Protocol for muscle fiber type and cross-sectional area analysis in cryosections of whole lower mouse hindlimbs.

We outline a protocol to visualize all mouse lower hindlimb skeletal muscles simultaneously. We describe procedures for orientating the whole lower hindlimb in gum tragacanth prior to freezing, simplifying the proceeding experimental steps, and enhancing the comprehensiveness of characterizations. We then detail steps for quantifying muscle fiber size and fiber type characteristics in a single cryosection using histochemistry and immunofluorescence. This protocol can be applied to histological and (immuno)histochemical evaluations such as muscle regeneration, fibrosis, enzymatic activity, and glycogen content.

A Protocol for the Isolation of Oval Cells without Preconditioning.

Oval cells (OCs) is the name of hepatic progenitor cells (HPCs) in rodents. They are a small population of cells in the liver with the remarkable ability to proliferate and regenerate hepatocytes and cholangiocytes in response to acute liver damage. Isolating OCs generally requires a pretreatment with special diets, chemicals, and/or surgery to induce hepatic damage and OC proliferation in mice. Unfortunately, these pretreatments are not only painful for the mice but also increase the cost of the assays, and the effects on the different organs as well as on various liver cells are still unclear. Therefore, the search for a protocol to obtain OCs without prior liver damage is mandatory. In our study, we present a protocol to isolate murine OCs from healthy liver (HL-OCs) and compare them with OCs isolated from mice pretreated with 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC-OCs). Our results demonstrated that cells derived from untreated mice exhibited similar behavior to those from treated mice in terms of surface marker expression, proliferation, and differentiation capacity. Therefore, given the impracticability of isolating human cells with prior hepatotoxic treatment, our model holds promise for enabling the isolation of progenitor cells from human tissue in the future. This advancement could prove invaluable for translational medicine in the understanding and treatment of liver diseases.

Isolation and transcriptional profiling of antigen-presenting cells from mouse lung and MLNs following intranasal immunization.

Dendritic cells (DCs) play a central role in the initiation of the adaptive immune response. Here, we present a protocol for isolating and transcriptionally profiling antigen-presenting cells (APCs) from the mouse lung and mediastinal lymph nodes (MLNs) following intranasal immunization. We describe steps for preparing single-cell suspensions from the lung and MLN, along with the detection and RNA sequencing (RNA-seq) of antigen-presenting DCs. This protocol offers a broadly applicable approach for identifying variations in DC subpopulations under diverse experimental conditions. For complete details on the use and execution of this protocol, please refer to Youhui et al.1.

Protocol for mapping T cell activation using single-cell RNA-seq.

Stimulation of CD4 T cells with anti-CD3/CD28 is a commonly used model to study T cell activation. Here, we present a protocol for investigating T cell activation based on anti-CD3/CD28 bead stimulation and single-cell RNA sequencing (scRNA-seq). We describe the workflow from the isolation of human peripheral blood mononuclear cells (PMBCs) and CD4 T cell enrichment to anti-CD3/CD28 bead stimulation, scRNA-seq, and data analysis. For complete details on the use and execution of this protocol, please refer to Li et al.1.

Protocol for isolating antigen-specific monoclonal antibodies from immunized mice utilizing the Beacon platform.

Isolation of antigen-specific plasma B cells had been challenging until the recent arrival of the Beacon platform. Leveraging light-sorting technology, Beacon can perform high-throughput screening of plasma B cells on a chip to sort single cells with the desired antigen specificity. Here, we present a protocol for isolating antigen-specific plasma B cells from immunized mice using Beacon, sequencing the encoded B cell receptors (BCRs), and cloning and expressing the resulting antibodies. This protocol can easily be extended to human samples.

Enrichment and separation technology for evaluation of circulating tumor cells.

Circulating tumor cells (CTCs) are tumor cells that exist in human peripheral blood, which could spread to other tissues or organs via the blood circulation system and develop into metastatic foci, leading to tumor recurrence or metastasis in postoperative patients and thereby increasing the mortality of malignant tumor patients. Evaluation of CTC levels can be used for tumor metastasis prediction, prognosis evaluation, drug exploitation, individualized treatment, liquid biopsy, etc., which exhibit outstanding clinical application prospects. In recent years, accurately capturing and analyzing CTCs has become a research hotspot in the early diagnosis and precise treatment of tumors. This review summarized various enrichment and isolation technologies for evaluating CTCs based on the design principle and discussed the challenges and perspectives in this field.

Protocol for isolating CD163+ Kupffer cells from human liver resections.

The liver microenvironment contains a wide variety of monocyte and macrophage populations. Here, we present a protocol for the specific isolation of liver-resident macrophages, known as Kupffer cells (KCs), from human liver resections. We describe steps for dissociating human liver tissues, separating non-parenchymal cells into fractions by a 2-phase iodixanol gradient, and positive selection of KCs based on the expression of CD163. We then provide instructions for validating the procedure by immunofluorescence to detect CD163. For complete details on the use and execution of this protocol, please refer to Roca Suarez, Plissonnier, et al.1.

Protocol for isolating innate lymphoid cells from murine lamina propria of the small intestine.

Innate lymphoid cells (ILCs) in the lamina propria of the small intestine (siLP) are essential for maintaining intestinal immune homeostasis; however, their isolation remains challenging. Here, we present a protocol for the rapid isolation of siLP ILCs. We describe steps for small intestine collection and trimming, epithelial cell dissociation, lamina propria digestion, and ILC analysis by flow cytometry. For complete details on the use and execution of this protocol, please refer to Zheng et al.1.

Protocol to characterize mouse dural mast cells by flow cytometry and immunofluorescence.

Mast cells, which constitute tissue-resident immune cells, are distributed in the dural meninges. Here, we provide procedural guidelines for investigating mouse dural mast cells using two techniques. First, we outline the procedures for dural tissue dissection, single-cell isolation, and subsequent surface staining for mast cell identification via flow cytometry. We then describe the techniques employed for whole dura tissue staining to visualize mast cells using confocal and slide scanning microscopy, followed by analysis using Nikon's NIS-Elements Advanced Research software. For complete details on the use and execution of this protocol, please refer to Lin et al.1.

Protocol for cell proliferation and cell death analysis of primary muscle stem cell culture using flow cytometry.

Skeletal muscle is critically dependent on the function of muscle stem cells (MuSCs) for effective muscle repair following injury. Here, we detail a protocol for the isolation of primary muscle cells and subsequent analysis of proliferation capacity in vitro using EdU (5-ethynyl-2'-deoxyuridine) on fixed cells. We also describe a cell death analysis on living cells with the identification of early- and late-apoptotic cells, as well as necrotic cells, through the incorporation of propidium iodide and YO-PRO-1 staining. For complete details on the use and execution of this protocol, please refer to Garcia et al.1.

Protocol for the dissociation of adult human primary cardiomyocytes using a methylcellulose-supplemented digestion solution.

Human primary cardiomyocytes are a valuable in vitro model for studying human heart physiology and disease. Here, we present a protocol for the dissociation of adult human primary cardiomyocytes using a methylcellulose-supplemented digestion solution. We describe steps for sample collection, tissue pre-processing, and cell dissociation. We then detail procedures for calcium reintroduction and viability assessment. This protocol can significantly improve the efficiency of cardiomyocyte isolation and subsequent cell function, making them an even more reliable model for cardiac research. For complete details on the use and execution of this protocol, please refer to Shi et al.1.

Spatially Controlled DNA Frameworks for Sensitive Detection and Specific Isolation of Tumor Cells.

High-affinity, specific, and sensitive probes are crucial for the specific recognition and identification of tumor cells from complex matrices. Multivalent binding is a powerful strategy, but the irrational spatial distribution of the functional moieties may reduce the probe performance. Here, we constructed a Janus DNA triangular prism nanostructure (3Zy1-JTP-3) for sensitive detection and specific isolation of tumor cells. Benefiting from spatial features of the triangular prism, the fluorescence intensity induced by 3Zy1-JTP-3 was almost 4 times that of the monovalent structure. Moreover, the DNA triangular prisms were connected to form hand-in-hand multivalent DNA triangular prism structures (Zy1-MTP), in which the fluorescence intensity and affinity were increased to 9-fold and 10-fold of 3Zy1-JTP-3, respectively. Furthermore, 3Zy1-JTP-3 and Zy1-MTP were combined with magnetic beads, and the latter showed higher capture efficiency (> 90%) in whole blood. This work provides a new strategy for the efficient capture of rare cells in complex biological samples.

Comparative Characteristic of the Methods of Isolation of Oocytes and Spermatozoa in Laboratory Animals (Review).

Over the past decade, there has been an increasing trend in the use of assisted reproductive technologies, which have significantly expanded the opportunities to overcome the problem of infertility. However, the problem of increasing the effectiveness of in vitro fertilization remains open. Isolation of germ cells from animals is a necessary process for various experimental studies. Animal germ cells can be used in experiments to study physical, chemical, genetic, immunological, and microbiological factors affecting reproduction efficiency and for the development of techniques that increase the effectiveness of in vitro fertilization. All of the above determines the relevance of studying existing methods of oocyte and sperm isolation for experimental in vitro studies. Here we discuss the existing methods of sperm and oocyte isolation from animals and their advantages and disadvantages, and also substantiate priority methods for use.

Protocol for quantum dot-based cell counting and immunostaining of pulmonary arterial cells from patients with pulmonary arterial hypertension.

Currently, there is no protocol for growing and culturing primary pulmonary arterial cells (PACs) available from the Pulmonary Hypertension Breakthrough Initiative (PHBI). Here, we present a protocol for cultivating and maintaining three major PACs collected from patients with pulmonary arterial hypertension (PAH): endothelial (PAH-ECs), smooth muscle (PAH-SMCs), and adventitial cells (PAH-ADCs). We describe steps for obtaining PACs from PHBI, evaluating the growth of cells labeled with quantum dots (QDs), and staining endothelial cell (EC) markers for immunofluorescence imaging. For complete details on the use and execution of this protocol, please refer to Al-Hilal et al.1.

Protocol for lipid mediator profiling and phenotyping of human M1- and M2-monocyte-derived macrophages during host-pathogen interactions.

Here, we present a protocol for primary, human immune cell isolation and stimulation for lipid mediator profiling. We describe steps for the isolation of monocytes from human leukocyte concentrates via density centrifugation and differentiation/polarization toward M1- or M2-monocyte-derived macrophages (MDMs). We detail stimulation approaches of MDMs with live bacteria or influenza A virus for lipid mediator profiling and sample preparation for subsequent analysis, such as enzyme expression, mRNA analysis, or surface marker determination. For complete details on the use and execution of this protocol, please refer to Jordan et al.1.

A Novel Approach for Mucosal and Bulbar Olfactory Ensheathing Cells Isolation Based on the Non-adherent Subculture Technique.

Introduction: Olfactory ensheathing cells (OECs) are widely used in transplantation studies. The high purification of this unique cell type is valuable for medical applications. Although recent improvements in OECs isolation procedures opened a new era in this field, the high purification efficacy and viability rate are still of concern. The most widely used OECs isolation techniques can be broadly classified based on adherence properties, particularly in olfactory bulb-derived OEC isolation. Considering the invasive nature of harvesting OECs from human olfactory bulbs, a highly efficient purification of these cells from olfactory mucosa can benefit clinical trials. In this study, we isolated OECs from rats' olfactory bulbs and mucosa due to their differential adherence properties and compared them. Methods: Cell preparations were characterized by NGFR p75 and S100ß antibodies, the specific markers for OECs, using immunocytochemistry and western blot analysis, respectively. OECs morphology and viability were monitored over time by microscopy and MTT (3-[4,5-dimethylthiazol2-yl]-2,5-diphenyltetrazolium bromide) assay. Results: We found that OECs could be purified from the olfactory mucosa using our suggested method as efficiently as the olfactory bulb. Both derived OECs showed high levels of NGFR p75 and S100ß expression, although the S100ß expression was higher in olfactory mucosa-derived OECs preparations (P<0.05). Moreover, there was no significant difference between the two sources in cell viability in our suggested protocol. Conclusion: Due to the non-invasive harvesting method, olfactory mucosa-derived OECs are preferred from a clinical point of view in transplantation studies.

Protocol for optimized nasal mucosa sample processing to obtain high-quality scRNA-seq and scATAC-seq data.

Examining nasal mucosa samples is crucial for nasal cavity disease research and diagnosis. Simultaneously obtaining high-quality data for single-cell transcriptomics (single-cell RNA sequencing [scRNA-seq]) and epigenomics (single-cell assay for transposase-accessible chromatin using sequencing [scATAC-seq]) of nasal mucosa tissues is challenging. Here, we present a protocol for processing human nasal mucosa samples to obtain data for both scRNA-seq and scATAC-seq. We describe steps for extracting human nasal mucosa tissue, mechanical and enzymatic dissociation, lysis of red blood cells, and a viability assay. We then detail procedures for library preparation and quality control.

Protocol for isolating high-purity natural killer cells from peripheral blood of septic patients using magnetic cell separation.

In human sepsis, myelocytosis and concomitant lymphopenia complicate the study of peripheral blood natural killer (NK) cells. Here, we present a protocol for isolating NK cells from peripheral blood of septic patients using magnetic cell separation. We describe steps for the depletion of non-NK cells and NK cell enrichment. We then detail procedures for comparing the results from this protocol to results obtained through the isolation procedures using two commercially available kits for NK cell isolation. For complete details on the use and execution of this protocol, please refer to Coulibaly et al.1.

Protocol for assessing murine cell doublet engagement and subsequent effects using flow cytometry and imaging flow cytometry.

Physical interactions between two immune cells or between immune and cancer cells play a major role in shaping the immune response in the tumor microenvironment, making them prime therapeutic targets for bispecific engagers. Here, we present a protocol for assessing murine cell doublet engagement and subsequent effects using flow cytometry and imaging flow cytometry. We describe steps for identifying bispecific cell engager antibodies at the cell-cell interface, doublet quantification, and characterizing cellular protein morphology and processes within the doublet. For complete details on the use and execution of this protocol, please refer to Shapir Itai et al.1.

Protocol for the processing, cryopreservation, and biobanking of patient-derived cells and tissues.

Biobanking of patient-derived specimens offers unique opportunities for retrospective testing that could potentially contribute to diagnosing and evaluating clinical conditions, advancing personalized medicine and translational biomedical discovery. In this protocol, we detail the collection, processing, and cryopreservation of peripheral blood, bone marrow, and lymph nodes from patients with hematological malignancies. This protocol can be used for multiomics to gain cellular and molecular insights into blood cancers and to test the therapeutic potential of compounds for translational biomedical research. For complete details on the use and execution of this protocol, please refer to Lim et al.1 and Rijal et al.2.