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.

scholarly journals A novel methodology for analysis of cell distribution in chimeric mouse organs using a strain specific antibody.

1988 ◽  
Vol 107 (1) ◽  
pp. 257-265 ◽  
Author(s):  
M Kusakabe ◽  
M Yokoyama ◽  
T Sakakura ◽  
T Nomura ◽  
H L Hosick ◽  
...  
Keyword(s):  
Effective Means ◽  
Specific Antigen ◽  
Cell Lineage ◽  
Cell Types ◽  
Mouse Strains ◽  
Corpora Lutea ◽  
Cell Renewal ◽  
Chimeric Mouse ◽  
Chimeric Mice ◽  
Lingual Papillae

Chimeric animals are very useful for analysis of cell lineage, homeostasis in tissue architecture, and cell-cell interactions during both organogenesis and carcinogenesis. However, there is not a generally effective means for marking cells of chimeric mice. We have therefore developed a polyclonal antibody that is useful for this purpose. This antibody specifically recognizes those cells derived from C3H strain mice. The specificity of this antibody was checked by both immunoblotting and immunoadsorption methods. The antigens were immunohistochemically detected in cytoplasm of both epithelial and mesenchymal cells of C3H/HeN strain mouse in many different organs, but not the corresponding cell types from BALB/c or C57BL/10 or several other mouse strains. The validity of these antibodies as markers for C3H cells was further checked by tissue recombination experiments and in mixed cultures of mouse and rat cells. In each case the antibody recognized only the C3H mouse cells. Next, chimeric mice were prepared between strains C3H/HeN and BALB/c, and C3H/HeN and C57BL/10 mice. Chimeras 2-mo old were examined for antigen distribution using the indirect immunofluorescence method. Many tissues in chimeric mice were composed of cells that were both stained and unstained by the anti-C3H specific antigen. The chimeric patterns were classified into four types, A-D. In well-defined structural units such as intestinal crypts, small intestinal villi, kidney convoluted tubules, exocrine gland acini, ovarian follicles, thyroid gland follicles, stomach glands, adrenal cortex, lingual papillae, etc., (A) each unit was composed entirely of either positive or negative cells, or else (B) in some organs each unit was composed of both types of cells. In the uniform tissues without such distinguishable units, such as stratified squamous epithelium, mesenchymal tissue, corpora lutea, pituitary gland, Islets of Langerhans, adrenal medulla etc., (C) the tissue was composed of definite small cell groups made entirely of either positive or negative cells, or else (D) the tissue was composed of both types of cells which were intermingled with one another. These findings strongly suggest that the chimeric patterns demonstrated here reflect the cell proliferative unit in each tissue. This cell marker system has proven useful for analysis of cell lineage and cell renewal systems in many organs of chimeric mice.

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.

scholarly journals The stream of precursors that colonizes the thymus proceeds selectively through the early T lineage precursor stage of T cell development

2008 ◽  
Vol 205 (5) ◽  
pp. 1187-1199 ◽  
Author(s):  
Claudia Benz ◽  
Vera C. Martins ◽  
Freddy Radtke ◽  
Conrad C. Bleul
Keyword(s):  
T Cell ◽  
T Cell Development ◽  
Cell Lineage ◽  
Cell Types ◽  
Cell Development ◽  
Precursor Cells ◽  
Precursor Cell ◽  
Lineage Tracing ◽  
Hematopoietic Precursor ◽  
The Common

T cell development in the thymus depends on continuous colonization by hematopoietic precursors. Several distinct T cell precursors have been identified, but whether one or several independent precursor cell types maintain thymopoiesis is unclear. We have used thymus transplantation and an inducible lineage-tracing system to identify the intrathymic precursor cells among previously described thymus-homing progenitors that give rise to the T cell lineage in the thymus. Extrathymic precursors were not investigated in these studies. Both approaches show that the stream of T cell lineage precursor cells, when entering the thymus, selectively passes through the early T lineage precursor (ETP) stage. Immigrating precursor cells do not exhibit characteristics of double-negative (DN) 1c, DN1d, or DN1e stages, or of populations containing the common lymphoid precursor 2 (CLP-2) or the thymic equivalent of circulating T cell progenitors (CTPs). It remains possible that an unknown hematopoietic precursor cell or previously described extrathymic precursors with a CLP, CLP-2, or CTP phenotype feed into T cell development by circumventing known intrathymic T cell lineage progenitor cells. However, it is clear that of the known intrathymic precursors, only the ETP population contributes significant numbers of T lineage precursors to T cell development.

scholarly journals Binary recombinase systems for high-resolution conditional mutagenesis

2014 ◽  
Vol 42 (6) ◽  
pp. 3894-3907 ◽  
Author(s):  
Mario Hermann ◽  
Patrick Stillhard ◽  
Hendrik Wildner ◽  
Davide Seruggia ◽  
Viktor Kapp ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Cell Lineage ◽  
Cell Types ◽  
Cre Recombinase ◽  
Lineage Tracing ◽  
Recombination Rates ◽  
Highly Active ◽  
Conditional Mutagenesis ◽  
Trans Splicing ◽  
Optimal Efficiency

Abstract Conditional mutagenesis using Cre recombinase expressed from tissue specific promoters facilitates analyses of gene function and cell lineage tracing. Here, we describe two novel dual-promoter-driven conditional mutagenesis systems designed for greater accuracy and optimal efficiency of recombination. Co-Driver employs a recombinase cascade of Dre and Dre-respondent Cre, which processes loxP-flanked alleles only when both recombinases are expressed in a predetermined temporal sequence. This unique property makes Co-Driver ideal for sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types. Co-InCre was designed for highly efficient intersectional conditional transgenesis. It relies on highly active trans-splicing inteins and promoters with simultaneous transcriptional activity to reconstitute Cre recombinase from two inactive precursor fragments. By generating native Cre, Co-InCre attains recombination rates that exceed all other binary SSR systems evaluated in this study. Both Co-Driver and Co-InCre significantly extend the utility of existing Cre-responsive alleles.

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.

Multipotential stem cells in adult mouse gastric epithelium

2002 ◽  
Vol 283 (3) ◽  
pp. G767-G777 ◽  
Author(s):  
Matthew Bjerknes ◽  
Hazel Cheng
Keyword(s):  
Stem Cells ◽  
Adult Mouse ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Gastric Epithelium ◽  
Chemical Mutagenesis ◽  
Cell Type ◽  
Mature Cell ◽  
Mature Cell Type

Previous studies of chimeric animals demonstrate that multipotential stem cells play a role in the development of the gastric epithelium; however, despite much effort, it is not clear whether they persist into adulthood. Here, chemical mutagenesis was used to label random epithelial cells by loss of transgene function in adult hemizygous ROSA26 mice, a mouse strain expressing the transgene lacZ in all tissues. Many clones derived from such cells contained all the major epithelial cell types, thereby demonstrating existence of functional multipotential stem cells in adult mouse gastric epithelium. We also observed clones containing only a single mature cell type, indicating the presence of long-lived committed progenitors in the gastric epithelium. Similar results were obtained in duodenum and colon, showing that this mouse model is suitable for lineage tracing in all regions of the gastrointestinal tract and likely useful for cell lineage studies in other adult renewing tissues.

scholarly journals Neural crest lineage analysis: from past to future trajectory

Development ◽  
2020 ◽  
Vol 147 (20) ◽  
pp. dev193193 ◽  
Author(s):  
Weiyi Tang ◽  
Marianne E. Bronner
Keyword(s):  
Neural Crest ◽  
Cell Fate ◽  
Single Molecule ◽  
Cell Lineage ◽  
Neural Crest Cell ◽  
Cell Types ◽  
Lineage Tracing ◽  
Migration Routes ◽  
Developmental Potential ◽  
Lineage Analysis

ABSTRACTSince its discovery 150 years ago, the neural crest has intrigued investigators owing to its remarkable developmental potential and extensive migratory ability. Cell lineage analysis has been an essential tool for exploring neural crest cell fate and migration routes. By marking progenitor cells, one can observe their subsequent locations and the cell types into which they differentiate. Here, we review major discoveries in neural crest lineage tracing from a historical perspective. We discuss how advancing technologies have refined lineage-tracing studies, and how clonal analysis can be applied to questions regarding multipotency. We also highlight how effective progenitor cell tracing, when combined with recently developed molecular and imaging tools, such as single-cell transcriptomics, single-molecule fluorescence in situ hybridization and high-resolution imaging, can extend the scope of neural crest lineage studies beyond development to regeneration and cancer initiation.

Cell Lineage Tracing and Cellular Diversity in Humans

2020 ◽  
Vol 21 (1) ◽  
pp. 101-116 ◽  
Author(s):  
Alexej Abyzov ◽  
Flora M. Vaccarino
Keyword(s):  
Methylation Status ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Data Types ◽  
Advantages And Disadvantages ◽  
Embryonic And Fetal Development ◽  
Distinct Lineage ◽  
Multiple Cell ◽  
Natural Mutation

Tracing cell lineages is fundamental for understanding the rules governing development in multicellular organisms and delineating complex biological processes involving the differentiation of multiple cell types with distinct lineage hierarchies. In humans, experimental lineage tracing is unethical, and one has to rely on natural-mutation markers that are created within cells as they proliferate and age. Recent studies have demonstrated that it is now possible to trace lineages in normal, noncancerous cells with a variety of data types using natural variations in the nuclear and mitochondrial DNA as well as variations in DNA methylation status. It is also apparent that the scientific community is on the verge of being able to make a comprehensive and detailed cell lineage map of human embryonic and fetal development. In this review, we discuss the advantages and disadvantages of different approaches and markers for lineage tracing. We also describe the general conceptual design for how to derive a lineage map for humans.

scholarly journals Cellular origins and lineage relationships of the intestinal epithelium

2021 ◽  
Author(s):  
Claudia Capdevila ◽  
Maria Trifas ◽  
Jonathan Miller ◽  
Troy Anderson ◽  
Peter A. Sims ◽  
...  
Keyword(s):  
Intestinal Epithelium ◽  
Developmental Trajectories ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Hierarchical Organization ◽  
Genetic Lineage ◽  
Intestinal Epithelial ◽  
Lineage Specification ◽  
Genetic Lineage Tracing

Knowledge of the development and hierarchical organization of tissues is key to understanding how they are perturbed in injury and disease, as well as how they may be therapeutically manipulated to restore homeostasis. The rapidly regenerating intestinal epithelium harbors diverse cell types and their lineage relationships have been studied using numerous approaches, from classical label-retaining and genetic lineage tracing methods to novel transcriptome-based annotations. Here, we describe the developmental trajectories that dictate differentiation and lineage specification in the intestinal epithelium. We focus on the most recent single-cell RNA-sequencing (scRNA-seq)-based strategies for understanding intestinal epithelial cell lineage relationships, underscoring how they have refined our view of the development of this tissue and highlighting their advantages and limitations. We emphasize how these technologies have been applied to understand the dynamics of intestinal epithelial cells in homeostatic and injury-induced regeneration models.

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.

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