Magnetic Bead-based Isolation Research Articles

Development of a Sampling and Storage Protocol of Extracellular Vesicles (EVs)-Establishment of the First EV Biobank for Polytraumatized Patients.

In the last few years, several studies have emphasized the existence of injury-specific EV "barcodes" that could have significant importance for the precise diagnosis of different organ injuries in polytrauma patients. To expand the research potential of the NTF (network trauma research) biobank of polytraumatized patients, the NTF research group decided to further establish a biobank for EVs. However, until now, the protocols for the isolation, characterization, and storage of EVs for biobank purposes have not been conceptualized. Plasma and serum samples from healthy volunteers (n = 10) were used. Three EV isolation methods of high relevance for the work with patients' samples (ultracentrifugation, size exclusion chromatography, and immune magnetic bead-based isolation) were compared. EVs were quantified using nanoparticle tracking analysis, EV proteins, and miRNAs. The effects of different isolation solutions; the long storage of samples (up to 3 years); and the sensibility of EVs to serial freezing-thawing cycles and different storage conditions (RT, 4/-20/-80 °C, dry ice) were evaluated. The SEC isolation method was considered the most suitable for EV biobanking. We did not find any difference in the quantity of EVs between serum and plasma-EVs. The importance of particle-free PBS as an isolation solution was confirmed. Plasma that has been frozen for a long time can also be used as a source of EVs. Serial freezing-thawing cycles were found to affect the mean size of EVs but not their amount. The storage of EV samples for 5 days on dry ice significantly reduced the EV protein concentration.

Isolation and culture of murine aortic cells and RNA isolation of aortic intima and media: Rapid and optimized approaches for atherosclerosis research

Background and aimsIsolation of cellular constituents from the mouse aorta is commonly used for expression or functional analyses in atherosclerosis research. However, current procedures to isolate primary cells are difficult, inefficient, and require separate mice. RNA extraction from aortic intima and media for transcriptomic analysis is also considered difficult with mixed RNA yields. To address these gaps, we provide: 1) a rapid, efficient protocol to isolate and culture diverse cell types concomitantly from the mouse aorta using immunomagnetic cell isolation; and 2) an optimized aortic intimal peeling technique for efficient RNA isolation from the intima and media. Methods and resultsAortic cells were obtained using an enzymatic solution and different cell types were isolated by magnetic beads conjugated to antibodies targeting endothelial cells (CD31+), leukocytes (CD45+), and fibroblast cells (CD90.2+), and smooth muscle cells were isolated by negative selection. Our protocol allows the isolation of relatively large numbers of cells (10,000 cells per aorta) in a predictable manner with high purity (>90%) verified by cell-marker gene expression, immunofluorescence, and flow cytometry. These cells are all functionally active when grown in cell culture. We also provide a rapid method to collect aortic intima-enriched RNA from Ldlr−/− mice utilizing an intima peeling approach and assess transcriptomic profiling associated with accelerated lesion formation. ConclusionsThis protocol provides an effective means for magnetic bead-based isolation of different cell types from the mouse aortic wall, and the isolated cells can be utilized for functional and mechanistic studies for a range of vascular diseases including atherosclerosis.

Abstract PO062: Isolation of tumor-infiltrating lymphocytes for higher sensitivity gene expression profiling

Abstract Gene expression profiling is a powerful approach to address the mechanism of action (MOA) of cancer immunotherapy-driven reprogramming of tumor-infiltrating lymphocytes (TILs) in the tumor microenvironment. However, TILs, particularly T and NK cells, are a very rare population within the tumor. Gene expression profiling using Nanostring or RNAseq is often not sensitive enough to detect expression changes in rare populations, and it is difficult to separate gene expression profiles between different cell subsets. Although single-cell RNAseq can distinguish gene expression profiles between different cell subsets, it is very costly and would require many cells to be sequenced before obtaining the rare cell type of interest. Classically, fluorescence-activated cell sorting (FACS) has been used to isolate rare populations, but this method is a long process that can affect cell phenotype and results in dramatic cell loss. Thus, we developed a protocol for rapid and reproducible magnetic bead-based isolation of tumor-infiltrating lymphocytes (TILs) for higher sensitivity MOA studies. CD8 and CD4 TILs were isolated from both MC38 and CT26.KSA tumor models with high purity and sufficient yield for further Nanostring gene expression analysis. As expected, CD8 and CD4 T cell gene expression profiles were dramatically enriched in the isolated TILs compared to the whole tumor. Thus, our protocol for isolating TILs from mouse tumors can be applied broadly to multiple tumor types and provides sufficient yield to perform downstream high-sensitivity gene expression profiling. Citation Format: Lindsay M. Webb, Bartholomew Naughton, Sireesha Yalavarthi, Clotilde Bourin, Jacques Moisan, Chunxiao Xu. Isolation of tumor-infiltrating lymphocytes for higher sensitivity gene expression profiling [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO062.

Isolation of Microglia and Analysis of Protein Expression by Flow Cytometry: Avoiding the Pitfall of Microglia Background Autofluorescence.

Microglia are a unique type of tissue-resident innate immune cell found within the brain, spinal cord, and retina. In the healthy nervous system, their main functions are to defend the tissue against infectious microbes, support neuronal networks through synapse remodeling, and clear extracellular debris and dying cells through phagocytosis. Many existing microglia isolation protocols require the use of enzymatic tissue digestion or magnetic bead-based isolation steps, which increase both the time and cost of these procedures and introduce variability to the experiment. Here, we report a protocol to generate single-cell suspensions from freshly harvested murine brains or spinal cords, which efficiently dissociates tissue and removes myelin debris through simple mechanical dissociation and density centrifugation and can be applied to rat and non-human primate tissues. We further describe the importance of including empty channels in downstream flow cytometry analyses of microglia single-cell suspensions to accurately assess the expression of protein targets in this highly autofluorescent cell type. This methodology ensures that observed fluorescence signals are not incorrectly attributed to the protein target of interest by appropriately taking into account the unique autofluorescence of this cell type, a phenomenon already present in young animals and that increases with aging to levels that are comparable to those observed with antibodies against highly abundant antigens.

Induction rate of regulatory T cells from conventional T cells is affected by substrate rigidity

Abstract The immune system maintains a balance between protection and tolerance. Regulatory T cells (Tregs) act as a tolerance mechanism to suppress effector immune cells. Recent studies suggest that the induction of Tregs from conventional T cells (Tconvs) has many practical and therapeutic advantages. Previously, both human and mouse T cells were reported to exhibit different responses to activating substrates of different rigidities as indicated in IL-2 secretion levels. In this work, we explore the previously unknown effect of substrate rigidity on the induction of Tregs from Tconvs. We used Sylgard 184 poly(dimethylsiloxane) (PDMS) to obtain rigidity ranging a few hundred kilopascals to megapascals. Mouse CD4+ T cells (Foxp3-GFP linked B6 mouse) were obtained from spleen and further isolated to CD25+ and CD25− cells using magnetic bead-based isolation kits. CD4+CD25− T cells (>99% Foxp3−) were then seeded onto the surfaces coated with antibodies to CD3 and CD28 in IL-2 and TGF-b-enriched media. Surprisingly, there was a significant increase in Treg induction rate at lower substrate rigidities (i.e., Young’s modulus, E ~ 100 kPa) compared to high rigidity (i.e., E ~ 3 MPa). To confirm that this significant difference in induction rate is truly related to T cell mechanosensing, we administered compound Y-27632 (cY) to inhibit myosin contractility. In the presence of cY, the difference in induction rate at varying rigidities was significantly reduced. This study furthers our understanding of mechanosensing properties of immune cells and raises questions about the underlying molecular mechanisms involved in this process of T cells choosing to proliferate or differentiate.

Versatile exclusion-based sample preparation platform for integrated rare cell isolation and analyte extraction.

Rare cell populations provide a patient-centric tool to monitor disease treatment, response, and resistance. However, understanding rare cells is a complex problem, which requires cell isolation/purification and downstream molecular interrogation - processes challenged by non-target populations, which vary patient-to-patient and change with disease. As such, cell isolation platforms must be amenable to a range of sample types while maintaining high efficiency and purity. The multiplexed technology for automated extraction (mTAE) is a versatile magnetic bead-based isolation platform that facilitates positive, negative, and combinatorial selection with integrated protein staining and nucleic acid isolation. mTAE is validated by isolating circulating tumor cells (CTCs) - a model rare cell population - from breast and prostate cancer patient samples. Negative selection yielded high efficiency capture of CTCs while positive selection yielded higher purity with an average of only 95 contaminant cells captured per milliliter of processed whole blood. With combinatorial selection, an overall increase in capture efficiency was observed, highlighting the potential significance of integrating multiple capture approaches on a single platform. Following capture (and staining), on platform nucleic acid extraction enabled the detection of androgen receptor-related transcripts from CTCs isolated from prostate cancer patients. The flexibility (e.g. negative, positive, combinatorial selection) and capabilities (e.g. isolation, protein staining, and nucleic acid extraction) of mTAE enable users to freely interrogate specific cell populations, a capability required to understand the potential of emerging rare cell populations and readily adapt to the heterogeneity presented across clinical samples.

Establishment of oral squamous cell carcinoma cell line and magnetic bead-based isolation and characterization of its CD90/CD44 subpopulations.

In this study, we describe the establishment of the human papillomavirus 18-positive, stage II, grade 1, T2N0M0 head and neck tumor primary cell line derived from oral squamous cell carcinoma of a non-smoking patient by using two different protocols. Furthermore, a preparation of subpopulations derived from this primary cell line according to the cluster of differentiation molecules CD44/CD90 status using magnetic bead-based separation and their characterization was performed. Impedance-based real-time cell analysis, enzyme-linked immunsorbant assay (ELISA), wound-healing assay, flow-cytometry, gene expression analysis, and MTT assay were used to characterize these four subpopulations (CD44+/CD90−, CD44−/CD90−, CD44+/CD90+, CD44−/CD90−). We optimised methodics for establishement of primary cell lines derived from oral squamous cell carcinoma tissue samples and subsequent separation of mesenchymal (CD90+) and epithelial (CD90−) types of tumorous cells. Primary cell line prepared by using trypsin proteolysis was more viable than the one prepared by using collagenase. According to our results, CD90 separation is a necessary step in preparation of permanent tumor-tissue derived cell lines. Based on the wound-healing assay, CD44+ cells exhibited stronger migratory capacity than CD44− subpopulations. CD44+ subpopulations had also significantly higher expression of BIRC5 and SOX2, lower expression of FLT1 and IL6, and higher levels of basal autophagy compared to CD44− subpopulations. Furthermore, co-cultivation experiments revealed that CD44−/CD90+ cells supported growth of epithelial tumor cells (CD44+/CD90−). On the contrary, factors released by CD44+/CD90+ type of cells seem to have rather inhibiting effect. The most cisplatin-resistant subpopulation with the shortest doubling time was CD44−/CD90+, but this subpopulation had a low migratory capacity.

Specific and Generic Isolation of Extracellular Vesicles with Magnetic Beads.

This chapter covers magnetic bead-based isolation and analysis of the smallest members of extracellular vesicles (EVs), the exosomes (30-150nm), generally regarded to originate from the multivesicular bodies (MVBs). Also included, are descriptions of how to prepare samples prior to isolations. The magnetic bead-based isolation workflow is dramatically shortened both by omitting the pre-enrichment step and providing an option for a very short capture time. Three direct exosome isolation strategies are described: (1) "Specific and Direct," (2) "Semi Generic and Direct" and (3) "Generic and Direct" as well as exosome release from the magnetic beads. Detailed description of downstream exosome analysis is included covering flow cytometry, Western blot and electron microscopy. Finally, a description of exosome isolation from more complex starting material including urine and serum/plasma is discussed.

Magnetic bead-based isolation of exosomes.

Exosomes are here defined as extracellular vesicles (EVs) in the approximate size range of 30-100 nm in diameter, and are observed in most body fluids containing typical exosomal markers such as CD9, CD63, and CD81. Potential subpopulations of exosomes can be captured by targeting these markers using magnetic beads. Magnetic beads are versatile tools for exosome isolation and downstream analysis. Here, we describe the workflow of immuno magnetic isolation and analysis of exosomes by flow cytometry, Western immunoblotting, and electron microscopy.

Flow-through immunomagnetic separation system for waterborne pathogen isolation and detection: Application to Giardia and Cryptosporidium cell isolation

Simultaneous sample washing and concentration of two waterborne pathogen samples were demonstrated using a rotational magnetic system under continuous flow conditions. The rotation of periodically arranged small permanent magnets close to a fluidic channel carrying magnetic particle suspension allows the trapping and release of particles along the fluidic channel in a periodic manner. Each trapping and release event resembles one washing cycle. The performance of the magnetic separation system (MSS) was evaluated in order to test its functionality to isolate magnetic-labelled protozoan cells from filtered, concentrated tap water, secondary effluent water, and purified water. Experimental protocols described in US Environmental Protection Agency method 1623 which rely on the use of a magnetic particle concentrator, were applied to test and compare our continuous flow cell separation system to the standard magnetic bead-based isolation instruments. The recovery efficiencies for Giardia cysts using the magnetic tube holder and our magnetic separation system were 90.5% and 90.1%, respectively, from a tap water matrix and about 31% and 18.5%, respectively, from a spiked secondary effluent matrix. The recovery efficiencies for Cryptosporidium cells using the magnetic tube holder and our magnetic separation system were 90% and 83.3%, respectively, from a tap water matrix and about 38% and 36%, respectively, from a spiked secondary effluent matrix. Recoveries from all matrices with the continuous flow system were typically higher in glass tubing conduits than in molded plastic conduits.

The HUPO World Congress at Long Beach, 2006

This year’s HUPO World Congress, Bench to Bedside, captured the excitement within the proteomics community over current developments and the anticipation of applying these developments to fundamental and clinical questions. This was best reflected in the organizers’ intention that the Long Beach meeting was not going to be “just another mass spectrometry meeting.” Vertical integration of the program captured the breadth of developments in the fast moving proteomics field and illustrated the power of current technologies to better understand both basic biological functions and the pathogenesis to disease phenotypes. The opening keynote address by Dr. Anna Barker highlighted the congress theme on translating proteomics technologies to advance medicine and to benefit society. The breadth of research featured in this congress is best illustrated by two lectures presented at the meeting. Mike Tyers encapsulated the breadth of modern technologies applied to the protein interactome, and Donald Hunt described new developments in mass spectrometry technologies that can be used to better understand regulation of transcription. The network of 12,000 protein interactions in yeast curated from the primary literature (see BioGRID (General Repository for Interaction Datasets), www.thebiogrid.org) forms a dense, uniform network that contains more hub-hub interactions than the sparsely connected networks derived from initial high throughput studies. Recent high throughput (HTP) 1 proteome-wide surveys by the Greenblatt and Superti-Furga groups support the notion that biological networks are highly interconnected. Similarly the exhaustive analysis of the phagosome presented by Michel Desjardins and of the nuclear pore presented by Brian Chait supported the notion that biological processes are controlled by a dense and dynamic web of protein interactions. An important discussion point raised by John Yates, namely the reliability of individual interactions in an HTP dataset versus the same interaction studied in depth “by a postdoc at the bench” elicited divergent views from the HTP and small scale camps. Regardless it is clear that the yeast interactome is far from complete as, for example, less than 30% of literature protein interactions are found in all HTP data combined. Tyers also cited examples of well studied signaling pathways for which less than 5% of known interactions are found in an HTP dataset. Reinterrogation of the protein interactome using rapid magnetic bead-based isolation methods developed by Brian Chait holds promise of detecting the transient signaling interactions that underlie cellular dynamics. Given the evident density and redundancy of biological networks, Tyers argued that systematic collections of small molecules will be needed to precisely modulate the proteome. An initial matrix of 4,000 chemical-genetic interactions has enabled successful prediction of small moleculesmall molecule interactions. Such interactions may enable highly specific antifungal and anticancer therapeutics.