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

Development of Immunoassay Using Graphene and Microfluidic Platforms.

Protein, as one of the most important functional biomolecules in the human body, plays a significant role in physiological responses and molecular diagnostics. Detecting the existence of proteins, quantifying concentration, and identifying protein types are therefore important techniques in many fields. Immunoassays are one of the major techniques relied on for protein detection. Immunoassays have been broadly applied in disease diagnosis, pharmaceutical development, food science, and environmental protection. The first part of this dissertation describes studies aimed at developing chemical vapor deposition (CVD) graphene as a large size protein biosensing platform. To utilize graphene as a biosensing platform, techniques to immobilize proteins on graphene are critical. In this dissertation work, carboxyl functional groups (-COOH) were created by graphene functionalization, and the functionalized graphene was characterized using Raman spectroscopy, X-ray photo spectroscopy (XPS), and fluorescence microscopy. The approach developed here provides information about protein coupling density and uniformity on large scale graphene (> cm2). The second and the third parts of the thesis describe the application of a microfluidic technique to two widely used protein detection methods – immunoblotting and dot blotting. The microfluidic systems were designed and fabricated to be easily interfaced with a common type of protein blotting membrane called polyvinylidene fluoride (PVDF) membrane. The microfluidic device was specifically applied to the antibody incubation step, which reduces antibody consumption and therefore also significantly reduces the cost of the assay. In microfluidic immunoblotting, an approach to activate the PVDF membrane to increase its protein binding capacity was developed. This was achieved by adding a surfactant Tween-20 to the antibody solution. The concentration of Tween-20 was optimized so that only the portion of the membrane within the channel region was activated. The system has been shown to be able to profile inflammatory signaling pathways. In microfluidic dot blotting, the influence of substrate hydrophobicity and protein concentrations on device design constraints were studied. Inflammatory cytokine detection using the developed microfluidic dot blotting system was determined. Altogether these experiments demonstrate that applying microfluidic techniques to protein immunoblotting and dot blotting improves detection efficiency, and reduces cost by utilizing less antibodies.PhDBiomedical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113501/1/huaining_1.pd

Biosensors for cardiac biomarkers detection: a review

The cardiovascular disease (CVD) is considered as a major threat to global health. Therefore, there is a growing demand for a range of portable, rapid and low cost biosensing devices for the detection of CVD. Biosensors can play an important role in the early diagnosis of CVD without having to rely on hospital visits where expensive and time-consuming laboratory tests are recommended. Over the last decade, many biosensors have been developed to detect a wide range of cardiac marker to reduce the costs for healthcare. One of the major challenges is to find a way of predicting the risk that an individual can suffer from CVD. There has been considerable interest in finding diagnostic and prognostic biomarkers that can be detected in blood and predict CVD risk. Of these, C-reactive protein (CRP) is the best known biomarker followed by cardiac troponin I or T (cTnI/T), myoglobin, lipoprotein-associated phospholipase A(2), interlukin-6 (IL-6), interlukin-1 (IL-1), low-density lipoprotein (LDL), myeloperoxidase (MPO) and tumor necrosis factor alpha (TNF-α) has been used to predict cardiovascular events. This review provides an overview of the available biosensor platforms for the detection of various CVD markers and considerations of future prospects for the technology are addressed

Label-Free Biosensors for Cyokine Detection.

Cytokines are protein biomarkers secreted by immune cells that serve as mediators in the immune system. The functional phenotypes of immune cells are important in recognizing immune functions and often determined by the dynamic cytokine secretion behaviors of immune cells. As a result, many researchers have attempted to quantify cytokines to develop a new approach to immune diagnosis and therapy. The lack of rapid, sensitive, multiplexed time-course cytokine monitoring techniques poses significant challenges to these research efforts. To fill this technological gap, this thesis has developed label-free biosensing platforms for rapid and sensitive cytokine detection. In the first part of this thesis, an MoS2-based field-effect transistor (FET) biosensor was developed to detect cytokines. This work advanced critical device physics by leveraging the excellent electronic/structural properties of TMDCs in biosensing applications as well as the research capability in analyzing biomolecular interactions with a fM-level sensitivity. In the second part, we demonstrated a nanoparticle based localized surface plasmon resonance (LSPR) biosensing device integrated with microfluidic technology. The quantitative characterization of cytokine secretion behaviors from T-cells under an immunomodulation was studied at high temporal resolution. The biosensors achieved precise measurements with low sample volume, short assay time, high-sensitivity, and negligible sensor crosstalk. Data obtained from this study provided a comprehensive picture of the time-varying cellular functional response during immunosuppression. In the last part, integrated LSPR biosensor within a microfluidic system was developed for cell-based immune functional analysis. By placing cells near the sensing elements, we achieved in-situ measurement of the cytokine secretion behavior of immune cells. The extended function of this platform may further allow us to measure cytokine secretion rate of cells to extract both the magnitude and time constant of the cellular response to an immunological environmental change. Compared to previous labeling techniques for cytokine detection, the label-free FET and LSPR cytokine detection techniques provide rapid, highly sensitive biosensing platforms, suitable for capturing the dynamic nature of immune response. Furthermore, the multiplexed detection capability integrated in a microfluidic system enables us to understand the cytokine-regulated functional characteristics of immune system. These platforms hold significant promise for point-of-care applications in clinical settings.PhDMechanical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133316/1/ohbr_1.pd

Development and Application of Analytical Techniques for Evaluating Function in Pancreatic Islets of Langerhans.

Type 1 diabetes is caused by autoimmune destruction of insulin-secreting beta-cells found in the islets of Langerhans of the pancreas. Severe cases can be treated in a minimally invasive way by islet transplantation; however, islet transplantation has been limited by an inability to measure islet viability and potency prior to transplant. To address this need, we have developed a microfluidic platform to measure both intracellular calcium flux and insulin secretion, two important indicators of beta-cell function, at high temporal resolution during glucose treatment. Combining these measures on islets required methods for measuring fluorescence at two separate locations on a microfluidic system. To accomplish this objective, we used a 2-chip system in which perfusate was collected in fractions while intracellular calcium was measured using fluorescence imaging. The perfusate was subsequently analyzed for insulin by microchip electrophoresis with laser-induced fluorescence detection (MCE-LIF) using the same fluorescence microscope. We were able to distinguish first and second phase insulin secretion from batches of 8-10 islets with 80 s temporal resolution. Measured basal and peak first phase insulin secretion correlated well with previously reported results. Total analysis time using this system was <90 min. For an alternative approach to islet evaluation, we developed a metabolomic method to identify potential biomarkers of islet health for transplant. Using a miniaturized sample preparation method and HPLC-TOF-MS, we were able to identify 62 metabolites reliably in whole islet samples. To mimic damage that can occur during islet transplant, we induced oxidative stress in islets using hydrogen peroxide and measured their immediate metabolomic response as well as their response 1-4 h following stress removal. Increased concentrations of pentose phosphates, glucose-6-phosphate, and fructose bisphosphate in the immediate response corresponded to glycolysis blockage and possibly increased flux through the pentose phosphate pathway. Post-stress responses included increased levels of free fatty acids, phospholipids, long chain CoAs, and HMG-CoA as well blunted malonyl CoA concentrations, potentially relating to alterations in the glycerolipid/free fatty acid cycle and mevalonate pathway. These metabolites could comprise a metabolic signature of stressed cells for islet evaluation prior to transplantation.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113374/1/ccipolla_1.pd

Microengineered Biomaterials and Biosystems for Systems Immunology, Cancer Biology, and Stem Cell-based Regenerative Medicine.

Many exciting topics exist at the interface between biology and micro/nanotechnology. This dissertation will discuss interdisciplinary researches that leveraging the engineering advances in biomaterials, microfluidics and advanced manufacturing for new and better solutions for emerging problems in cancer biology, systems immunology, and stem cell-based regenerative medicine. First, this dissertation will discuss the potential of integrated microfluidic immunophenotyping assay device to perform rapid, accurate, and sensitive functional cellular immunophenotyping assays for target subpopulations of immune cells isolated directly from patient blood. This dissertation will also explore the possible technique using nanotopographic substrates for efficient capture of circulating tumor cells regardless of surface protein expression and cancer type, critical for early cancer diagnosis and for fundamental understanding of cancer metastasis. This dissertation will also provide a comprehensively profiling of the biophysical characteristics of inflammatory breast cancer stem cells at the single-cell level using multiple microengineered tools to delineate the live cell phenotypic characteristics of the model of the most metastatic breast cancer subtype. Last, this dissertation will further explore synthetic micro/nanoscale ex vivo cellular microenvironment for study and regulating human embryonic stem cell behaviors that are desirable for functional tissue engineering and regenerative medicine. These novel micro/nanoengineered functional biomaterials and biosystems will not only permit advances in engineering but also greatly contribute to improving human health.PhDMechanical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/108939/1/wqchen_1.pd

Lab-on-a-chip Thermoelectric and Solid-phase Immunodetection of Biochemical Analytes and Extracellular Vesicles: Experimental and Computational Analysis

Microfluidics is the technology of controlling and manipulating fluids at the microscale. Microfluidic platforms provide precise fluidic control coupled with low sample volume and an increase in the speed of biochemical reactions. Lab-on-a-chip platforms are used for detection and quantification of biochemical analytes, capture, and characterization of various proteins, sensitive analysis of cytokines, and isolation and detection of extracellular vesicles (EVs). This study focuses on the development of microfluidic and solid-phase capture pin platforms for the detection of cytokines, extracellular vesicles, and cell co-culture. The fabrication processes of the devices, experimental workflows, numerical analysis to identify optimal design parameters, and reproducibility studies have been discussed. Layer-by-layer assembly of polyelectrolytes has been developed to functionalize glass and stainless-steel substrates with biotin for the immobilization of streptavidinconjugated antibodies for selective capture of cytokines or EVs. Microstructure characterization techniques (SEM, EDX, and fluorescence microscopy) have been implemented to assess the efficiency of substrate functionalization. A detailed overview of current methods for purification and analysis of EVs is discussed as well. Additionally, the dissertation demonstrates the feasibility of a calorimetric microfluidic immunosensor with an integrated antimony-bismuth (Sb/Bi) thermopile sensor for the detection of cytokines with picomolar sensitivity. The developed platform can be used for the universal detection of both exothermic or endothermic reactions. A three-dimensional numerical model was developed to define the critical design parameters that enhance the sensitivity of the platform. Mathematical analyses identified the optimal combinations of substrate material and dimensions that will maximize the heat transfer to the sensor. Lab-on-a-chip cell co-culture platform with integrated pneumatic valve was designed, numerically characterized, and fabricated. This device enables the reversible separation of two cell culture chambers and serves as a tool for the effective analysis of cell-to-cell communication. Intercellular communication is mediated by extracellular vesicles. A protocol for the functionalization of stainless-steel probe with exosomespecific CD63 antibody was developed. The efficiency of the layer-by-layer deposition of polyelectrolytes and the effectiveness of biotin and streptavidin covalent boding were characterized using fluorescent and scanning electron microscopy

Manufacturing of human mesenchymal stem cells: the analytical challenges

It has been repeatedly proven that cell therapies can address many current unmet clinical treatment needs and also improve on current treatment options for various diseases, from neurological disorders to bone repair (Rosset et al. 2014; Corey et al. 2017). Though the potential of cell therapies has been demonstrated at a relatively small scale, the realisation of bringing cell based treatments to a larger market is hindered by the complexity of the product along with safety concerned and high production cost. Safety concerns can be informed with more in-depth analytical analysis of the product, however this in turn increase the costs involved in producing a cell therapy (Davie et al. 2012). Consequently the cost of analytical techniques also needs to be reduced, to address this need the area of microfluidic based bioanalytics holds much promise (Titmarsh et al. 2014). The culturing of human mesenchymal stem cells (hMSC) was used as a proof of concept model to demonstrate where improved bioanalytical and bioassay methods could be utilised in the production of cell therapies. Cells from four donors were cultured under three different oxygen environments and the conditioned medium assessed for pro-angiogenic capabilities using a tube formation bioassay and a proportion of the cytokine secretome profile measured using Luminex technology. Thorough secretome analysis it was shown that predicting cytokine levels based solely on the donor was not possible as the handling of the cells also had an influence on the secretome profile. The donor expression profiles did not behave in the same manner across all oxygen environments, for example in some donors IL-8 levels increased per cell at lower oxygen where as other donors showed a decrease per cell. While the tube formation assay showed some differences between donors in pro-angiogenic capabilities it also highlights the challenges with interpreting large data sets. The feasibility of using a microcapillary film (MCF) based enzyme-linked immunosorbent assay (ELISA) to detected two relevant cytokines, IL-8 and hepatocyte growth factor (HGF) was investigated. Following on from this work the development of a combined MCF ELISA assay with hMSC cell culture to produce a fully closed cell screening system was initiated. It was shown that it was feasible to measure IL-8 and HGF using the MCF ELISA platform but further work would need to be done to make the system more compatible with the manufacturing environment. In order to adapt the MCF to also be an hMSC culture platform the first challenge was to functionalise the Fluorinated Ethylene Propylene (FEP) surface of the MCF. It was concluded that a poly (vinyl- alcohol) (PVA) and gelatin mixture produced a homogenous coating to which a consistent level of hMSC would attach. This work was carried out on a flat surface; therefore steps were taken to adapt this knowledge into the MCF, while there was evidence of hMSCs present inside the MCF more work will need to be done to bring this concept to an established platform