Practicalities of Cell Sorting

Cell sorting is a technique commonly used in academic and biotechnology laboratories in order to separate out cells or particles of interest from heterogeneous populations. Cell sorters use the same principles as flow cytometry analyzers, but instead of cell populations passing to the waste of the instrument, they can be collected for further studies including DNA sequencing as well as other genomic, in vitro and in vivo experiments. This chapter aims to give an overview of cell sorting, the different types of cell sorters, details on how a cell sorter works, as well as protocols that are useful when embarking on a journey with cell sorting.

Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset

Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.

CUT & RUN to Profile Chromatin-Bound Proteins in Primary Mouse Neural Progenitor Cells

Cleavage under targets and release using nuclease (CUT & RUN) is an innovative method to profile histone modifications and chromatin-bound proteins genome-wide. CUT & RUN offers two distinct advantages of requiring much fewer cells and providing strong signal-to-noise ratios in deep-sequencing data. Here, we describe a workflow starting from dissociation and sorting of mouse embryonic brains, CUT & RUN, and DNA library preparation to deep sequencing. With our workflow, researchers can obtain high-quality sequencing data to profile histones and chromatin-associated proteins by using as few as 100,000 neural progenitor cells (NPCs).

Fishing for Developmental Regulatory Regions: Zebrafish Tissue-Specific ATAC-seq

Interactions between transcription factors and regulatory DNA can be described by gene regulatory networks. These networks provide a systems-level view of embryonic tissue development. Here, we describe a protocol for the isolation, identification, and experimental manipulation of tissue-specific cis-regulatory elements during zebrafish embryonic development using low-input ATAC-seq. With the methods described, genome-wide assessments of regulatory DNA in small populations of developing tissues can be identified, allowing for the construction of gene regulatory networks.

Detection of Circulating and Tissue Myeloid-Derived Suppressor Cells (MDSC) by Flow Cytometry

Flow cytometry allows the multiparameter analysis of heterogeneous cell populations and is an essential tool for detecting and characterizing different cell populations from peripheral blood and dissociated tissues. Myeloid-derived suppressor cells (MDSC) are a heterogeneous and plastic group of myeloid precursors with immune-suppressive capacity, which are a characteristic feature of chronic inflammation, such as cancer. The optimal measurement of MDSC levels could be used as a biomarker for clinicians for prognosis and/or management and for researchers to track and understand the role of MDSC in different pathological diseases.The criteria for defining MDSC include phenotypic surface markers, but ideally should also include the functional immunosuppressive effect on T cells, and, if possible, assessing the main biochemical and molecular features. Two major functional mechanisms to suppress T cell responses are the production of arginase-1 and reactive oxygen species (ROS) molecules. Here is presented a nine-parameter seven-color flow cytometric assay to identify and quantify MDSC from both peripheral blood mononuclear cells (PBMC) and dissociated tissue (e.g., tumor) by using fluorescence-tagged antibodies against surface markers. Also, the intracellular levels of arginase-1 and superoxide (O₂^-) content were performed to potentially distinguish their functional status.

Tracking de novo protein synthesis in the activated sludge microbiome using BONCAT-FACS

In order to ensure stable performance of engineered biotechnologies that rely on mixed microbial community systems, it is important to identify process-specific microbial traits and study their in-situ activity and responses to changing environmental conditions and system operational parameters. We used BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT) in combination with Fluorescence-Activated Cell Sorting (FACS) and 16S rRNA gene amplicon sequencing to identify translationally active cells in activated sludge. We found that only a subset of the activated sludge microbiome is translationally active during the aerobic treatment phase of a full-scale sequencing batch reactor designed to enhance biological phosphorus removal from municipal wastewater. Relative abundance of amplicon sequence variants was not a reliable predictor of species activity. BONCAT-positive and -negative cells revealed a broad range of population-wide and taxa-specific translational heterogeneity. BONCAT-FACS in combination with amplicon sequencing can provide new insights into the ecophysiology of highly dynamic microbiomes in activated sludge systems.

Feeder-Free Differentiation Assay for Mouse Hematopoietic Stem and Progenitor Cells

Hematopoietic stem cells (HSCs) are responsible for replenishing immune cells and reside in bone marrow (BM) niches, which provide all cellular and molecular components required for their lifelong maintenance and differentiation. Although HSCs have been extensively analyzed and characterized, their ex vivo expansion, which constitutes a promising approach for therapeutic development in regenerative medicine, remains challenging. Here, we describe an original in vitro system allowing to quantify by flow cytometry the differentiation of mouse HSCs into lineage-primed multipotent hematopoietic progenitors (MPPs) in a cytokine-supplemented feeder-free medium.

Development of a nanotechnology-based approach for capturing and detecting nucleic acids by using flow cytometry

Nucleic acid-based molecular diagnosis has gained special importance for the detection and early diagnosis of genetic diseases as well as for the control of infectious disease outbreaks. The development of systems that allow for the detection and analysis of nucleic acids in a low-cost and easy-to-use way is of great importance. In this context, we present a combination of a nanotechnology-based approach with the already validated dynamic chemical labeling (DCL) technology, capable of reading nucleic acids with single-base resolution. This system allows for the detection of biotinylated molecular products followed by simple detection using a standard flow cytometer, a widely used platform in clinical and molecular laboratories, and therefore, is easy to implement. This proof-of-concept assay has been developed to detect mutations in KRAS codon 12, as these mutations are highly important in cancer development and cancer treatments.

Study of Mesenchymal Stem Cell-Mediated Mitochondrial Transfer in In Vitro Models of Oxidant-Mediated Airway Epithelial and Smooth Muscle Cell Injury

Mesenchymal stem cells (MSCs) have emerged as an attractive candidate for cell-based therapy. In the past decade, many animal and pilot clinical studies have demonstrated that MSCs are therapeutically beneficial for the treatment of obstructive lung diseases such as asthma and chronic obstructive pulmonary disease (COPD). However, due to the scarcity of adult human MSCs, human-induced pluripotent stem cells mesenchymal stem cells (iPSCs) are now increasingly used as a source of MSCs. iPSCs are derived by reprogramming somatic cells from a wide variety of tissues such as skin biopsies and then differentiating them into iPSC-MSCs. One of the mechanisms through which MSCs exert their protective effects is mitochondrial transfer. Specifically, transfer of mitochondria from iPSC-MSCs to lung cells was shown to protect lung cells against oxidative stress-induced mitochondrial dysfunction and apoptosis and to reduce lung injury and inflammation in in vivo models of lung disease. In this chapter, we detail our methods to visualize and quantify iPSC-MSC-mediated mitochondrial transfer and to study its effects on oxidant-induced airway epithelial and smooth muscle cell models of acute airway cell injury.

Improved fucoxanthin and docosahexaenoic acid productivities of a sorted self-settling Tisochrysis lutea phenotype at pilot scale

This work aimed to select a Tisochrysis lutea phenotype with higher biomass and fucoxanthin productivities using fluorescence-activated cell sorting (FACS). A novel phenotype was obtained after 2 rounds of selection, based on high-fucoxanthin fluorescence. The resulting phenotype forms cell aggregates, has no flagella, and was stable after 15 months. Optimal temperature (30 °C) and light (300 µmol m^-2 s^-1) were obtained at laboratory scale, identical to the original strain. The biomass productivity was higher than the original strain: 1.9× at laboratory scale (0.4 L), and 4.5× under outdoor conditions (190 L). Moreover, compared to the original strain, the productivity of fucoxanthin increased 1.6-3.1× and docosahexaenoic acid 1.5-1.9×. These are the highest ever reported outdoor productivities, obtained with a robust new phenotype from a T. lutea monoculture isolated with FACS without genetic manipulation. The resulting phenotype shows high potential for industrial production.

Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry

Objective

Chromovert® Technology is presented as a new cell engineering technology to detect and purify living cells based on gene expression.

Methods

The technology utilizes fluorogenic oligonucleotide signaling probes and flow cytometry to detect and isolate individual living cells expressing one or more transfected or endogenously-expressed genes.

Results

Results for production of cell lines expressing a diversity of ion channel and membrane proteins are presented, including heteromultimeric epithelial sodium channel (αβγ-ENaC), sodium voltage-gated ion channel 1.7 (NaV1.7-αβ1β2), four unique γ-aminobutyric acid A (GABA_A) receptor ion channel subunit combinations α1β3γ2s, α2β3γ2s, α3β3γ2s and α5β3γ2s, cystic fibrosis conductance regulator (CFTR), CFTR-Δ508 and two G-protein coupled receptors (GPCRs) without reliance on leader sequences and/or chaperones. In addition, three novel plasmid-encoded sequences used to introduce 3′ untranslated RNA sequence tags in mRNA expression products and differentially-detectable fluorogenic probes directed to each are described. The tags and corresponding fluorogenic signaling probes streamline the process by enabling the multiplexed detection and isolation of cells expressing one or more genes without the need for gene-specific probes.

Conclusions

Chromovert technology is provided as a research tool for use to enrich and isolate cells engineered to express one or more desired genes.

Flow Cytometry-Based Analysis of the Mouse Bone Marrow Stromal and Perivascular Compartment

Bone marrow stromal cells (BMSCs) account for an extremely small percentage of total bone marrow cells; therefore, it is technically challenging to harvest a good quantity of BMSCs with good viability using fluorescence-activated cell sorting (FACS). Here, we describe the methods to effectively isolate BMSCs for flow cytometry analyses and subsequent FACS. Use of transgenic reporter lines facilitates FACS-based isolation of BMSCs, aiding to uncover fundamental characteristics of these diverse cell populations.

A Mouse Model of Pseudomonas aeruginosa Pneumonia

The rapid innate immune response to respiratory infection is essential to prevent the systemic dissemination of pathogens. This chapter outlines an experimental mouse model of respiratory infection by gram-negative Pseudomonas aeruginosa and analyses of leukocyte trafficking in the lungs. The reader will learn two methods to induce respiratory infection in mice that differ in whether the initial bolus is targeted within a specific lobe of the lung. We then describe a technique based on tissue digestion and flow cytometry that allows the investigator to distinguish leukocytes within different compartments of the lung, and discuss the advantages and limitations to such an approach.

Production and high throughput quantification of fucoxanthin and lipids in Tisochrysis lutea using single-cell fluorescence

This work aimed to investigate the accumulation of fucoxanthin and lipids in Tisochrysis lutea during growth (N+) and nitrogen-starvation (N-) and to correlate these products with single-cell emissions using fluorescence-activated cell sorting (FACS). Fucoxanthin content decreased 52.94% from N+ to N- in batch cultivation; increased 40.53% as dilution rate changed from 0.16 to 0.55 d^-1 in continuous cultivation. Total lipids (N-) were constant (~250 mg/g), but the abundance of neutral lipids increased from 4.87% to 40.63%. Nile red can stain both polar and neutral lipids. However, in vivo, this differentiation is limited due to an overlapping of signals between 600 and 660 nm, caused by neutral lipids concentrations above 3.48% (W/W). Chlorophyll autofluorescence (720 nm) was reported for the first time as a proxy for fucoxanthin (R² = 0.90) and polar lipids (R² = 0.98). FACS can be used in high throughput quantification of pigments and lipids and to select and sort cells with high-fucoxanthin/lipids.

A unified design allows fine-tuning of biosensor parameters and application across bacterial species

In recent years, transcriptional biosensors have become valuable tools in metabolic engineering as they allow semiquantitative determination of metabolites in single cells. Although being perfectly suitable tools for high-throughput screenings, application of transcriptional biosensors is often limited by the intrinsic characteristics of the individual sensor components and their interplay. In addition, biosensors often fail to work properly in heterologous host systems due to signal saturation at low intracellular metabolite concentrations, which typically limits their use in high-level producer strains at advanced engineering stages.

We here introduce a biosensor design, which allows fine-tuning of important sensor parameters and restores the sensor response in a heterologous expression host. As a key feature of our design, the regulator activity is controlled through the expression level of the respective gene by different (synthetic) constitutive promoters selected for the used expression host. In this context, we constructed biosensors responding to basic amino acids or ring-hydroxylated phenylpropanoids for applications in Corynebacterium glutamicum and Escherichia coli. Detailed characterization of these biosensors in liquid cultures and during single-cell analysis using flow cytometry showed that the presented sensor design enables customization of important biosensor parameters as well as application of these sensors in relevant heterologous hosts.

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Development of a unified biosensor design for C. glutamicum and E. coli.

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Gradual expression of the regulator gene allows for biosensor fine-tuning.

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Biosensor response in a heterologous host can be restored.

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Biosensor characterization on the single-cell level prior to FACS is mandatory.

In tube immunocytochemistry for fluorescence-activated cell sorting that prevents RNA degradation in sorted cells

Fluorescence-activated cell sorting (FACS) is a powerful tool for analyzing stem cells. When using fixed cells, however, it is sometimes difficult to analyze RNA extracted from sorted cells due to RNA degradation. We established a protocol for immunocytochemistry before FACS to prevent RNA degradation. Cells were fixed with a methanol-based fixative (UM-Fix), then subjected to immunocytochemistry. The addition of RNase inhibitor and dithiothreitol (DTT) to some buffers used for immunocytochemistry increased RNA integrity after cell recovery. We found increased copy numbers of mRNA in recovered cells using quantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis. When RNase inhibitor and DTT were added, amplification of mRNA using T7 promoter was possible with RNA extracted from recovered cells after FACS. Our protocol ensures high quality RNA in cells recovered by FACS; therefore, gene expression analysis with a smaller number of cells is possible using pre-amplification of mRNAs. Our protocol for immunocytochemistry also might be applicable to RNA recovery after immunostaining.

Purification of Myogenic Progenitors from Human Muscle Using Fluorescence-Activated Cell Sorting (FACS)

Primary myoblasts derived from human tissue are a valuable tool in research of muscle disease and pathophysiology. However, skeletal muscle biopsies, especially from diseased muscle, contain a plethora of non-myogenic cells, necessitating purification of the myogenic cell population. This protocol describes techniques for dissociation of cells from human skeletal muscle biopsies and enrichment for a highly myogenic population by fluorescence-activated cell sorting (FACS). We also describe methods for assessing myogenicity and population expansion for subsequent in vitro study.

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.

Determination and Isolation of Immune Populations from Brain Tumor Microenvironments

Flow cytometry analysis and fluorescence-activated cell sorting (FACS) allow the determination and isolation of different cell types from a given tumor sample. Here we describe and comment a method consisting of the preparation of a single cell suspension from a freshly dissected mouse brain tumor mass, staining with a combination of fluorescently labeled antibodies and analysis by flow cytometry to determine, characterize, and isolate different immune populations.

FACS - based isolation of human eosinophils allows purification of high quality RNA

Here we extensively describe a FACS-based protocol for isolating intact non-stained human eosinophils from peripheral blood; a stop forward from our recently published initial study. This method of purification could be accomplished in <3 h with only small volumes of whole blood necessary, even in healthy subjects generally exhibiting low levels of circulating eosinophils. Eosinophil activation during the isolation steps appeared to be minimal and this purification procedure yielded high quality RNA. Moreover, these FACS-isolated eosinophils had prolonged viability in culture and were suitable for further activation assays.

Isolation of pH-Sensitive Antibody Fragments by Fluorescence-Activated Cell Sorting and Yeast Surface Display

Fluorescence-activated cell sorting (FACS) in combination with yeast surface display (YSD) has proven to be a valuable tool for the engineering of antibodies. It enables the fast and robust identification and isolation of candidates with prescribed characteristics from combinatorial libraries. A novel application for FACS and YSD that has recently evolved addresses the engineering of antibodies toward pH-switchable antigen binding, aiming at reduced binding at acidic pH, compared to neutral pH. Therefore, we give guidance for the incorporation of such pH switches into antibody variable domains using combinatorial histidine scanning libraries. The protocol describes a flow cytometric sorting technique for the enrichment of antigen-specific molecules. Moreover, we provide information on how to screen the obtained antibody pools from initial sorting to isolate and characterize pH-sensitive variants.

Purification of Immune Cell Populations from Freshly Isolated Murine Tumors and Organs by Consecutive Magnetic Cell Sorting and Multi-parameter Flow Cytometry-Based Sorting

It is well established that tumors evolve together with nonmalignant cells, such as fibroblasts, endothelial cells, and immune cells. These cells constantly entangle and interact with each other creating the tumor microenvironment. Immune cells can exert both tumor-promoting and tumor-protective functions. Detailed phenotypic and functional characterization of intra-tumoral immune cell subsets has become increasingly important in the field of cancer biology and cancer immunology. In this chapter, we describe a method for isolation of viable and pure immune cell subsets from freshly isolated murine solid tumors and organs. First, we describe a protocol for the generation of single-cell suspensions from tumors and organs using mechanical and enzymatic strategies. In addition, we describe how immune cell subsets can be purified by consecutive magnetic cell sorting and multi-parameter flow cytometry-based cell sorting.

Methods to Study the Innate Immune Response to Sepsis

This chapter describes techniques to measure the innate immune response in the mouse cecal ligation and puncture model of sepsis. The reader will learn how to perform retro-orbital bleeds to harvest serum from mice and learn how to perform peritoneal lavage to harvest cells and inflammatory mediators from this compartment. The enzyme-linked immunosorbent assay (ELISA) technique is described as a method to measure the levels of cytokines and chemokines in these fluids. Additionally, this chapter describes techniques to stain the cellular fraction of the peritoneal lavage with fluorescently labeled antibodies, and perform fluorescence activated cell sorting (FACS) to quantify macrophages and neutrophils in this compartment.

Fluorescence-Activated Cell Sorting of Murine Mammary Cancer Stem-Like Cell Subpopulations with HIF Activity

Fluorescence-activated cell sorting (FACS) is a common method to identify and to isolate subpopulations within a complex mixture of cells based on their light scatter and fluorescent staining profiles. FACS is widely used to enrich for normal tissue and tumor cells that have stem cell potential. Whereas FACS protocols using conventional breast cancer cell lines are relatively routine, additional technical challenges are encountered when sorting for cell populations from freshly digested solid tumors, particularly for use in downstream cancer stem cell (CSC) assays. First, it is more difficult to isolate live, single cells from whole tumors, and second, single tumor cells prepared from enzymatically digested tumors are typically more sensitive to cell death following the physical stresses of digestion, pipetting, and sorting. Herein methods are described that have been optimized to harvest and to FACS profile viable tumor epithelial cells digested from late-stage mammary tumors originating in the mouse mammary tumor virus (MMTV)-polyomavirus middle T antigen (PyMT) transgenic mouse. Protocols were designed to enrich for single, viable, MMTV-PyMT tumor cell populations sorted by FACS and to facilitate the collection of sorted cell subpopulations suitable for head-to-head comparison of CSC activity by tumorsphere assays in vitro or limiting dilution transplantation in vivo.

The Use of Somatic Hypermutation for the Affinity Maturation of Therapeutic Antibodies

The engineering of antibodies and antibody fragments for affinity maturation, stability, and other biophysical characteristics is a common aspect of therapeutic development. Maturation of antibodies in B cells during the adaptive immune response is the result of a process called somatic hypermutation (SHM), in which the activation-induced cytidine deaminase (AID) acts to introduce mutations into immunoglobulin (Ig) genes. Iterative selection and clonal expansion of B cells containing affinity-enhancing mutations drive an increase in the overall affinity of antibodies. Here we describe the use of SHM coupled with mammalian cell surface display for the maturation of antibodies in vitro and the complementarity of these methods with the mining of immune lineages using next-generation sequencing (NGS).

A Method to Monitor Protein Turnover by Flow Cytometry and to Screen for Factors that Control Degradation by Fluorescence-Activated Cell Sorting

The protein quality control network consists of multiple proteins or protein complexes that monitor proteome integrity by mediating protein folding and the removal of proteins that cannot be folded. An integral component of this network is the ubiquitin-proteasome system, which controls the degradation of thousands of cellular proteins. A number of questions remain unanswered regarding the degradation of misfolded proteins. For example, how are substrates recognized and triaged? What are the identities of the components involved? And finally, what substrates are targeted by any given component of the quality control network? Finding answers to these questions is what inspires our work in protein quality control. Further characterization of protein quality control mechanisms requires methods that can reliably quantify turnover rates of model substrates. One such method is based on flow cytometry. Here, we present protocols detailing how to assess protein stability with flow cytometry and how fluorescence-activated cell sorting (FACS) can be used to screen for factors important for protein quality control and protein turnover.

High-Resolution Cell-Type Specific Analysis of Cytokinins in Sorted Root Cell Populations of Arabidopsis thaliana

We describe a method combining fluorescence-activated cell sorting (FACS) with one-step miniaturized isolation and accurate quantification of cytokinins (CKs) using ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) to measure these phytohormones in specific cell types of Arabidopsis thaliana roots. The methodology provides information of unprecedented resolution about spatial distributions of CKs, and thus should facilitate attempts to elucidate regulatory networks involved in root developmental processes.

Efficient Generation of Gene-Modified Mice by Haploid Embryonic Stem Cell-Mediated Semi-cloned Technology

Haploid embryonic stem cells can be derived from androgenetic embryos produced by injection of sperm into enucleated oocytes or by removal of the female pronucleus from zygotes. These cells, termed AG-haESCs, can be used in place of sperm to produce the so-called semi-cloned (SC) mice. Importantly, AG-haESCs carrying H19-DMR and IG-DMR knockouts (DKO-AG-haESCs) can efficiently and stably support the generation of SC mice via intracytoplasmic AG-haESCs injection (ICAHCI), which provides a new route to obtain genetically modified mice. In this chapter, we describe the procedures for AG-haESCs culturing, enrichment of haploid cells by FACS, genomic manipulation in DKO-AG-haESCs by CRISPR/Cas9 and generation of live SC mice with gene-modified DKO-AG-haESCs.

Histone Modifications in Major Depressive Disorder and Related Rodent Models

Major depressive disorder (MDD) is a multifactorial disease, weakly linked to multiple genetic risk factors. In contrast to that, environmental factors and "gene × environment" interaction between specific risk genes and environmental factors, such as severe or early stress exposure, have been strongly linked to MDD vulnerability. Stressors can act on the interface between an organism and the environment, the epigenome. The molecular foundation for the impact of stressors on the risk to develop MDD is based on the hormonal stress response itself: the glucocorticoid receptor (GR, encoded by NR3C1). NR3C1 can directly interact with the epigenome in the cell nucleus. Besides DNA methylation, histone modifications have been reported to be crucial targets for the interaction with the stress response system. Here, we review critical findings on the impact of the most relevant histone modifications, i.e. histone acetylation and methylation, in the context of MDD and related animal models. We discuss new treatment options which have been based on these findings, including histone deacetylase inhibitors (HDACis) and drugs targeting specific histone marks, closely linked to psychiatric disease. In this context we talk about contemporary and future approaches required to fully understand (1) the epigenetics of stress-related disease and (2) the mode of action of potential MDD drugs targeting histone modifications. This includes harnessing the unprecedented potentials of genome-wide analysis of the epigenome and transcriptome, in a cell type-specific manner, and the use of epigenome editing technologies to clearly link epigenetic marks on specific genomic loci to functional relevance.

Isolation of Primary Human Skeletal Muscle Cells

Primary myoblast culture is a valuable tool in research of muscle disease, pathophysiology, and pharmacology. This protocol describes techniques for dissociation of cells from human skeletal muscle biopsies and enrichment for a highly myogenic population by fluorescence-activated cell sorting (FACS). We also describe methods for assessing myogenicity and population expansion for subsequent in vitro study.

Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression

BACKGROUND

Previously, drug-based synchronization procedures were used for characterizing the cell cycle dependent transcriptional program. However, these synchronization methods result in growth imbalance and alteration of the cell cycle machinery. DNA content-based fluorescence activated cell sorting (FACS) is able to sort the different cell cycle phases without perturbing the cell cycle. MiRNAs are key transcriptional regulators of the cell cycle, however, their expression dynamics during cell cycle has not been explored.

METHODS

Following an optimized FACS, a complex initiative of high throughput platforms (microarray, Taqman Low Density Array, small RNA sequencing) were performed to study gene and miRNA expression profiles of cell cycle sorted human cells originating from different tissues. Validation of high throughput data was performed using quantitative real time PCR. Protein expression was detected by Western blot. Complex statistics and pathway analysis were also applied.

RESULTS

Beyond confirming the previously described cell cycle transcriptional program, cell cycle dependently expressed genes showed a higher expression independently from the cell cycle phase and a lower amplitude of dynamic changes in cancer cells as compared to untransformed fibroblasts. Contrary to mRNA changes, miRNA expression was stable throughout the cell cycle.

CONCLUSIONS

Cell cycle sorting is a synchronization-free method for the proper analysis of cell cycle dynamics. Altered dynamic expression of universal cell cycle genes in cancer cells reflects the transformed cell cycle machinery. Stable miRNA expression during cell cycle progression may suggest that dynamical miRNA-dependent regulation may be of less importance in short term regulations during the cell cycle.

Breast Cancer Stem Cell Isolation

Cells within the tumor are highly heterogeneous. Only a small portion of the cells within the tumor is capable to generate a new tumor. These cells are called cancer stem cells. Theoretically, cancer stem cells are originally from normal stem cells or early progenitor cells which accumulate the random mutations and undergo an altered version of the normal differentiation process. The cancer stem cell drives tumor progression and its recurrence. Thus, the technique to identify and purify the cancer stem cell is the key in any cancer stem cell research. In this protocol, we provide the basic technology of identification and purification of breast cancer stem cells as well as further functional assays to help the researchers achieve their research goals.

Analyzing the Tumor Microenvironment by Flow Cytometry

Flow cytometry is an essential tool for studying the tumor microenvironment. It allows us to quickly quantify and identify multiple cell types in a heterogeneous sample. A brief overview of flow cytometry instrumentation and the appropriate considerations and steps in building a good flow cytometry staining panel are discussed. In addition, a lymphoid tissue and solid tumor leukocyte infiltrate flow cytometry staining protocol and an example of flow cytometry data analysis are presented.

Analyzing Persister Physiology with Fluorescence-Activated Cell Sorting

Bacterial persisters are phenotypic variants that exhibit an impressive ability to tolerate antibiotics. Persisters are hypothesized to cause relapse infections, and therefore, understanding their physiology may lead to novel therapeutics to treat recalcitrant infections. However, persisters have yet to be isolated due to their low abundance, transient nature, and similarity to the more highly abundant viable but non-culturable cells (VBNCs), resulting in limited knowledge of their phenotypic state. This technical hurdle has been addressed through the use of fluorescence-activated cell sorting (FACS) and quantification of persister levels in the resulting sorted fractions. These assays provide persister phenotype distributions, which can be compared to the phenotype distributions of the entire population, and can also be used to examine persister heterogeneity. Here, we describe two detailed protocols for analysis of persister physiology with FACS. One protocol assays the metabolic state of persisters using a fluorescent metabolic stain, whereas the other assays the growth state of persisters with use of a fluorescent protein.

Inactivation of GDP-fucose transporter gene (Slc35c1) in CHO cells by ZFNs, TALENs and CRISPR-Cas9 for production of fucose-free antibodies

Removal of core fucose from N-glycans attached to human IgG1 significantly enhances its affinity for the receptor FcγRIII and thereby dramatically improves its antibody-dependent cellular cytotoxicity activity. While previous works have shown that inactivation of fucosyltransferase 8 results in mutants capable of producing fucose-free antibodies, we report here the use of genome editing techniques, namely ZFNs, TALENs and the CRISPR-Cas9, to inactivate the GDP-fucose transporter (SLC35C1) in Chinese hamster ovary (CHO) cells. A FACS approach coupled with a fucose-specific lectin was developed to rapidly isolate SLC35C1-deficient cells. Mass spectrometry analysis showed that both EPO-Fc produced in mutants arising from CHO-K1 and anti-Her2 antibody produced in mutants arising from a pre-existing antibody-producing CHO-HER line lacked core fucose. Lack of functional SLC35C1 in these cells does not affect cell growth or antibody productivity. Our data demonstrate that inactivating Slc35c1 gene represents an alternative approach to generate CHO cells for production of fucose-free antibodies.

Cells with surface expression of CD133highCD71low are enriched for tripotent colony-forming progenitor cells in the adult murine pancreas

Progenitor cells in the adult pancreas are potential sources of endocrine beta cells for treating type 1 diabetes. Previously, we identified tri-potent progenitor cells in the adult (2-4month-old) murine pancreas that were capable of self-renewal and differentiation into duct, acinar, and endocrine cells in vitro. These progenitor cells were named pancreatic colony-forming units (PCFUs). However, because PCFUs are a minor population in the pancreas (~1%) they are difficult to study. To enrich PCFUs, strategies using cell-surface marker analyses and fluorescence-activated cell sorting were developed. We found that CD133(high)CD71(low) cells, but not other cell populations, enriched PCFUs by up to 30 fold compared to the unsorted cells. CD133(high)CD71(low) cells generated primary, secondary, and subsequent colonies when serially re-plated in Matrigel-containing cultures, suggesting self-renewal abilities. In the presence of a laminin hydrogel, CD133(high)CD71(low) cells gave rise to colonies that contained duct, acinar, and Insulin(+)Glucagon(+) double-hormonal endocrine cells. Colonies from the laminin hydrogel culture were implanted into diabetic mice, and five weeks later duct, acinar, and Insulin(+)Glucagon(-) cells were detected in the grafts, demonstrating tri-lineage differentiation potential of CD133(high)CD71(low) cells. These CD133(high)CD71(low) cells will enable future studies of putative adult pancreas stem cells in vivo.

Isolation, enrichment and primary characterisation of vitelline cells from Schistosoma mansoni obtained by the organ isolation method

In the emerging era of post-genomic research on schistosomes, new methods are required to functionally analyse genes of interest in more detail. Among other tools, schistosome cell lines are needed to overcome present research constraints. Based on a recently established organ isolation protocol for adult Schistosoma mansoni, we report here on the successful enrichment of vitellarium tissue and isolation of vitelline cells. Morphological analyses performed by bright field, fluorescence, scanning and transmission electron microscopy showed typical features of S1 to S4 stage vitelline cells. In addition, molecular analyses using reverse transcription-PCR confirmed the identity of vitelline cells. Cytological and physiological studies included staining experiments with viability dyes and a neutral lipid stain, as well as calcium (Ca2+) imaging. Together they demonstrated cell viability, the possibility to define the differentiation stage of individual vitelline cells, and the suitability to investigate Ca(2+)-associated processes herein. Finally, fluorescence-activated cell sorting was shown to be a convenient way to separate and enrich S1 to S4 stage vitelline cells. In summary, these results demonstrate the expedience of the organ isolation protocol to obtain vitellarium tissue. Importantly, the protocol allows vitelline cells representing defined differentiation stages to be purified, which can be cultured in vitro and used to investigate diverse aspects of schistosome reproductive biology in the post-genomic era.