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Cell Nov 2015Recent advances in single-cell sequencing hold great potential for exploring biological systems with unprecedented resolution. Sequencing the genome of individual cells... (Review)
Review
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 -
International Journal of Molecular... Apr 2020Plant cell walls surround cells and provide both external protection and a means of cell-to-cell communication [...].
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 -
Nature Cell Biology Jan 2019Tissue repair is critical for animal survival. The skin epidermis is particularly exposed to injuries, which necessitates rapid repair. The coordinated action of... (Review)
Review
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 -
Journal of Hepatology Oct 2014The liver has the unique capacity to regenerate in response to a damaging event. Liver regeneration is hereby largely driven by hepatocyte proliferation, which in turn... (Review)
Review
The liver has the unique capacity to regenerate in response to a damaging event. Liver regeneration is hereby largely driven by hepatocyte proliferation, which in turn relies on cell cycling. The hepatocyte cell cycle is a complex process that is tightly regulated by several well-established mechanisms. In vitro, isolated hepatocytes do not longer retain this proliferative capacity. However, in vitro cell growth can be boosted by immortalization of hepatocytes. Well-defined immortalization genes can be artificially overexpressed in hepatocytes or the cells can be conditionally immortalized leading to controlled cell proliferation. This paper discusses the current immortalization techniques and provides a state-of-the-art overview of the actually available immortalized hepatocyte-derived cell lines and their applications.
Topics: Animals; Cell Culture Techniques; Cell Proliferation; Cells, Cultured; Cellular Senescence; Hepatocytes; Humans
PubMed: 24911463
DOI: 10.1016/j.jhep.2014.05.046 -
Allergy Jun 2021Basophils and mast cells contribute to the development of allergic reactions. Whereas these mature effector cells are extensively studied, the differentiation...
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 -
Cellular Physiology and Biochemistry :... 2018A 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... (Review)
Review
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 -
Science (New York, N.Y.) May 2018The 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...
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 -
Nature Cell Biology Feb 2019Despite advances in the differentiation of insulin-producing cells from human embryonic stem cells, the generation of mature functional β cells in vitro has remained...
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 -
Genes To Cells : Devoted To Molecular &... Dec 2019We used single-cell RNA sequencing (seq) on several human induced pluripotent stem (iPS) cell-derived neural stem cell (NSC) lines and one fetal brain-derived NSC line...
We used single-cell RNA sequencing (seq) on several human induced pluripotent stem (iPS) cell-derived neural stem cell (NSC) lines and one fetal brain-derived NSC line to study inherent cell type heterogeneity at proliferating neural stem cell stage and uncovered predisposed presence of neurogenic and gliogenic progenitors. We observed heterogeneity in neurogenic progenitors that differed between the iPS cell-derived NSC lines and the fetal-derived NSC line, and we also observed differences in spontaneous differentiation potential for inhibitory and excitatory neurons between the iPS cell-derived NSC lines and the fetal-derived NSC line. In addition, using a recently published glia patterning protocol we enriched for gliogenic progenitors and generated glial cells from an iPS cell-derived NSC line.
Topics: Cell Line; Cell Lineage; Cells, Cultured; Human Embryonic Stem Cells; Humans; Induced Pluripotent Stem Cells; Neural Stem Cells; Neurogenesis; Neuroglia; Single-Cell Analysis
PubMed: 31651061
DOI: 10.1111/gtc.12731 -
Cells Jan 2021The concept of "symmetry breaking" has become a mainstay of modern biology, yet you will not find a definition of this concept specific to biological systems in...
The concept of "symmetry breaking" has become a mainstay of modern biology, yet you will not find a definition of this concept specific to biological systems in Wikipedia [...].
Topics: Animals; Cell Polarity; Cell Surface Extensions; Cells; Developmental Biology; Epithelial Cells; Humans; Morphogenesis
PubMed: 33430209
DOI: 10.3390/cells10010086