Coupling immuno-magnetic capture with LC-MS/MS(MRM) as a sensitive, reliable, and specific assay for SARS-CoV-2 identification from clinical samples.

Recently, numerous diagnostic approaches from different disciplines have been developed for SARS-CoV-2 diagnosis to monitor and control the COVID-19 pandemic. These include MS-based assays, which provide analytical information on viral proteins. However, their sensitivity is limited, estimated to be 5 × 104 PFU/ml in clinical samples. Here, we present a reliable, specific, and rapid method for the identification of SARS-CoV-2 from nasopharyngeal (NP) specimens, which combines virus capture followed by LC-MS/MS(MRM) analysis of unique peptide markers. The capture of SARS-CoV-2 from the challenging matrix, prior to its tryptic digestion, was accomplished by magnetic beads coated with polyclonal IgG-α-SARS-CoV-2 antibodies, enabling sample concentration while significantly reducing background noise interrupting with LC-MS analysis. A sensitive and specific LC-MS/MS(MRM) analysis method was developed for the identification of selected tryptic peptide markers. The combined assay, which resulted in S/N ratio enhancement, achieved an improved sensitivity of more than 10-fold compared with previously described MS methods. The assay was validated in 29 naive NP specimens, 19 samples were spiked with SARS-CoV-2 and 10 were used as negative controls. Finally, the assay was successfully applied to clinical NP samples (n = 26) pre-determined as either positive or negative by RT-qPCR. This work describes for the first time a combined approach for immuno-magnetic viral isolation coupled with MS analysis. This method is highly reliable, specific, and sensitive; thus, it may potentially serve as a complementary assay to RT-qPCR, the gold standard test. This methodology can be applied to other viruses as well.

In Vitro Detection of Cellular Adjuvant Properties of Human Invariant Natural Killer T Cells.

Invariant natural killer T (iNKT) cells are a subset of T lymphocytes that play a crucial role in the tumor surveillance. The activation of iNKT cells by their specific ligand α-galactosylceramide (α-GalCer) induces the activation of dendritic cells (DCs) via reciprocal interaction, which results in the generation of cellular immunity against cancer. Here we describe a method to detect DC-mediated cellular adjuvant properties of human iNKT cells in vitro.

Clonogenic Culture of Mouse Thymic Epithelial Cells.

The thymus plays an essential role in the development and selection of T cells by providing a unique microenvironment that is mainly composed of thymic epithelial cells (TECs). We previously identified stem cells of medullary TECs (mTECs) that are crucial for central tolerance induction using a novel clonogenic culture system. We also found that medullary thymic epithelial stem cells (mTESCs) maintain life-long mTECs regeneration and central T cell self-tolerance in mouse models. The clonogenic efficiency of TECs in vitro is highly correlated to the TEC reconstitution activity in vivo. Here, we describe the clonogenic culture system to evaluate the self-renewing activity of TESCs. The colonies are derived from TESCs, are visualized and quantified by rhodamine-B staining on a feeder layer, and can be passaged in vitro. Thus, our system enables quantitative evaluation of TESC activity and is useful for dissecting the mechanisms that regulate TESC activity in physiological aging as well as in various clinical settings.

Electronic profiling of membrane antigen expression via immunomagnetic cell manipulation.

Membrane antigens control cell function by regulating biochemical interactions and hence are routinely used as diagnostic and prognostic targets in biomedicine. Fluorescent labeling and subsequent optical interrogation of cell membrane antigens, while highly effective, limit expression profiling to centralized facilities that can afford and operate complex instrumentation. Here, we introduce a cytometry technique that computes surface expression of immunomagnetically labeled cells by electrically tracking their trajectory under a magnetic field gradient on a microfluidic chip with a throughput of >500 cells per min. In addition to enabling the creation of a frugal cytometry platform, this immunomagnetic cell manipulation-based measurement approach allows direct expression profiling of target subpopulations from non-purified samples. We applied our technology to measure epithelial cell adhesion molecule expression on human breast cancer cells. Once calibrated, surface expression and size measurements match remarkably well with fluorescence-based measurements from a commercial flow cytometer. Quantitative measurements of biochemical and biophysical cell characteristics with a disposable cytometer have the potential to impact point of care testing of clinical samples particularly in resource limited settings.

Rapid prototyping of Nanoroughened polydimethylsiloxane surfaces for the enhancement of immunomagnetic isolation and recovery of rare tumor cells.

Traditional immunomagnetic assays for the isolation and recovery of circulating tumor cells (CTCs) usually require sophisticated device or intense magnetic field to simultaneously achieve high capture efficiency and high throughout. In this study, a simple microfluidic chip featured with nanoroughened channel substrate was developed for effectively capture and release of CTCs based on an immunomagnetic chip-based approach. The nanoroughened substrate aims to increase the cell-surface contact area, facilitate the immobilization of magnet particles (MPs) and accommodate cell attachment tendency. Hep3B tumor cells were firstly conjugated with MPs that were functionalized with anti-EpCAM. Comparing with the flat channel, MPs modified tumor cells can be more effectively captured on nanoroughened substrate at the presence of the magnetic field. Upon the removal of magnetic field, these captured cells can be released from the device and collected for further analysis. Under the optimum operating conditions, the capture efficiency of tumor cells was obtained as high as ~90% with a detection limit of 10 cell per mL. Additionally, recovery rates of trapped tumor cells at various densities all exceeded 90% and their biological potencies were well retained by investigating the cell attachment and proliferation. Therefore, the present approach may potentially be used in clinical CTC analysis for cancer diagnosis and prognosis as well as the fundamental understanding of tumor metastasis.

Magnetic nanocomposites: versatile tool for the combination of immunomagnetic separation with flow-based chemiluminescence immunochip for rapid biosensing of Staphylococcal enterotoxin B in milk.

Immunomagnetic separation (IMS) was combined with flow-based chemiluminescence sandwich immunoassays (CL-SIA) for the quantification of Staphylococcal enterotoxin B in milk. Therefore, iron oxide-shell silica-core magnetic nanocomposites were conjugated to biotinylated anti-SEB antibodies (MNC-IgGs). MNC-IgGs were applied successfully for (i) capturing SEB in milk samples by an affinity reaction, (ii) magnetophoretic collection on antibody spots in a channel of a flow-based immunochip, and (iii) sensitive enzymatic chemiluminescence detection of biotin labels by poly(horseradish peroxidase)-streptavidin. IMS was performed in 0.6 mL and 100 mL milk samples resulting in detection limits of 50 ng L-1 and 0.39 ng L-1, respectively, for the combined analytical method. It was shown that the assay sensitivity was dramatically improved by the combination of IMS with flow-based CL-SIA compared to CL-SIA directly applied with milk samples (detection limit 130 ng L-1). The IMS-CL-SIA has a time-to-result of 2-3 h. The reported combined analytical method can be used for a rapid control of SEB in complex food matrices such as milk. In future, even the monitoring of multiple contaminants in food or water may be performed by IMS-CL-SIA. Graphical abstract.

An integrated magnetic microfluidic chip for rapid immunodetection of the prostate specific antigen using immunomagnetic beads.

The authors describe an integrated microfluidic chip for immunodetection of the prostate specific antigen (PSA) by using giant magnetoimpedance (GMI) sensor. This chip contains an immunoreaction platform and a biomarker detection system. The immunoreaction platform contains an incubation chamber and a reactive chamber to implement immunological reaction in microfluidics. The system can detect PSA rapidly with ultra-high sensitivity. Both are fabricated by MEMS technology. Immunomagnetic beads (If PSA binds to its antibody (that is labeled with immunomagnetic beads; IMBs) it will be trapped on the surface of self-assembled film. Trapped IMBs generate a stray magnetic field under the magnetization of the external applied magnetic field and can be detected by the GMI sensor. The chip can detect PSA with a detection limit as low as 0.1 ng ∙ mL-1 and works in the 0.1 ng ∙ mL-1 to 20 ng ∙ mL-1 concentration range. Compared to established GMI biosensors, the magnetic microfluidic chip reduces assay time, and lends itself to fast detection. It also avoids complex handling steps, enhances reaction efficiency and decreases experimental errors. Graphical abstract An integrated magnetic microfluidic chip which contains immunoreaction platform and biomarker detection system was designed and microfabricated by micro-electromechanical systems (MEMS) technology to detect prostate specific antigen (PSA) rapidly, and has promise in Point-of-care (PoC) diagnostic applications.

A flyover style microfluidic chip for highly purified magnetic cell separation.

White blood cells (WBCs) isolated from peripheral blood have been verified as important biomarkers for the diagnosis, treatment and prognosis of cancer. However, it's still under challenge to acquire high-purity WBCs, even by taking advantage of current microfluidic technology. Considering the universality of clinical magnetic activated cell sorting (MACS) method, new developments on microfluidic chip in combination of magnetic cells separation technologies may provide a fascinating approach for high-purity WBCs sorting and widely clinical application. Here, we present a flyover style microfluidic chip which has been elaborately embedded with two-stage magnetic separation in continuous flow for WBCs sorting. Immunomagnetic micro/nano-particles (IMNPs) labeled WBC (WBC@IMNPs) were sequentially separated by a lateral magnetic force and a vertical magnetic force, and the final separation purity of WBCs reached up to 93 ±â€¯1.67% at a flow rate of 20 µL min-1. Furthermore, the WBCs viability was up to 97.5 ±â€¯1.8%. Consequently, this novel flyover style microfluidic-chip with magnetic separation technology has been successfully demonstrated as cut-in-edge method for high-purity WBCs sorting, and obviously it's easy to extend for other types of cells sorting under great potential application in biomedical fields.

Tumor-Associated Macrophage Isolation and In Vivo Analysis of Their Tumor-Promoting Activity.

Characterization of individual cell populations from the tumor microenvironment is critical to understand their functional contribution to tumor progression. Magnetic bead enrichment and fluorescence-activated cell sorting (FACS) allow for the isolation of specific cell types that can be used in downstream applications, including in vitro and in vivo functional studies and molecular profiling. In this chapter, we describe the process of isolation of tumor-associated macrophages (TAMs) from primary murine breast tumors subsequent to therapeutic or experimental intervention. Additionally, we further detail how to analyze their ability to support tumor cell growth by co-injecting isolated TAMs with tumor cells orthotopically into the mammary gland of immune-deficient hosts, and monitoring tumor progression by live imaging and caliper measurement.

Purification of Leukemia-Derived Exosomes to Study Microenvironment Modulation.

Exosomes are membrane-enclosed vesicles released by different cell types into the extracellular space. As mediators of intercellular communication, they are involved in multiple physiological processes, but they are also associated with the pathogenesis of human malignancies including leukemia. Isolation of exosomes enables the characterization of their role in microenvironment modulation as well as their participation in disease pathology. A variety of strategies and techniques exists to purify exosomes from many biological fluids (e.g., blood, urine, and saliva). Here, we describe the efficient production of large quantities of exosomes from leukemic cell lines by using CELLine bioreactors based on two-compartment technology, as well as their isolation and purification by combining differential centrifugation and ultracentrifugation through a density gradient (17% OptiPrep™ cushion). Thus, exosomes are appropriately prepared for characterization by western blotting to detect exosome markers or imaging flow cytometry (ImageStream), and for downstream analyses such as the internalization in microenvironmental cells by confocal imaging or flow cytometry, methods which are also described in this chapter.

Molecular Characterization of Circulating Tumor Cells to Study Cancer Immunoevasion.

Cancer cells leaving the primary tumor immunosuppressive microenvironment become vulnerable to active immune surveillance and require mechanisms of immunoevasion to survive in the circulation. Studies have identified several pathways by which circulating tumor cells (CTCs) might escape the immune system/immunotherapy attack. The PD-1/PD-L1 axis is an immune checkpoint regulator, playing a major role in maintaining self-tolerance. It is now well recognized that tumor cells co-opt the PD-1/PD-L1 axis of immune regulation to interfere with cytotoxic T lymphocyte function. Transcriptional changes in CTCs, leading to the upregulation of PD-L1, might enable them to survive in circulation. Very recent data revealed a previously unappreciated role of epithelial-mesenchymal transition (EMT) in reprogramming the immune response in the local tumor microenvironment and a mutual regulation between EMT and immunoevasion is becoming apparent. In this chapter, we will describe in detail both EpCAM-dependent and -independent approaches that allow the identification of PD-L1 expression and EMT-like features in circulating tumor cells.

Microfluidic communicating vessel chip for expedited and automated immunomagnetic assays.

Rapid, sensitive analysis of protein biomarkers is of tremendous biological and clinical significance. Immunoassays are workhorse tools for protein analysis and have been under continuous investigation to develop new methods and to improve the analytical performance. Herein we report a pneumatically gated microfluidic communicating vessel (µCOVE) chip for rapid and sensitive immunomagnetic ELISA. A distinct feature of our device is that it employs the communicating vessel principle as a simple means to generate a fast transient hydrodynamic flow to enable effective flow washing without the need for excessive incubation, which greatly simplifies and expedites the assay workflow, compared to conventional microfluidic flow-based immunoassays. Stationary multi-phase microfluidic techniques have been developed for fast bead washing. However, they have some limitations, such as the need for careful control of interfacial properties, large bead quantity required for reliable interphase bead transport, and relatively high bead loss during surface tension-gated traverse. Our single-phase µCOVE chip can overcome such limitations and facilitate the manipulation of magnetic beads to streamline the assay workflow. We showed that the µCOVE device affords highly sensitive quantification of the CEA and EGFR proteins with a LOD down to the sub-picogram per mL level. Direct detection of the EGFR in the crude A431 cell lysate was also demonstrated to further validate the ability of our device for rapid and quantitative analysis of complex biological samples. Overall, our work presents a unique platform that combines the merits of the stationary multi-phase systems and the flow-based microfluidics. This novel immunoassay microsystem has promising potential for a broad range of biological and clinical applications, owing to its simplicity and high performance.

Combined immunomagnetic capture coupled with ultrasensitive plasmonic detection of circulating tumor cells in blood.

We demonstrate enhanced on-chip circulating tumor cell (CTC) detection through the incorporation of plasmonic-enhanced near-infrared (NIR) fluorescence screening. Specifically, the performance of plasmonic gold coated chips was evaluated on our previously reported immunomagnetic CTC capture system and compared to the performance of a regular chip. Three main performance metrics were evaluated: capture efficiency, capture reproducibility, and clinical efficacy. Use of the plasmonic chip to capture SK-BR-3 cells in PBS, resulted in a capture efficiency of 82%, compared to 76% with a regular chip. Both chips showed excellent capture reproducibility for all three cells lines evaluated (MCF-7, SK-BR-3, Colo 205) in both PBS and peripheral blood, with R2 values ranging from 0.983 to 0.996. Finally, performance of the plasmonic chip was evaluated on thirteen peripheral blood samples in patients with both breast and prostate cancer. The regular chip detected 2-8 cells per 5 mL of blood, while the plasmonic chip detected 8-85 cells per 5 mL of blood in parallel samples. In summary, we successfully demonstrate improved CTC capture and detection capabilities through use of plasmonic-enhanced near-infrared (NIR) fluorescence screening in both in vitro and ex vivo experiments. This work not only has the potential to improve clinical outcomes though improved CTC analysis, but also demonstrates successful interface design between plasmonic materials and cell capture for bioanalytical applications.

Microfluidics-enabled rational design of immunomagnetic nanomaterials and their shape effect on liquid biopsy.

Microfluidics brings unique opportunities for the synthesis of nanomaterials toward efficient liquid biopsy. Herein, we developed the microreactor-enabled flow synthesis of immunomagnetic nanomaterials with controllable shapes (sphere, cube, rod, and belt) by simply tuning the flow rates. The particle shape-dependent screening efficiency of circulating tumor cells was first investigated and compared with commercial ferrofluids, providing new insights into the rational design of a particulate system toward the screening and analysis of circulating tumor biomarkers.

Circulatory Tumor Cells in Esophageal Adenocarcinoma.

While circulating tumor cells (CTCs) within peripheral blood of cancer patients are no new phenomenon in many carcinomas, there is a lack of information on the biological and clinical implications of CTCs in esophageal adenocarcinomas. Limited evidence suggests that the CTCs are frequently detected in esophageal adenocarcinomas when compared to esophageal squamous cell carcinoma suggesting the potential difference in the pathogenesis between these two carcinomas. In addition, the varied CTC levels between adenocarcinoma and squamous cell carcinomas of the esophagus could be attributed to the varied expression pattern of epithelial markers such as epithelial cell adhesion molecule (EpCAM) and cytokeratin (CK). In esophageal adenocarcinomas, CTC levels correlated with pathological T stages, lymph node metastasis, and patient survival. Thus, detection of CTCs potentially acts as a noninvasive and real-time biomarker for predicting patient prognosis in esophageal adenocarcinomas. Although the CTC detection is currently performed using various methods, the only Food and Drug Administration (FDA) of USA approved CTC detection method in clinics is the CELLSEARCH® system. This chapter will discuss various biological characteristics of CTC and its potential implications in esophageal adenocarcinomas. In addition, a quick overview of CTC detection methodology is outlined.

Generation of alloreactivity-reduced donor lymphocyte products retaining memory function by fully automatic depletion of CD45RA-positive cells.

BACKGROUND AIMS: For patients needing allogeneic stem cell transplantation but lacking a major histocompatibility complex (MHC)-matched donor, haplo-identical (family) donors may be an alternative. Stringent T-cell depletion required in these cases to avoid lethal graft-versus-host disease (GVHD) can delay immune reconstitution, thus impairing defense against virus reactivation and attenuating graft-versus-leukemia (GVL) activity. Several groups reported that GVHD is caused by cells residing within the naive (CD45RA+) T-cell compartment and proposed use of CD45RA-depleted donor lymphocyte infusion (DLI) to accelerate immune reconstitution. We developed and tested the performance of a CD45RA depletion module for the automatic cell-processing device CliniMACS Prodigy and investigated quality attributes of the generated products. METHODS: Unstimulated apheresis products from random volunteer donors were depleted of CD45RA+ cells on CliniMACS Prodigy, using Good Manufacturing Practice (GMP)-compliant reagents and methods throughout. Using phenotypic and functional in vitro assays, we assessed the cellular constitution of CD45RA-depleted products, including T-cell subset analyses, immunological memory function and allo-reactivity. RESULTS: Selections were technically uneventful and proceeded automatically with minimal hands-on time beyond tubing set installation. Products were near-qualitatively CD45RA+ depleted, that is, largely devoid of CD45RA+ T cells but also of almost all B and natural killer cells. Naive and effector as well as γ/δ T cells were greatly reduced. The CD4:CD8 ratio was fivefold increased. Mixed lymphocyte reaction assays of the product against third-party leukocytes revealed reduced allo-reactivity compared to starting material. Anti-pathogen responses were retained. DISCUSSION: The novel, closed, fully GMP-compatible process on Prodigy generates highly CD45RA-depleted cellular products predicted to be clinically meaningfully depleted of GvH reactivity.

Detection of membrane-bound and soluble antigens by magnetic levitation.

Magnetic levitation is a technique for measuring the density and the magnetic properties of objects suspended in a paramagnetic field. We describe a novel magnetic levitation-based method that can specifically detect cell membrane-bound and soluble antigens by measurable changes in levitation height that result from the formation of antibody-coated bead and antigen complex. We demonstrate our method's ability to sensitively detect an array of membrane-bound and soluble antigens found in blood, including T-cell antigen CD3, eosinophil antigen Siglec-8, red blood cell antigens CD35 and RhD, red blood cell-bound Epstein-Barr viral particles, and soluble IL-6, and validate the results by flow cytometry and immunofluorescence microscopy performed in parallel. Additionally, employing an inexpensive, single lens, manual focus, wifi-enabled camera, we extend the portability of our method for its potential use as a point-of-care diagnostic assay.

An integrated method for cell isolation and migration on a chip.

Tumour cell migration has an important impact on tumour metastasis. Magnetic manipulation is an ascendant method for guiding and patterning cells. Here, a unique miniaturized microfluidic chip integrating cell isolation and migration assay was designed to isolate and investigate cell migration. The chip was fabricated and composed of a magnet adapter, a polytetrafluoroethylene(PDMS) microfluidic chip and six magnetic rings. This device was used to isolate MCF-7 cells from MDA-MB-231-RFP cells and evaluate the effects of TGF-ß on MCF-7 cells. First, the two cell types were mixed and incubated with magnetic beads modified with an anti-EpCAM antibody. Then, they were slowly introduced into the chip. MCF-7 cells bond to the magnetic beads in a ring-shaped pattern, while MDA-MB-231-RFP cells were washed away by PBS. Cell viability was examined during culturing in the micro-channel. The effects of TGF-ß on MCF-7 cells were evaluated by migration distance and protein expression. The integrated method presented here is novel, low-cost and easy for performing cell isolation and migration assay. The method could be beneficial for developing microfluidic device applications for cancer metastasis research and could provide a new method for biological experimentation.

Negative Enrichment and Isolation of Circulating Tumor Cells for Whole Genome Amplification.

Circulating tumor cells (CTCs) are a rare population of cells found in the peripheral blood of patients with many types of cancer such as breast, prostate, colon, and lung cancers. Higher numbers of these cells in blood are associated with a poorer prognosis of patients. Genomic profiling of CTCs would help characterize markers specific for the identification of these cells in blood, and also define genomic alterations that give these cells a metastatic advantage over other cells in the primary tumor. Here, we describe an immunomagnetic method to enrich CTCs from the blood of patients with breast cancer, followed by single-cell laser capture microdissection to isolate single CTCs. Whole genome amplification of isolated CTCs allows for many downstream applications to be performed to aide in their characterization, such as whole genome or exome sequencing, Single Nucleotide Polymorphism (SNP) and copy number analysis, and targeted sequencing or quantitative Polymerase Chain Reaction (qPCR) for genomic analyses.

Enumeration of Circulating Tumor Cells and Disseminated Tumor Cells in Blood and Bone Marrow by Immunomagnetic Enrichment and Flow Cytometry (IE/FC).

Enumerating circulating tumor cells (CTCs) in blood and disseminated tumor cells (DTCs) in bone marrow has shown to be clinically useful, as elevated numbers of these cells predict poor clinical outcomes. Accurate detection and quantification is, however, difficult and technically challenging because CTCs and DTCs are extremely rare. We have developed a novel quantitative detection method for enumeration of CTCs and DTCs. Our approach consists of two steps: (1) EPCAM-based immunomagnetic enrichment followed by (2) flow cytometry (IE/FC). The assay takes approximately 2 h to complete. In addition to tumor cell enumeration, IE/FC offers opportunities for direct isolation of highly pure tumor cells for downstream molecular characterization.