A protocol for isolating and imaging large extracellular vesicles or midbody remnants from mammalian cell culture

Traditionally, midbody remnants (MBRs) are isolated from cell culture medium using ultracentrifugation, which is expensive and time consuming. Here, we present a protocol for isolating MBRs or large extracellular vesicles (EVs) from mammalian cell culture using either 1.5% polyethylene glycol 6000 (PEG6000) or PEG5000-coated gold nanoparticles. We describe steps for growing cells, collecting media, and precipitating MBRs and EVs from cell culture medium. We then detail characterization of MBRs through immunofluorescent antibody staining and immunofluorescent imaging.

Generation of mouse models carrying B cell restricted single or multiplexed loss-of-function mutations through CRISPR-Cas9 gene editing

Here, we present a protocol to generate B cell restricted mouse models of loss-of-function genetic drivers typical of lymphoproliferative disorders, using stem cell engineering of murine strains carrying B cell restricted Cas9 expression. We describe steps for preparing lentivirus expressing sgRNA-mCherry, isolating hematopoietic stem and progenitor cells, and in vitro transduction. We then detail the transplantation of engineered cells into recipient mice and verification of gene edits. These mouse models represent versatile platforms to model complex disease traits typical of lymphoproliferative disorders. For complete details on the use and execution of this protocol, please refer to ten Hacken et al.,1 ten Hacken et al.,2 and ten Hacken et al.3.

An optimized protocol for isolation of hepatic leukocytes retrieved from murine and NASH liver biopsies

Immune dysregulation and inflammation by hepatic-resident leukocytes is considered a key step in disease progression of non-alcoholic fatty liver disease and non-alcoholic steatohepatitis toward cirrhosis and hepatocellular carcinoma. Here, we provide a protocol for isolation and characterization of liver-resident immune cells from fine-needle biopsies obtained from a rodent model and humans. We describe steps for isolating leukocytes, cell sorting, and RNA extraction and sequencing. We then detail procedures for low-input mRNA sequencing analyses.

Protocol for the purification and transcriptomic analysis of mouse astrocytes using GFAT

Astrocytes are glial cells of the central nervous system that modulate neuronal function. Here, we present glyoxal-fixed astrocyte nuclei transcriptomics (GFAT), a protocol for the purification and transcriptomic analysis of astrocyte nuclei from the cortex and cerebellum of adult and aged fresh mouse brain. We describe steps for tissue dissection, glyoxal fixation, homogenization, nuclei isolation, antibody staining, fluorescence-activated cell sorting, and RT-qPCR or bulk RNA sequencing. GFAT does not require transgenic lines or viral injection and allows parallel astrocyte and neuron profiling.

Protocol for the in vitro isolation and culture of mature adipocytes and white adipose tissue explants from humans and mice

White adipose tissue (WAT) explants culture allows the study of this tissue ex vivo, maintaining its structure and properties. Concurrently, isolating mature adipocytes facilitates research into fat cell metabolism and hormonal regulation. Here, we present a protocol for obtaining, isolating, and processing mature adipocytes, alongside the cultivation of WAT explants from humans and mice. We describe steps for WAT retrieval, culturing of WAT explants, WAT digestion, and adipocytes separation. We then detail procedures for culturing isolated mature adipocytes. For complete details on the use and execution of this protocol, please refer to Villanueva-Carmona et al. (2023).1.

Protocol for high-sensitivity western blot on murine hematopoietic stem cells

Hematopoietic stem cells (HSCs) sustain hematopoiesis during homeostasis and regeneration. However, their limited availability poses a challenge for protein analysis. Here, we present a protocol for performing high-sensitivity western blot on HSCs using two techniques that enhance HSC isolation from mice and boost sensitivity for low cell numbers. We describe steps for isolating murine bone marrow cells, antibody staining, and cell sorting and post-sort analysis. We then detail a western blot procedure suitable for low numbers of HSCs. For complete details on the use and execution of this protocol, please refer to Li et al (2022).1,2.

Ultrasound-guided lymph node fine-needle aspiration for evaluating post-vaccination germinal center responses in humans

The lymph node (LN) is a critical biological site for immune maturation after vaccination as it includes several cell populations critical for priming the antibody response. Here, we present a protocol for sampling the LN and isolating cell populations to evaluate immunogens targeting germline cells. We describe steps for media and tube preparation and sample collection using an ultrasound-guided LN fine-needle aspiration procedure. This protocol is safe, quick, low-cost, and less invasive than excisional biopsy. For complete details on the use and execution of this protocol, please refer to Leggat et al. (2022).1.

Protocol for cytokine and uterine immune cell characterization in a mouse model of LPS-induced preterm birth

Inflammation-driven preterm birth (PTB) is modeled in mice using lipopolysaccharide (LPS) challenge. Here, we present a protocol for cytokine and uterine immune cell characterization in a mouse model of LPS-induced PTB. We describe steps for LPS challenge, in vivo cytokine capture assay, and isolation of uterine immune cells for flow cytometry. These techniques allow examination of systemic inflammation in vivo and immune cell characterization at the maternal-fetal interface, facilitating exploration of inflammatory dynamics in mouse models of PTB susceptibility. For complete details on the use and execution of this protocol, please refer to Doll et al.1.

Protocol for isolating single cells from human pancreatic cancer tissues and analyzing major immune cell populations using flow cytometry

Here, we present a protocol for collecting, dissociating, isolating, staining, and analyzing immune cells from pancreatic cancer tissues for flow cytometry. The isolated cells can also be used for single-cell RNA sequencing and other related procedures. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2023).1.

Protocol for acquiring samples to assess the impact of microplastics on immune microenvironments in the mouse intestine

Environmental nano- and microplastics (NMPs) pose serious environmental issues, yet there is no established technique to assess their impact on health through oral ingestion. Here, we present a protocol to assess the impact of NMPs in the intestinal immune microenvironments by employing chronic exposure to NMPs in a mouse model. We describe steps for administration of NMPs, feces and tissue collection, and colonic gut digestion. We then detail procedures for isolation of intestinal immune cells and RNA isolation. For complete details on the use and execution of this protocol, please refer to Harusato et al.1.

Sample enrichment for single-nucleus sequencing using concanavalin A-conjugated magnetic beads

Single-cell/nucleus sequencing has been increasingly used to study specific cell populations. However, cells/nuclei often become diluted during isolation steps and are difficult to reconcentrate through centrifugation. Here, we present a protocol for sample enrichment using concanavalin A-conjugated magnetic beads. We describe steps for dissection, nuclei isolation, and fluorescence-activated cell sorting (FACS). We then detail procedures for nuclei enrichment and library preparation. This protocol enables efficient retrieval and enrichment of cells/nuclei following FACS and integrates into existing workflows of various 10× Genomics applications.

Protocol for isolation and spectral flow cytometry analysis of immune cells from the murine exocrine and endocrine pancreas

Diabetes mellitus is a disease of the hormone-secreting endocrine pancreas. However, increasing evidence suggests that the exocrine pancreas is also involved in the pathogenesis of diabetes. In this protocol, we describe how to harvest both isolated islets and exocrine tissue from one mouse pancreas, followed by a detailed explanation of how to isolate and analyze immune cells using full-spectrum flow cytometry.

A protocol for selection in mice of highly metastatic ovarian cancer cell with omental tropism

Preclinical models mimicking spontaneous omental metastasis from ovarian cancer (OC) can benefit the study of anti-metastatic therapies for OC patients. Here, we present a protocol to establish a highly metastatic (HM) mouse model with omental tropism by in vivo selection. We describe the processes of implanting OC cells in the ovaries of mice and obtaining HM sublines from their omental metastases. HM cells can metastasize from the ovary to the omentum within 2 weeks. For complete details on the use and execution of this protocol, please refer to Ying et al.1.

Protocol to characterize the melanoma tumor immune microenvironment in mice from single cell to flow cytometry analysis

Here, we present a protocol to study and describe immune cells that surround or infiltrate tumor cells or get through the body of a melanoma syngeneic mice model. We describe steps for creating and establishing the syngeneic mouse model, euthanasia, and tumor or organ harvest. We then detail procedures to rapidly achieve a single-cell suspension from different tissue samples to further quantify and analyze the phenotype of the immune cell population (lymphocytes T and B, tumor-associated macrophages, and myeloid-derived suppressor cells) by flow cytometry.

Quantification of cell energetics in human subcutaneous adipose progenitor cells after target gene knockdown

Pro-preadipocytes are adipocyte progenitor cells within subcutaneous adipose tissue that are conserved in human adipose tissue with distinct cellular energetics. Here, we detail a protocol to quantify cellular oxygen consumption rates of primary human cells harvested from adipose tissue. We describe steps for primary cell expansion, cell seeding, transfection, differentiation, and respirometry followed by Agilent Seahorse Analytics. The measurement of bioenergetic profiles and resulting data further expand our knowledge of the functional properties of primary cells isolated from adipose tissue. For complete details on the use and execution of this protocol, please refer to Chen et al. (2023).1.

Proteomics protocol for obtaining extracellular vesicle from human plasma using asymmetrical flow field-flow fractionation technology

Plasma extracellular vesicles (EVs) represent a potential resource for biomarkers of multiple diseases. Here, we present a protocol for obtaining EVs from human plasma using asymmetrical flow field-flow fractionation technology. We describe steps for using tandem mass tags to perform comparative proteomic studies of a large clinical cohort. We then detail targeted quantitative analysis of differential proteins based on a parallel reaction monitoring technique. For complete details on the use and execution of this protocol, please refer to Wu et al. (2020)1 and Li et al. (2023).2.

Isolation of murine hepatic myeloid cells with high yield and purity using immunomagnetic beads for subset analysis

There are numerous established techniques for isolating hepatic myeloid cells; however, preserving their phenotypic and functional characteristics can be challenging. We present a straightforward and efficient method to isolate hepatic myeloid cells, including Kupffer cells and lymphocyte antigen 6 complex, locus C+ (Ly6C+) monocytes/macrophages. The procedure involves perfusion of the liver with collagenase and purification with immunomagnetic particles. This protocol ensures the isolation of large quantities of purified, viable, and functional cells without influencing their physiological characteristics. For complete details on the use and execution of this protocol, please refer to Wu et al. (2019).1.

Protocol for isolating mice skeletal muscle myoblasts and myotubes via differential antibody validation

Isolation of skeletal muscles allows for the exploration of many complex diseases. Here, we present a protocol for isolating mice skeletal muscle myoblasts and myotubes that have been differentiated through antibody validation. We describe steps for collecting and preparing murine skeletal tissue, myoblast cell maintenance, plating, and cell differentiation. We then detail procedures for cell incubation, immunostaining, slide preparation and storage, and imaging for immunofluorescence validation.

Protocol to dissociate and isolate wide-diversity single cells by density gradient centrifugation from human hepatoblastoma tissue

Single-cell transcriptome sequencing can characterize various cell types in human liver tissue and facilitate understanding of hepatoblastoma heterogeneity. Here, we present a protocol for isolating hepatocytes and immune cells from human hepatoblastoma samples with high viability. We describe steps for tissue processing, enzymatic digestion, Percoll density gradient separation, cell lysis, cell suspension quality control, and scRNA library construction. We then detail sequencing and data analysis. This protocol is applicable to preparing single-cell suspensions from other human liver tissue samples.

Large-scale single-cell cloning of genome-edited cultured human cells by On-chip SPiS

Single-cell cloning is the simplest strategy to isolate genome-edited cell clones, although its scalability has been an issue. Here, we present a protocol to establish genome-edited human cultured cell clones using the On-chip SPiS, a single-cell auto-dispensing device with image recognition technology. Human cultured cells are transfected with plasmids of the CRISPR-Cas9 components, and Cas9-expressing cells are sorted and individually plated into multi-well plates by the On-chip SPiS. For complete details on the use and execution of this protocol, please refer to Takahashi et al. (2022).1.

Intracellular ATP delivery to in vitro expanded mouse CD27- γδ T cells

Intracellular ATP supports the function of γδT17 cells in mice. Here, we present a protocol for intracellular ATP delivery to in vitro expanded mouse CD27- γδ T cells. We describe steps for pre-coating well plates, preparing lymphocytes, culturing CD27- γδ T cells, and ATP delivery. We then detail functional evaluation of γδ T cells by flow cytometry. Appropriate concentrations of control and ATP vesicles are detailed for intracellular ATP delivery, which can also be applied to other immune cells. For complete details on the use and execution of this protocol, please refer to Wang et al. (2023).1.

Protocol for the isolation and purification of human follicular dendritic cells for functional assays

In this protocol, we detail how to isolate and purify human follicular dendritic cells (FDCs) from lymphoid tissues. FDCs play a vital role in antibody development by presenting antigens to B cells in germinal centers. The assay involves enzymatic digestion and fluorescence-activated cell sorting and is successfully applied to various lymphoid tissues, including tonsils, lymph nodes, and tertiary lymphoid structures. Our robust technique enables the isolation of FDCs and facilitates downstream functional and descriptive assays. For complete details on the use and execution of this protocol, please refer to Heesters et al.1.

Isolation and profiling of viable tumor cells from human ex vivo glioblastoma cultures through single-cell transcriptomics

Single-cell RNA-sequencing (scRNA-seq) is becoming a ubiquitous method in profiling the cellular transcriptomes of both malignant and non-malignant cells from the human brain. Here, we present a protocol to isolate viable tumor cells from human ex vivo glioblastoma cultures for single-cell transcriptomic analysis. We describe steps including surgical tissue collection, sectioning, culturing, primary tumor cells inoculation, growth tracking, fluorescence-based cell sorting, and population-enriched scRNA-seq. This comprehensive methodology empowers in-depth understanding of brain tumor biology at the single-cell level. For complete details on the use and execution of this protocol, please refer to Ravi et al.1.

Protocol for identifying immune checkpoint on circulating tumor cells of human pancreatic ductal adenocarcinoma by single-cell RNA sequencing

Circulating tumor cells (CTCs) are regarded as the "seeds" of tumor metastasis. Identifying immune checkpoints on CTCs is essential for establishing efficient immunotherapies to prevent tumor metastasis. Here, we present a protocol for isolating CTCs and obtaining single-cell suspensions from pancreatic ductal adenocarcinoma liver metastatic patients. We describe steps for biospecimen acquisition, CTC isolation, and tissue dissociation. We then detail procedures for performing single-cell RNA-seq, annotating cell types, and identifying immune checkpoints on CTCs. For complete details on the use and execution of this protocol, please refer to Liu et al. (2023).1.

Enzyme-free isolation of mesenchymal stem cells from decidua basalis of the human placenta

Mesenchymal stem cells (MSCs), also referred to as "medicinal signaling cells," have gained prominence as candidates for cell-based therapy and in clinical trials owing to their regenerative and therapeutic properties. Here, we present a protocol for isolating MSCs from the decidua basalis layer of human placenta using an explant culture approach. We describe steps for collecting, disinfecting, and plating placental tissue. We then detail procedures for characterizing the isolated MSCs through flow cytometry and in vitro differentiation.

Protocol for density gradient neutrophil isolation and flow cytometry-based characterization from human peripheral blood

Neutrophils are the first immune responders to bacterial or viral infection and play key roles in the host immune response; however, handling and investigating fresh neutrophils can be challenging. Here, we present a protocol for isolating neutrophils from the peripheral blood of healthy donors using density gradient separation method. We describe steps for morphology analysis by cytospin and immunophenotyping by flow cytometry analysis. This protocol can be used for the isolation of neutrophils from healthy and diseased individuals. For complete details on the use and execution of this protocol, please refer to Parthasarathy et al.1.

A protocol to establish cell line models from rare pediatric solid tumors

Pediatric cell line models are important for basic and translational research. However, their establishment has been hampered by low success rates and the lack of a unified approach. Here, we present a protocol to establish pediatric cancer cell lines from rare childhood tumors. We describe the requirements for successful establishment, including an optimized dissociation technique, and the appropriate media conditions necessary for several types of rare but lethal forms of childhood cancers. For complete details on the use and execution of this protocol, please refer to Sun et al.1.

Protocol for isolating human BCAM-positive corneal progenitor cells by flow cytometry and cell sorting

BCAM-positive basal limbal epithelial cells are an early transit-amplifying cell population (TAC) capable of holoclone formation and corneal epithelial differentiation. Here, we present a protocol for isolating BCAM-positive cells from human donor corneas by flow cytometry and cell sorting. We describe steps for cell dissection and dissociation, antibody staining, and flow cytometry. We then detail procedures for culturing the purified BCAM-positive and BCAM-negative cells for holoclone and cell sheet formation assays to study the factors that regulate corneal regeneration. For complete details on the use and execution of this protocol, please refer to Sasamoto et al.1.

Protocol to isolate human normal and neoplastic pancreatic cells for single-cell omic analyses

The high-throughput sequencing at single-cell resolution requires high-quality samples of inputted 100-10,000 cells with at least 80%-90% viability according to the applied platform. Here, we present a protocol for single-cell isolation from normal and neoplastic human pancreas. We describe steps for sample harvesting, procurement, tissue digestion, and cell purification. Subsequently, isolated cells can be further applied to single-cell profiling, for example, single-cell RNA sequencing and single-cell ATAC-seq using 10× Genomics platform. For complete details on the use and execution of this protocol, please refer to Peng et al. (2019)1 and Li et al. (2021).2.

Protocol for enrichment, purification, and cytocentrifugation of mouse liver endothelial cells

Liver endothelial cells (LECs) are critical in maintaining liver homeostasis. To understand the mechanistic processes occurring in these cells, high-quality isolation protocols must be in place. Here, we present a protocol for LEC enrichment, subsequent LEC purification using fluorescence-assisted cell sorting, and cytocentrifugation of sorted LECs for imaging. We describe steps for isolation of LEC-enriched population from mouse livers, immunolabeling and sorting, and cytospin and immunostaining. We then mention procedures for downstream analysis. For complete details on the use and execution of this protocol, please refer to Drzewiecki et al. (2021).1.

Protocol to establish an oviduct epithelial cell line derived from Gallus gallus using Percoll for in vitro validation of recombinant proteins

In vitro validation of therapeutic and recombinant proteins expressed from transgenic chickens is limited by the co-culture of fibroblasts. Here, we present a protocol for isolating pure epithelial cells derived from the magnum tubular glands of the chicken oviduct. We describe steps for preparing solutions and buffers, tissue collection, processing, dissociation, and Percoll density centrifugation to separate the epithelial cells from co-isolated fibroblasts. We then detail procedures for expressing a recombinant IgG antibody in the Percoll-derived epithelial cell line.

Tracking the growth fate of single cells and isolating slow-growing cells in human colorectal cancer organoids

Patient-derived tumor organoids are three-dimensionally cultured cancer cells that enable a suitable platform for studying heterogeneity and plasticity of cancer. We present a protocol for tracking the growth fate of single cells and isolating slow-growing cells in human colorectal cancer organoids. We describe steps for organoid preparation and culturing using the cancer-tissue-originating spheroid method, maintaining cell-cell contact throughout. We then detail a single-cell-derived spheroid-forming and growth assay, confirming single-cell plating, monitoring growth over time, and isolating slow-growing cells. For complete details on the use and execution of this protocol, please refer to Coppo et al.1.

Protocol for the isolation of mouse senescence-associated CD4+ T cells using flow cytometry and functional assays

Senescence-associated (SA) CD4+ T cells, which increase with age, may underlie the development of autoimmunity and chronic inflammation, but their pathological function remains understudied. Here, we present a protocol to isolate CD153+ SA-T cells and evaluate their characteristic responses upon T cell receptor stimulation. We describe steps for the isolation of CD153+ SA-T cells using flow cytometry and in vitro culture with stimulatory antibodies against CD3, CD28, and CD153. We then detail the assessment of the proliferation capacity and cytokine production. For complete details on the use and execution of this protocol, please refer to Fukushima et al. (2022).1.

Isolation of human cutaneous immune cells for single-cell RNA sequencing

Single-cell RNA sequencing (scRNA-seq) allows for high-resolution analysis of transcriptionally dysregulated cell subpopulations in inflammatory diseases. However, it can be challenging to properly isolate viable immune cells from human skin for scRNA-seq due to its barrier properties. Here, we present a protocol to isolate high-viability human cutaneous immune cells. We describe steps for obtaining and enzymatically dissociating a skin biopsy specimen and isolating immune cells using flow cytometry. We then provide an overview of downstream computational techniques to analyze sequencing data. For complete details on the use and execution of this protocol, please refer to Cook et al. (2022)¹ and Liu et al. (2022).².

Protocol for analyzing transforming growth factor β signaling in dextran-sulfate-sodium-induced colitic mice using flow cytometry and western blotting

Transforming growth factor β (TGF-β) is critical to the maintenance of intestinal immune homeostasis. Here, we present techniques for analyzing Smad molecules downstream of TGF-β receptor signaling in dextran-sulfate-sodium-induced colitic mice. We describe colitis induction, cell isolation, and flow cytometric cell sorting of dendritic cells and T cells. We then detail intracellular staining of phosphorylated Smad2/3 and western blotting analysis of Smad7. This protocol can be performed on a limited number of cells from many sources. For complete details on the use and execution of this protocol, please refer to Garo et al.¹.

A scalable workflow to test "shock and kill" therapeutic approaches against the HIV-1 latent reservoir in blood cells ex vivo

Integrated HIV-1 DNA persists in cells of people living with HIV during antiretroviral treatment, but its quantification is hindered by its rarity. Here, we present an optimized protocol to evaluate "shock and kill" therapeutic strategies, including both the latency reactivation ("shock") and elimination of infected cells ("kill") stages. We describe steps for the sequential use of nested PCR-based assays and viability sorting to allow for scalable and rapid screening of candidate therapeutics in patient-derived blood cells. For complete details on the use and execution of this protocol, please refer to Shytaj et al..¹.

Generating a mouse model for relapsed Sonic Hedgehog medulloblastoma

Tumor relapse is the leading adverse prognostic factor in medulloblastoma (MB). However, there is still no established mouse model for MB relapse, impeding our efforts to develop strategies to treat relapsed MB. We present a protocol for generating a mouse model for relapsed MB using irradiation by optimizing mouse breeding and age, as well as irradiation dosage and timing. We then detail procedures for determining tumor relapse based on tumor cell trans-differentiation in MB tissue, immunohistochemistry, and tumor cell isolation. For complete details on the use and execution of this protocol, please refer to Guo et al. (2021).¹.

Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis

Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) allows the dissection of transcriptional changes in immune cells with HIV infection. Here, we isolate PBMCs from HIV-infected individuals. After counting the cell number and verifying cell viability, we perform scRNA-seq for PBMCs on the 10× Genomics protocol and the Illumina NovaSeq 6000 sequencing platform. Furthermore, we analyze the function and cellular trajectories of B cell subsets and B cell receptor (BCR) repertoire after filtering raw sequences data and normalizing gene expression. For complete details on the use and execution of this protocol, please refer to Jia et al. (2022).¹.

Optimized protocol for direct cardiac reprogramming in mice using Ascl1 and Mef2c

Direct cardiac reprogramming refers to the conversion of fibroblasts into cardiomyocyte-like cells (iCMs) without going through an intermediate progenitor stage. Here, we present a protocol for direct cardiac reprogramming in mice using Ascl1 and Mef2c. We describe steps for isolating primary neonatal mouse cardiac fibroblast, preparing retrovirus encoding reprogramming factors, and efficient cardiac reprogramming with Ascl1 and Mef2c. The resulting iCMs display cardiomyocyte-like sarcomere structure, gene expression, and calcium flux. For complete details on the use and execution of this protocol, please refer to Wang et al. (2022).¹.

Chimerism and phenotypic analysis of intraepithelial and lamina propria T cells isolated from human ileal biopsies after intestinal transplantation

Understanding immune cell dynamics after intestinal transplantation has provided new insights into human lymphocyte biology. However, isolating and characterizing such cells can be challenging. Here, we provide a protocol to isolate intraepithelial and lamina propria lymphocytes from human ileal biopsies. We describe techniques for flow cytometric analysis and determination of multilineage chimerism and T lymphocyte phenotypes. This protocol can be modified to isolate and analyze lymphocytes from other tissues. For complete details on the use and execution of this protocol, please refer to Fu et al. (2019)¹ and Fu et al. (2021).².

In vitro expansion of Wilms' tumor protein 1 epitope-specific primary T cells from healthy human peripheral blood mononuclear cells

Wilms' tumor protein 1 (WT1) is a tumor-associated antigen overexpressed in various cancers. As a self-antigen, negative selection reduces the number of WT1-specific T cell receptors (TCRs). Here, we provide a protocol to generate WT137-45-specific TCRs using healthy human peripheral blood mononuclear cells. We describe the expansion of WT1-specific T cell clones by two consecutive in vitro stimulations with autologous WT137-45-pulsed dendritic cells and peripheral blood lymphocytes. We then detail the detection with human leukocyte antigen/WT137-45 tetramers.

Whole-mount immunofluorescence imaging and isolation of mesothelium-bound immune cell aggregates during mouse peritoneal inflammation

Resident peritoneal macrophages (resMØs) are crucial for repairing peritoneal injuries and controlling infections by forming mesothelium-bound resMØ-aggregates in the peritoneal wall and omentum. Here we present a protocol to analyze these structures in mouse models of peritoneal inflammation. We describe the dissection, fixation, immunofluorescent staining, and mounting of whole peritoneal wall and omentum samples and subsequent confocal microscopy imaging of resMØ-aggregates. We also detail the steps to isolate resMØ-aggregates for additional studies, including flow cytometry and electron-microscopy-based analysis. For complete details on the use and execution of this protocol, please refer to Vega-Pérez et al. (2021).1.

B-cell ELISpot assay to analyze human memory B cell and plasmablast responses specific to SARS-CoV-2 receptor-binding domain

B-cell ELISpot is an extremely sensitive assay based on the secretion of antibodies by B cells that requires the differentiation of B cells into antibody-secreting cells. Here, we describe the procedure to analyze both plasmablast (PB) and memory B cell (MBC) responses specific to SARS-CoV-2 receptor-binding domain (RBD) in the context of acute SARS-CoV-2 infection and vaccination. We detail steps for MBC stimulation, MBC and PB plating, detection, and counting of total IgG and RBD-specific spots. For complete details on the use and execution of this protocol, please refer to Tay et al. (2022).1.

Protocol for the induction of hindlimb ischemia and isolation of muscle endothelial cells in mice

A mouse model of hindlimb ischemia is an important tool for studying diverse therapeutic approaches for vascularization with high surgical success and low mortality rates. Here, we present a protocol for the induction of hindlimb ischemia in mice, including the surgery procedure and steps to analyze blood perfusion in the ischemic area using a laser speckle contrast analyzer. We also detail the isolation of endothelial cells from thigh muscles using flow cytometry after ischemic surgery. For complete details on the use and execution of this protocol, please refer to Park et al. (2016).1.

Protocol for in vivo and ex vivo assessment of hyperglycemia and islet function in diabetic mice

Mouse hyperglycemia model and islet function assessment are essential in diabetes research. Here, we provide a protocol to evaluate glucose homeostasis and islet functions in diabetic mice and isolated islets. We describe steps for establishing type 1 and 2 diabetes, glucose tolerance test, insulin tolerance test, glucose stimulated insulin secretion (GSIS) assay, and histological analysis for islet number and insulin expression in vivo. We then detail islet isolation, islet GSIS, β-cell proliferation, apoptosis, and programming assays ex vivo. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).1.

Assessing lineage and cytolytic functional potential of murine tissue-resident innate lymphocytes

Group 1 innate lymphocytes are heterogeneous, and their ontogeny and function remain ambiguous. Here, we describe a protocol to measure cell ontogeny and effector functions of natural killer (NK) and ILC1 subsets based on current understanding of their differentiation pathways. We use cre drivers to genetically fate-map cells, tracking plasticity between mature NK and ILC1. We describe innate lymphoid cell precursor transfer studies that determine ontogeny of granzyme-C-expressing ILC1. Additionally, we detail in vitro killing assays that test cytolytic potential of ILC1s. For complete details on the use and execution of this protocol, please refer to Nixon et al. (2022).1.

Protocol for bulk RNA sequencing of enriched human neutrophils from whole blood and estimation of sample purity

Although neutrophils are the most abundant leukocyte in healthy individuals and impact outcomes of diseases ranging from sepsis to cancer, they remain understudied due to technical constraints of isolation, preservation, and sequencing. We present a modified Smart-Seq2 protocol for bulk RNA sequencing of neutrophils enriched from whole blood. We describe steps for neutrophil isolation, cDNA generation, library preparation, and sample purity estimation via a bioinformatic approach. Our approach permits the collection of large cohorts and enables detection of neutrophil transcriptomic subtypes. For complete details on the use and execution of this protocol, please refer to LaSalle et al. (2022)1 and Boribong et al. (2022).2.

Protocol for direct measurement of stability and activity of mitochondria electron transport chain complex II

Mitochondria electron transport chain (ETC) complex II is essential for steroid metabolism. Here, we present a protocol to measure the stability and activity of mitochondria ETC complex II. We first describe mitochondria isolation from cell lines and tissues. We then detail how to determine the stability of ETC complex II using isothermal calorimetry and quantification of steroidogenesis using activity assays in parallel. Finally, we describe the steps to perform radioimmunoassay (RIA) to confirm the activity of ETC complex II. For complete details on the use and execution of this protocol, please refer to Bose et al. (2020).1.

Isolation of slow-cycling cancer cells from lung patient-derived xenograft using carboxyfluorescein-succinimidyl ester retention-mediated cell sorting

The slow-cycling subpopulation plays an important role in anticancer drug resistance and tumor recurrence. Here, we describe a clinically relevant patient-derived xenograft model and a carboxyfluorescein succinimidyl ester dye that is diluted in a cell proliferation-dependent manner. We detail steps to separate active-cycling cancer cells and slow-cycling cancer cells (SCCs) in heterogeneous cancer populations to confirm their different cellular properties. This protocol can be used to distinguish SCCs, investigate their biology, and develop strategies for anticancer therapeutics. For complete details on the use and execution of this protocol, please refer to Cho et al. (2021).¹.

Leukocyte Reduction Filters Are Reliable and Economic Source for Natural Killer Cell Preparation

BACKGROUND

An issue that hinders researchers' access to Natural Killer (NK) cells is their low proportion in peripheral blood leukocytes. This issue is currently addressed by methods involving a series of differentiation and expansions that are time-consuming and expensive.

OBJECTIVE

We have investigated whether the used leukocyte reduction filters, a by-product in the blood transfusion practice that currently is considered waste, can be utilized as a source of the NK cells.

METHODS

Following the blood donation of 46 donors based on the Iranian Blood Transfusion Organization's protocols, a sample of peripheral blood of each donor and the leukocyte reduction filter used in their donation procedure have been obtained. The entrapped cells were flushed back from the leukocyte reduction filters. Both groups of samples were analyzed using an automatic hematological analyzer. NK cell isolation was done by the MACS negative selection method. The samples have been comparatively analyzed utilizing flow cytometry data of NK cells' subpopulation compositions, viability, degranulation patterns, and cytotoxic capacity against the K562 cell line.

RESULTS

Every major leukocyte population was abundant in the samples extracted from the used leukocyte reduction filters. The NK cells extracted from leukocyte reduction filters did not show any statistically meaningful differences (P<0.5) from peripheral blood samples in terms of subpopulation composition, viability, degranulation potency, and cytotoxic capacity.

CONCLUSION

Used leukocyte reduction filters can be considered an economic, easy to obtain, and robust source of abundant research-grade NK cells.