Review

Authors: Dominic Grün, Alexander van Oudenaarden

Recent advances in single-cell sequencing hold great potential for exploring biological systems with unprecedented resolution. Sequencing the genome of individual cells can reveal somatic mutations and allows the investigation of clonal dynamics. Single-cell transcriptome sequencing can elucidate the cell type composition of a sample. However, single-cell sequencing comes with major technical challenges and yields complex data output. In this Primer, we provide an overview of available methods and discuss experimental design and single-cell data analysis. We hope that these guidelines will enable a growing number of researchers to leverage the power of single-cell sequencing.

Topics: Animals; Cells; Gene Expression Profiling; Guidelines as Topic; Humans; Sequence Analysis, DNA; Sequence Analysis, RNA; Single-Cell Analysis

PubMed: 26544934
DOI: 10.1016/j.cell.2015.10.039

Authors: Elisabeth Jamet, Christophe Dunand

Plant cell walls surround cells and provide both external protection and a means of cell-to-cell communication [...].

Topics: Cell Membrane; Cell Wall; Plant Cells; Plant Development; Plant Proteins

PubMed: 32326416
DOI: 10.3390/ijms21082731

Review

Authors: Sophie Dekoninck, Cédric Blanpain

Tissue repair is critical for animal survival. The skin epidermis is particularly exposed to injuries, which necessitates rapid repair. The coordinated action of distinct epidermal stem cells recruited from various skin regions together with other cell types, including fibroblasts and immune cells, is required to ensure efficient and harmonious wound healing. A complex crosstalk ensures the activation, migration and plasticity of these cells during tissue repair.

Topics: Animals; Cell Movement; Cell Plasticity; Cell Proliferation; Endothelial Cells; Fibroblasts; Humans; Keratinocytes; Stem Cells; Wound Healing

PubMed: 30602767
DOI: 10.1038/s41556-018-0237-6

Authors: Fiona K Hamey, Winnie W Y Lau, Iwo Kucinski...

BACKGROUND

Basophils and mast cells contribute to the development of allergic reactions. Whereas these mature effector cells are extensively studied, the differentiation trajectories from hematopoietic progenitors to basophils and mast cells are largely uncharted at the single-cell level.

METHODS

We performed multicolor flow cytometry, high-coverage single-cell RNA sequencing analyses, and cell fate assays to chart basophil and mast cell differentiation at single-cell resolution in mouse.

RESULTS

Analysis of flow cytometry data reconstructed a detailed map of basophil and mast cell differentiation, including a bifurcation of progenitors into two specific trajectories. Molecular profiling and pseudotime ordering of the single cells revealed gene expression changes during differentiation. Cell fate assays showed that multicolor flow cytometry and transcriptional profiling successfully predict the bipotent phenotype of a previously uncharacterized population of peritoneal basophil-mast cell progenitors.

CONCLUSIONS

A combination of molecular and functional profiling of bone marrow and peritoneal cells provided a detailed road map of basophil and mast cell development. An interactive web resource was created to enable the wider research community to explore the expression dynamics for any gene of interest.

Topics: Animals; Basophils; Bone Marrow Cells; Cell Differentiation; Mast Cells; Mice; Stem Cells

PubMed: 33078414
DOI: 10.1111/all.14633

Review

Authors: Paula Müller, Heiko Lemcke, Robert David...

A large number of clinical trials have shown stem cell therapy to be a promising therapeutic approach for the treatment of cardiovascular diseases. Since the first transplantation into human patients, several stem cell types have been applied in this field, including bone marrow derived stem cells, cardiac progenitors as well as embryonic stem cells and their derivatives. However, results obtained from clinical studies are inconsistent and stem cell-based improvement of heart performance and cardiac remodeling was found to be quite limited. In order to optimize stem cell efficiency, it is crucial to elucidate the underlying mechanisms mediating the beneficial effects of stem cell transplantation. Based on these mechanisms, researchers have developed different improvement strategies to boost the potency of stem cell repair and to generate the "next generation" of stem cell therapeutics. Moreover, since cardiovascular diseases are complex disorders including several disease patterns and pathologic mechanisms it may be difficult to provide a uniform therapeutic intervention for all subgroups of patients. Therefore, future strategies should aim at more personalized SC therapies in which individual disease parameters influence the selection of optimal cell type, dosage and delivery approach.

Topics: Embryonic Stem Cells; Heart; Heart Diseases; Hepatic Stellate Cells; Humans; Induced Pluripotent Stem Cells; Myoblasts, Skeletal; Regeneration; Stem Cell Transplantation; Ventricular Remodeling

PubMed: 30121644
DOI: 10.1159/000492704

Review

Authors: Shin-Jeong Lee, Cholomi Jung, Jee Eun Oh...

Red blood cell (RBC) transfusion is a lifesaving medical procedure that can treat patients with anemia and hemoglobin disorders. However, the shortage of blood supply and risks of transfusion-transmitted infection and immune incompatibility present a challenge for transfusion. The in vitro generation of RBCs or erythrocytes holds great promise for transfusion medicine and novel cell-based therapies. While hematopoietic stem cells and progenitors derived from peripheral blood, cord blood, and bone marrow can give rise to erythrocytes, the use of human pluripotent stem cells (hPSCs) has also provided an important opportunity to obtain erythrocytes. These hPSCs include both human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs). As hESCs carry ethical and political controversies, hiPSCs can be a more universal source for RBC generation. In this review, we first discuss the key concepts and mechanisms of erythropoiesis. Thereafter, we summarize different methodologies to differentiate hPSCs into erythrocytes with an emphasis on the key features of human definitive erythroid lineage cells. Finally, we address the current limitations and future directions of clinical applications using hiPSC-derived erythrocytes.

Topics: Humans; Induced Pluripotent Stem Cells; Cell Differentiation; Erythrocytes; Pluripotent Stem Cells; Hematopoietic Stem Cells

PubMed: 37296674
DOI: 10.3390/cells12111554

Authors: Christopher T Fincher, Omri Wurtzel, Thom de Hoog...

The transcriptome of a cell dictates its unique cell type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and represents a powerful approach to metazoan biology.

Topics: Animals; Atlases as Topic; Cell Lineage; Cells; Gene Expression Profiling; Planarians; Sequence Analysis, RNA; Single-Cell Analysis; Stem Cells; Transcriptome

PubMed: 29674431
DOI: 10.1126/science.aaq1736

Authors: Gopika G Nair, Jennifer S Liu, Holger A Russ...

Despite advances in the differentiation of insulin-producing cells from human embryonic stem cells, the generation of mature functional β cells in vitro has remained elusive. To accomplish this goal, we have developed cell culture conditions to closely mimic events occurring during pancreatic islet organogenesis and β cell maturation. In particular, we have focused on recapitulating endocrine cell clustering by isolating and reaggregating immature β-like cells to form islet-sized enriched β-clusters (eBCs). eBCs display physiological properties analogous to primary human β cells, including robust dynamic insulin secretion, increased calcium signalling in response to secretagogues, and improved mitochondrial energization. Notably, endocrine cell clustering induces metabolic maturation by driving mitochondrial oxidative respiration, a process central to stimulus-secretion coupling in mature β cells. eBCs display glucose-stimulated insulin secretion as early as three days after transplantation in mice. In summary, replicating aspects of endocrine cell clustering permits the generation of stem-cell-derived β cells that resemble their endogenous counterparts.

Topics: Animals; Cell Differentiation; Cells, Cultured; Embryonic Stem Cells; Endocrine Cells; Fibroblasts; Glucose; Human Embryonic Stem Cells; Humans; Insulin Secretion; Insulin-Secreting Cells; Islets of Langerhans; Mice; Mitochondria

PubMed: 30710150
DOI: 10.1038/s41556-018-0271-4

Authors: Tullia Maraldi, David Vauzour, Cristina Angeloni...

Topics: Cell Differentiation; Cell Proliferation; Cells; Diet; Disease; Inflammation; Oxidation-Reduction; Polyphenols; Signal Transduction; Stem Cells

PubMed: 24672636
DOI: 10.1155/2014/576363

Authors: Leonardo D'Aiuto, Yun Zhi, Dhanjit Kumar Das...

Induced pluripotent stem cell (iPSC)-based technologies offer an unprecedented opportunity to perform high-throughput screening of novel drugs for neurological and neurodegenerative diseases. Such screenings require a robust and scalable method for generating large numbers of mature, differentiated neuronal cells. Currently available methods based on differentiation of embryoid bodies (EBs) or directed differentiation of adherent culture systems are either expensive or are not scalable. We developed a protocol for large-scale generation of neuronal stem cells (NSCs)/early neural progenitor cells (eNPCs) and their differentiation into neurons. Our scalable protocol allows robust and cost-effective generation of NSCs/eNPCs from iPSCs. Following culture in neurobasal medium supplemented with B27 and BDNF, NSCs/eNPCs differentiate predominantly into vesicular glutamate transporter 1 (VGLUT1) positive neurons. Targeted mass spectrometry analysis demonstrates that iPSC-derived neurons express ligand-gated channels and other synaptic proteins and whole-cell patch-clamp experiments indicate that these channels are functional. The robust and cost-effective differentiation protocol described here for large-scale generation of NSCs/eNPCs and their differentiation into neurons paves the way for automated high-throughput screening of drugs for neurological and neurodegenerative diseases.

Topics: Batch Cell Culture Techniques; Cell Differentiation; Cell Proliferation; Cells, Cultured; Humans; Induced Pluripotent Stem Cells; Neural Stem Cells; Neurons

PubMed: 25629202
DOI: 10.1080/15476278.2015.1011921