by a fully automated programmable microfluidic system. High sensitivity with high reliability can be obtained with a nine-graphene sensor layout on a single chip. The portable graphene curve reader also provides a tunable electrical parameter setup and straightforward data acquisition. Fluidic control was performed through a multi-position valve, allowing sequential commands for liquid injection into the polydimethylsiloxane (PDMS) flow cell mounted on the sensing chip. The flow cell design with impinging jet geometry and the microfluidic system packaging offer high precision and portability as a less laborious and low-cost sensing setup. The merged system allows for various functionalities, including probe DNA (pDNA) immobilization, a blocking step, and DNA hybridization with stable signal output autonomously, even in a long-run experimental setup. As a DNA sensor, the proposed prototype has demonstrated a high sensitivity of ~44 mV/decade of target DNA concentration, with an outstanding limit of detection (LoD) of ~0.642 aM, making it one of the most sensitive sensors reported up to date. The programmable device has demonstrated essential versatilities for biomolecular detection in a fully portable and automated platform.This research is supported by PORTGRAPHE-Control of Port and Douro Wines authenticity using graphene DNA sensors project co-funded by Fundação para a Ciência e a Tecnologia (FCT) Portugal (PTDC/BIA-MOL/31069/2017) and the ERDF through COMPETE2020 (POCI-01–0145-FEDER-031069). One of the authors (Telma Domingues) acknowledges a Ph.D. grant from Fundação para a Ciência e a Tecnologia (FCT) Portugal (SFRH/BD/08181/2020). FCT partially supported University of Minho´s research in the Strategic Funding UIDB/04650/2020

Microfluidic Flow Sensing Approaches

Precise flow metrology has an increasing demand in many microfluidic related applications. At the scale and scope of interests, Capillary number instead of Reynold number defines the flow characteristics. The interactions between fluid medium and flow channel surface or the surface tension, cavitation, dissolution, and others play critical roles in microfluidic flow metrology. Conventional flow measurement approaches are not sufficient for solving these issues. This chapter will review the currently available products on the market, their microfluidic flow sensing technologies, the technologies with research and development, the major factors impacting flow metrology, and the prospective sensing approaches for future microfluidic flow sensing

Microfluidic Selection of Aptamers towards Applications in Precision Medicine

Precision medicine represents a shift in medicine where large datasets are gathered for massive patient groups to draw correlations between disease cohorts. An individual patient can then be compared to these large datasets to determine the best treatment strategy. While electronic health records and next generation sequencing techniques have enabled much of the early applications for precision medicine, the human genome only represents a fraction of the information present and important to a person’s health. A person’s proteome (peptides and proteins) and glycome (glycans and glycosylation patterns) contain biomarkers that indicate health and disease; however, tools to detect and analyze such biomarkers remain scarce. Thus, precision medicine databases are lacking a major source of phenotypic data due to the absence of available methods to explore these domains, despite the potential of such data to allow further stratification of patients and individualized therapeutic strategies. Available methods to detect non-nucleic acid biomarkers are currently not well suited to address the needs of precision medicine. Mass spectrometry techniques, while capable of generating high throughput data, lack standardization, require extensive preparative steps, and have many sources of errors. Immunoassays rely on antibodies which are time consuming and expensive to produce for newly discovered biomarkers. Aptamers, analogous to antibodies but composed of nucleotides and isolated through in vitro methods, have potential to identify non-nucleic acid biomarkers but methods to isolate aptamers remain labor and resource intensive and time consuming. Recently, microfluidic technology has been applied to the aptamer discovery process to reduce the aptamer development time, while consuming smaller amounts of reagents. Methods have been demonstrated that employ capillary electrophoresis, magnetic mixers, and integrated functional chambers to select aptamers. However, these methods are not yet able to fully integrate the entire aptamer discovery process on a single chip and must rely on off-chip processes to identify aptamers. In this thesis, new approaches for aptamer selection are developed that aim to integrate the entire process for aptamer discovery on a single chip. These approaches are capable of performing efficient aptamer selection and polymerase chain reaction based amplification while utilizing highly efficient bead-based reactions. The approaches use pressure driven flow, electrokinetic flow or a combination of both to transfer aptamer candidates through multiple rounds of affinity selection and PCR amplification within a single microfluidic device. As such, the approaches are capable of isolating aptamer candidates within a day while consuming <500 µg of a target molecule. The utility of the aptamer discovery approach is then demonstrated with examples in precision medicine over a broad spectrum (small molecule to protein) of molecular targets. Seeking to demonstrate the potential of the device to generate probes capable of accessing the human glycome (an emerging source of precision medicine biomarkers), aptamers are isolated against gangliosides GM1, GM3, and GD3, and a glycosylated peptide. Finally, personalized, patient specific aptamers are isolated against a multiple myeloma patient serum sample. The aptamers have high affinity only for the patient derived antibody

Investigation into the Use of Microfluidics in the Manufacture of Metallic Gold-Coated Iron Oxide Hybrid Nanoparticles

Hybrid iron oxide-gold nanoparticles are of increasing interest for applications in nanomedicine, photonics, energy storage, etc. However, they are often difficult to synthesise without experience or 'know-how'. Additionally, standard protocols do not allow for scale up, and this is significantly hindering their future potential. In this study, we seek to determine whether microfluidics could be used as a new manufacturing process to reliably produce hybrid nanoparticles with the line of sight to their continuous manufacture and scaleup. Using a Precision Nano NanoAssemblr Benchtop(R) system, we were able to perform the intermediate coating steps required in order to construct hybrid nanoparticles around 60 nm in size with similar chemical and physical properties to those synthesised in the laboratory using standard processes, with Fe/Au ratios of 1:0.6 (standard) and 1:0.7 (microfluidics), indicating that the process was suitable for their manufacture with optimisation required in order to configure a continuous manufacturing plant

Microfluidic Processes for Synthesis of Plasmonic Nanomaterials

Ph.DDOCTOR OF PHILOSOPH

A Portable and Automatic Biosensing Instrument for Detection of Foodborne Pathogenic Bacteria in Food Samples

Foodborne diseases are a growing public health problem. In recent years, many rapid detection methods have been reported, but most of them are still in lab research and not practical for use in the field. In this study, a portable and automatic biosensing instrument was designed and constructed for separation and detection of target pathogens in food samples using nanobead-based magnetic separation and quantum dots (QDs)-labeled fluorescence measurement. The instrument consisted of a laptop with LabVIEW software, a data acquisition card (DAQ), a fluorescent detector, micro-pumps, stepper motors, and 3D printed tube holders. First, a sample in a syringe was mixed with magnetic nanobead-antibody (MNB-Ab) conjugates and then injected to a low binding reaction tube. After incubation and magnetic separation, target bacterial cells were captured and collected and the solution was pumped out. Then the QD-antibody (QD-Ab) conjugates were pumped into the reaction tube to form the MNB-Ab-cell-Ab-QD complexes that were then collected by magnetic separation and resuspended in PBS buffer solution through air pressure control. Finally, the sample solution was pushed into the detection tube by an air pump and the fluorescence intensity was measured using a fluorescent detector. A virtual instrument (VI) was programmed using LabVIEW software to provide a platform for magnetic separation, fluorescent measurement, data processing, and control. The DAQ was used for data communication. The results showed that the separation efficiency of this instrument was 78.3 ± 3.4% and 60.7 ± 4.2% for E. coli O157:H7 in pure culture and ground beef samples, respectively. The limit of detection was 3.98 × 103 and 6.46 × 104 CFU/mL in pure culture and ground beef samples, respectively. Sample preparation and detection could be finished in 2 hours. The instrument was portable and automatic with great potential to serve as a more effective tool for in-field/on-line detection of foodborne pathogenic bacteria in food products

SCALABLE CONTINUOUS-FLOW PROCESSES FOR MANUFACTURING PLASMONIC NANOMATERIALS

Master'sMASTER OF ENGINEERIN

Microfluidic devices interfaced to matrix-assisted laser desorption/ionization mass spectrometry for proteomics

Microfluidic interfaces were developed for off-line matrix-assisted laser desorption/ionization mass spectrometry (MALDI). Microfluidic interfaces allow samples to be manipulated on-chip and deposited onto a MALDI target plate for analysis. For this research, microfluidic culturing devices and automated digestion and deposition microfluidic chip platforms were developed for the identification of proteins. The microfluidic chip components were fabricated on a poly(methyl methacrylate), PMMA, wafer using the hot embossing method and a molding tool with structures prepared via micromilling. One of the most important components of the chip system was a trypsin microreactor. An open channel microreactor was constructed in a 100 µm wide and 100 µm deep channel with a 4 cm effective channel length. This device integrated frequently repeated steps for MALDI-based proteomics such as digestion, mixing with a matrix solution, and depositing onto a MALDI target. The microreactor provided efficient digestion of proteins at a flow rate of 1 µL/min with a residence time of approximately 24 s in the reaction channel. An electrokinetically driven microreactor was also developed using a micropost structured chip for digestion. The micropost chip had a higher digestion efficiency due to the higher surface area-to-volume ratio in the channel. Also, the electrokinetic flow eliminated the need for an external pumping system and gave a flat flow profile in the microchannel. The post microreactor consisted of a 4 cm × 200 µm × 50 µm microfluidic channel with trypsin immobilized on an array of 50 µm in diameter micropost support structures with a 50 µm edge-to-edge inter-post spacing. This micropost reactor was also used for fingerprint analysis of whole bacterial cells. The entire tryptic digestion and deposition procedure for intact bacteria took about 1 min. A contact deposition solid-phase bioreactor coupled with MALDI-TOF MS allowed for low-volume fraction deposition with a smaller spot size and a higher local concentration of the analyte. A bacterial cell-culturing chip was constructed for growing cells on-chip followed by off-line MALDI analysis. Coupling MALDI-TOF MS whole cell analysis with microfluidic culturing resulted in more consistent spectra as well as reduction of the total processing time. The microfluidic cell culturing was performed in a PMMA chip with a polydimethylsiloxane (PDMS) cover to allow gas permeation into the culture channel, which contained a 2.1 μL volume active culture chamber. After incubation of E. coli in a microfluidic culture device at 37 ℃ for 24 h, the cultured cells were analyzed with MALDI MS. Also, a microfluidic cell culture device containing continuous perfusion of culture medium was developed using a polycarbonate membrane. This microfluidic culturing format was improved with a fluidic manifold and thermostatted microheaters. Fingerprint mass spectra distinguishing E. coli strains tested were obtained after a 6 h incubation time, which was shorter compared to the 24 h incubation time using conventional culturing techniques. In addition, an enhanced identification procedure for bacteria was achieved by integrating on-chip digestion of cultured bacteria

High Throughput Screening for Enzyme Modulators Using Segmented Flow Coupled to Electrospray Ionization-Mass Spectrometry.

In drug discovery, it is important to use high throughput screening (HTS) technologies to rapidly identify active compounds for biological targets (usually enzymes) from large chemical libraries. The state of art strategy for HTS is coupling multiwell-plates (MWPs) to optical readers. Higher throughput, less reagent use and minimal labeling are always pursued in HTS. Mass spectrometry (MS) is a powerful label-free analyzer due to its high speed and sensitivity. Segmented flow (droplets) can reliably manipulate nanoliter samples and miniaturize reactions with high precision and automation. Novel high throughput screening systems have been developed by interfacing oil-segmented droplets to electrospray ionization (ESI)-MS. To miniaturize a screening, we designed an all-droplet system for conducting assays inside nanoliter droplets. A microfabricated reagent addition device was used for injecting multiple reagents into the droplet array of test compounds to initiate enzymatic reactions. The reaction droplets were directly analyzed by ESI-MS. This all-droplet system was demonstrated by a cathepsin B inhibitor screening with high reliability (Z-factor = 0.8), high analysis rate (0.8 Hz) and straightforward interpretation. Reagents consumption was at picomoles to femtomole level, which is 1000-fold less than the traditional MWP-based assays. Integrating droplet-ESI-MS with existing MWPs screening workflow can extend the application of both systems. With this concept, we developed a ‘MS plate reader’ (MSPR). It can reformat 3072 samples from eight 384-well plates into oil-segmented droplets in 13 min (4.5 Hz), and then analyze them in 30 min (up to 2 Hz). Using MSPR, a label-free screen for cathepsin B inhibitors against 1280 chemicals was completed in 45 min (triplicate assay, 1.6 Hz). 11 novel inhibitors were identified and validated. We also developed MS assays for two health beneficial enzymes: SIRT1 and SIRT6. Both assays are applicable to large-scale screenings using MSPR. An 80-compound pilot screening for SIRT1 modulators identified 4 strong inhibitors (> 50% inhibition), all of which were confirmed by dose-dependent experiments. A 25-compound test screening of SIRT6 modulators demonstrated the reliability of this assay by identifying the known activator (> 200% activation). It also showed that the single assay is as robust (Z-factor=0.6) as the replicated assay.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111582/1/shuwens_1.pd