scholarly journals Single Cell Profiling Reveals Sex, Lineage and Regional Diversity in the Mouse Kidney

2019 ◽  
Author(s):  
Andrew Ransick ◽  
Nils O. Lindström ◽  
Jing Liu ◽  
Zhu Qin ◽  
Jin-Jin Guo ◽  
...  
Keyword(s):  
Single Cell ◽  
Disease Modeling ◽  
Cell Lineage ◽  
Kidney Injury ◽  
Cell Types ◽  
Mouse Kidney ◽  
Lineage Tracing ◽  
Mammalian Kidney ◽  
Organ Systems ◽  
Cell Diversity

SummaryChronic kidney disease affects 10% of the population with notable differences in ethnic and sex-related susceptibility to kidney injury and disease. Kidney dysfunction leads to significant morbidity and mortality, and chronic disease in other organ systems. A mouse organ-centered understanding underlies rapid progress in human disease modeling, and cellular approaches to repair damaged systems. To enhance an understanding of the mammalian kidney, we combined anatomy-guided single cell RNA sequencing of the adult male and female mouse kidney with in situ expression studies and cell lineage tracing. These studies reveal cell diversity and marked sex differences, distinct organization and cell composition of nephrons dependent on the time of nephron specification, and lineage convergence, in which contiguous functionally-related cell types are specified from nephron and collecting system progenitor populations. A searchable database integrating findings to highlight gene-cell relationships in a normal anatomical framework will facilitate study of the mammalian kidney.

scholarly journals Understanding the Adult Mammalian Heart at Single-Cell RNA-Seq Resolution

2021 ◽  
Vol 9 ◽  
Author(s):  
Ernesto Marín-Sedeño ◽  
Xabier Martínez de Morentin ◽  
Jose M. Pérez-Pomares ◽  
David Gómez-Cabrero ◽  
Adrián Ruiz-Villalba
Keyword(s):  
Single Cell ◽  
Single Gene ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Cardiac Cell ◽  
Rna Seq ◽  
Cardiovascular Research ◽  
Cell Diversity ◽  
Unbiased Manner

During the last decade, extensive efforts have been made to comprehend cardiac cell genetic and functional diversity. Such knowledge allows for the definition of the cardiac cellular interactome as a reasonable strategy to increase our understanding of the normal and pathologic heart. Previous experimental approaches including cell lineage tracing, flow cytometry, and bulk RNA-Seq have often tackled the analysis of cardiac cell diversity as based on the assumption that cell types can be identified by the expression of a single gene. More recently, however, the emergence of single-cell RNA-Seq technology has led us to explore the diversity of individual cells, enabling the cardiovascular research community to redefine cardiac cell subpopulations and identify relevant ones, and even novel cell types, through their cell-specific transcriptomic signatures in an unbiased manner. These findings are changing our understanding of cell composition and in consequence the identification of potential therapeutic targets for different cardiac diseases. In this review, we provide an overview of the continuously changing cardiac cellular landscape, traveling from the pre-single-cell RNA-Seq times to the single cell-RNA-Seq revolution, and discuss the utilities and limitations of this technology.

scholarly journals Massively parallel single cell lineage tracing using CRISPR/Cas9 induced genetic scars

2017 ◽  
Author(s):  
Bastiaan Spanjaard ◽  
Bo Hu ◽  
Nina Mitic ◽  
Jan Philipp Junker
Keyword(s):  
Single Cell ◽  
Computational Analysis ◽  
Systematic Approach ◽  
Single Cells ◽  
Cell Lineage ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Lineage Tracing ◽  
Lineage Trees ◽  
Different Cell Types

A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many different cell types. Single-cell RNA-sequencing (scRNA-seq) has become a widely-used method due to its ability to identify all cell types in a tissue or organ in a systematic manner 1–3. However, a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here, we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses, LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences) can be used as a systematic approach for identifying the lineage origin of novel cell types, or of known cell types under different conditions.

EPCO-26. INTEGRATIVE MULTI-OMICS IDENTIFIES CONVERGING DEVELOPMENTAL ORIGINS OF DISTINCT MEDULLOBLASTOMA SUBGROUPS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi7-vi7
Author(s):  
Kyle Smith ◽  
Laure Bihannic ◽  
Brian Gudenas ◽  
Qingsong Gao ◽  
Parthiv Haldipur ◽  
...  
Keyword(s):  
Single Cell ◽  
Developmental Trajectories ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Group 4 ◽  
Group 3 ◽  
Mechanistic Basis ◽  
Rhombic Lip

Abstract Understanding the interplay between normal development and tumorigenesis, including the identification and characterization of lineage-specific origins of MB, is a fundamental challenge in the field. Recent studies have highlighted novel associations between biologically distinct MB subgroups and diverse murine cerebellar lineages via cross-species single-cell transcriptomics. Specifically, Group 4-MB correlated with the unipolar brush cell lineage and Group 3-MB resembled Nestin+ stem cells of the early cerebellum. However, these analyses were hampered by low resolution due to the sparsity of pertinent cerebellar cell types and the cross-species nature of the approach. Herein, we profoundly expand the depth of these rare developmental populations in the murine cerebellum using a combination of lineage tracing and integrative multi-omics. Isolation and enrichment of spatially and temporally unique developmental trajectories of key rhombic lip-derived glutamatergic lineages provided an enhanced reference for mapping MB subgroups based on molecular overlap, especially for poorly defined Group 3- and Group 4-MB. Further comparisons to a novel single-cell atlas of the human fetal cerebellum, companioned with laser-capture microdissected transcriptional and epigenetic datasets, reinforced developmental insights extracted from the mouse. Characterization of compartment-specific transcriptional programs and co-expression networks identified in the human upper rhombic lip implicated convergent cellular correlates of Group 3- and Group 4-MB, suggestive of a common developmental link. Together, our results strongly implicate developmental lineages of the upper rhombic lip as the probable origins of poorly defined Group 3- and Group 4-MB. These important findings will shape future efforts to accurately model the biological heterogeneity underlying these subgroups and provide unprecedented opportunities to explore their cellular and mechanistic basis.

scholarly journals From Cell States to Cell Fates: How Cell Proliferation and Neuronal Differentiation Are Coordinated During Embryonic Development

2022 ◽  
Vol 15 ◽  
Author(s):  
Carla Belmonte-Mateos ◽  
Cristina Pujades
Keyword(s):  
Progenitor Cells ◽  
Progenitor Cell ◽  
New Technologies ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Vertebrate Brain ◽  
Proliferation And Differentiation ◽  
Cell Diversity ◽  
The Right

The central nervous system (CNS) exhibits an extraordinary diversity of neurons, with the right cell types and proportions at the appropriate sites. Thus, to produce brains with specific size and cell composition, the rates of proliferation and differentiation must be tightly coordinated and balanced during development. Early on, proliferation dominates; later on, the growth rate almost ceases as more cells differentiate and exit the cell cycle. Generation of cell diversity and morphogenesis takes place concomitantly. In the vertebrate brain, this results in dramatic changes in the position of progenitor cells and their neuronal derivatives, whereas in the spinal cord morphogenetic changes are not so important because the structure mainly grows by increasing its volume. Morphogenesis is under control of specific genetic programs that coordinately unfold over time; however, little is known about how they operate and impact in the pools of progenitor cells in the CNS. Thus, the spatiotemporal coordination of these processes is fundamental for generating functional neuronal networks. Some key aims in developmental neurobiology are to determine how cell diversity arises from pluripotent progenitor cells, and how the progenitor potential changes upon time. In this review, we will share our view on how the advance of new technologies provides novel data that challenge some of the current hypothesis. We will cover some of the latest studies on cell lineage tracing and clonal analyses addressing the role of distinct progenitor cell division modes in balancing the rate of proliferation and differentiation during brain morphogenesis. We will discuss different hypothesis proposed to explain how progenitor cell diversity is generated and how they challenged prevailing concepts and raised new questions.

scholarly journals Lineage recording of zebrafish embryogenesis reveals historical and ongoing lineage commitments

2020 ◽  
Author(s):  
Zhuoxin Chen ◽  
Chang Ye ◽  
Zhan Liu ◽  
Shanjun Deng ◽  
Xionglei He ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Cell Type ◽  
Single Cell Sequencing ◽  
Sequencing Technologies ◽  
Development And Differentiation ◽  
Zebrafish Embryogenesis

AbstractIt has been challenging to characterize the lineage relationships among cells in vertebrates, which comprise a great number of cells. Fortunately, recent progress has been made by combining the CRISPR barcoding system with single-cell sequencing technologies to provide an unprecedented opportunity to track lineage at single-cell resolution. However, due to errors and/or dropouts introduced by amplification and sequencing, reconstruction of accurate lineage relationships in complex organisms remains a challenge. Thus, improvements in both experimental design and computational analysis are necessary for lineage inference. In this study, we employed single-cell Lineage tracing On Endogenous Scarring Sites (scLOESS), a lineage recording strategy based on the CRISPR-Cas9 system, to trace cell fate commitments for zebrafish larvae. With rigorous quality control, we demonstrated that lineage commitments of complex organisms could be inferred from a limited number of barcoding sites. Together with cell-type characterization, our method could homogenously recover lineage information. In combination with the cell-type and lineage information, we depicted the development histories for germ layers as well as cell types. Furthermore, when combined with trajectory analysis, our methods could capture and resolve the ongoing lineage commitment events to gain further biological insights into later development and differentiation in complex organisms.

scholarly journals In vivo single-cell lineage tracing in zebrafish using high-resolution infrared laser-mediated gene induction microscopy

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Sicong He ◽  
Ye Tian ◽  
Shachuan Feng ◽  
Yi Wu ◽  
Xinwei Shen ◽  
...  
Keyword(s):  
Single Cell ◽  
Zebrafish Embryo ◽  
Cell Lineage ◽  
Cell Types ◽  
Infrared Laser ◽  
Lineage Tracing ◽  
Cell Labeling ◽  
Specific Cell ◽  
Blood Island

Heterogeneity broadly exists in various cell types both during development and at homeostasis. Investigating heterogeneity is crucial for comprehensively understanding the complexity of ontogeny, dynamics, and function of specific cell types. Traditional bulk-labeling techniques are incompetent to dissect heterogeneity within cell population, while the new single-cell lineage tracing methodologies invented in the last decade can hardly achieve high-fidelity single-cell labeling and long-term in-vivo observation simultaneously. In this work, we developed a high-precision infrared laser-evoked gene operator heat-shock system, which uses laser-induced CreERT2 combined with loxP-DsRedx-loxP-GFP reporter to achieve precise single-cell labeling and tracing. In vivo study indicated that this system can precisely label single cell in brain, muscle and hematopoietic system in zebrafish embryo. Using this system, we traced the hematopoietic potential of hemogenic endothelium (HE) in the posterior blood island (PBI) of zebrafish embryo and found that HEs in the PBI are heterogeneous, which contains at least myeloid unipotent and myeloid-lymphoid bipotent subtypes.

scholarly journals Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection

2020 ◽  
Author(s):  
Sergio Triana ◽  
Megan L. Stanifer ◽  
Mohammed Shahraz ◽  
Markus Mukenhirn ◽  
Carmon Kee ◽  
...  
Keyword(s):  
Immune Response ◽  
Single Cell ◽  
Cell Lineage ◽  
Enteric Virus ◽  
Cell Types ◽  
Intestinal Cell ◽  
Intestinal Epithelial ◽  
Proliferating Cells ◽  
Interferon Stimulated Genes ◽  
Human Intestinal Epithelium

AbstractHuman intestinal epithelial cells form a primary barrier protecting us from pathogens, yet only limited knowledge is available about individual contribution of each cell type to mounting an immune response against infection. Here, we developed a pipeline combining single-cell RNA-Seq and highly-multiplex RNA imaging and applied it to human intestinal organoids infected with human astrovirus, a model human enteric virus. We found that interferon controls the infection and that astrovirus infects all major cell types and lineages with a preferential infection of proliferating cells. Intriguingly, each intestinal epithelial cell lineage has a unique basal expression of interferon-stimulated genes and, upon astrovirus infection, undergoes an antiviral transcriptional reprogramming by upregulating distinct sets of interferon-stimulated genes. These findings suggest that in the human intestinal epithelium, each cell lineage plays a unique role in resolving virus infection. Our pipeline can be applicable to other organoids and viruses, opening new avenues to unravel roles of individual cell types in viral pathogenesis.

Formation of the egg-laying system inPristionchus pacificusrequires complex interactions between gonadal, mesodermal and epidermal tissues and does not rely on single cell inductions

Development ◽  
2001 ◽  
Vol 128 (18) ◽  
pp. 3395-3404
Author(s):  
Benno Jungblut ◽  
André Pires-daSilva ◽  
Ralf J. Sommer
Keyword(s):  
Single Cell ◽  
Lateral Inhibition ◽  
Cell Lineage ◽  
Egg Laying ◽  
C Elegans ◽  
Complex Interactions ◽  
Organ Systems ◽  
Vulval Precursor Cells ◽  
Sex Myoblasts ◽  
Multiple Cells

The invariant cell lineage of nematodes allows the formation of organ systems, like the egg-laying system, to be studied at a single cell level. The Caenorhabditis elegans egg-laying system is made up of the vulva, the mesodermal gonad and muscles and several neurons. The gonad plays a central role in patterning the underlying ectoderm to form the vulva and guiding the migration of the sex myoblasts to their final position. In Pristionchus pacificus, the egg-laying system is homologous to C. elegans, but comparative studies revealed several differences at the cellular and molecular levels during vulval formation. For example, the mesoblast M participates in lateral inhibition, a process that influences the fate of two vulval precursor cells. Here, we describe the M lineage in Pristionchus and show that both the dorsal and ventral M sublineages are involved in lateral inhibition. Mutations in the homeotic gene Ppa-mab-5 cause severe misspecification of the M lineage, resembling more the C. elegans Twist than the mab-5 phenotype. Ectopic differentiation of P8.p in Ppa-mab-5 results from at least two separate interactions between M and P8.p. Thus, interactions among the Pristionchus egg-laying system are complex, involving multiple cells of different tissues occurring over a distance.

scholarly journals Comparison of the Opn-CreER and Ck19-CreER Drivers in Bile Ducts of Normal and Injured Mouse Livers

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 380 ◽  
Author(s):  
Lesaffer ◽  
Verboven ◽  
Van Huffel ◽  
Moya ◽  
van Grunsven ◽  
...  
Keyword(s):  
Bile Ducts ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Tamoxifen Treatment ◽  
Mouse Strains ◽  
Recombination Efficiency ◽  
Cre Recombination ◽  
Low Efficiency ◽  
Toxic Liver Injury

Inducible cyclization recombinase (Cre) transgenic mouse strains are powerful tools for cell lineage tracing and tissue-specific knockout experiments. However, low efficiency or leaky expression can be important pitfalls. Here, we compared the efficiency and specificity of two commonly used cholangiocyte-specific Cre drivers, the Opn-iCreERT2 and Ck19-CreERT drivers, using a tdTomato reporter strain. We found that Opn-iCreERT2 triggered recombination of the tdTomato reporter in 99.9% of all cholangiocytes while Ck19-CreERT only had 32% recombination efficiency after tamoxifen injection. In the absence of tamoxifen, recombination was also induced in 2% of cholangiocytes for the Opn-iCreERT2 driver and in 13% for the Ck19-CreERT driver. For both drivers, Cre recombination was highly specific for cholangiocytes since recombination was rare in other liver cell types. Toxic liver injury ectopically activated Opn-iCreERT2 but not Ck19-CreERT expression in hepatocytes. However, ectopic recombination in hepatocytes could be avoided by applying a three-day long wash-out period between tamoxifen treatment and toxin injection. Therefore, the Opn-iCreERT2 driver is best suited for the generation of mutant bile ducts, while the Ck19-CreERT driver has near absolute specificity for bile duct cells and is therefore favorable for lineage tracing experiments.

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