An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

Bowling, Sarah; Sritharan, Duluxan; Osorio, Fernando G.; Nguyen, Maximilian; Cheung, Priscilla; Rodriguez-Fraticelli, Alejo; Patel, Sachin; Yuan, Wei; Fujiwara, Yuko; Li, Bin E.; Orkin, Stuart H.; Hormoz, Sahand; Camargo, Fernando D.

doi:10.1016/j.cell.2020.06.018

Cited by 48 publications

(24 citation statements)

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“…If concerns still remain about material transfer in lineage tracing, various recent single-cell lineage tracing tools should be implemented, involving either permanent genomic alterations (scGESTALT [CRISPR in zebrafish; ( Raj et al, 2018 )]; CLARIN [CRISPR in mouse; ( Bowling et al, 2020 )]; and Polylox [Cre-recombinase in mouse; ( Pei et al, 2017 )]) or somatic mutations ( Ludwig et al, 2019 ). Adoption of these tools will help verify previous lineage tracing studies and provide additional information on how cell state affects lineage decisions.…”

Section: Retinal Progenitor Cells—the Evolving Transcriptome Of Rpcs Across Developmentmentioning

confidence: 99%

A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq

Shiau

Ruzycki

Clark

2021

Developmental Biology

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Recent advances in high throughput single-cell RNA sequencing (scRNA-seq) technology have enabled the simultaneous transcriptomic profiling of thousands of individual cells in a single experiment. To investigate the intrinsic process of retinal development, researchers have leveraged this technology to quantify gene expression in retinal cells across development, in multiple species, and from numerous important models of human disease. In this review, we summarize recent applications of scRNA-seq and discuss how these datasets have complemented and advanced our understanding of retinal progenitor cell competence, cell fate specification, and differentiation. Finally, we also highlight the outstanding questions in the field that advances in single-cell data generation and analysis will soon be able to answer.

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Section: Retinal Progenitor Cells—the Evolving Transcriptome Of Rpcs Across Developmentmentioning

confidence: 99%

A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq

Shiau

Ruzycki

Clark

2021

Developmental Biology

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“…Similarly, pseudo-temporal ordering is difficult when differentiation to a specific cell type occurs over a wide range of time during development. Alternative approaches that aim at merging single-cell analysis with lineage relationships are rapidly evolving, using the estimation of transcriptional derivatives (RNA velocity) (La Manno et al, 2018), time series experiments (Fischer et al, 2019;Schiebinger et al, 2019), or by simultaneous direct recording of cell histories, with promising but still partial coverage (Bowling et al, 2020;Chan et al, 2019;Kalhor et al, 2018;Raj et al, 2018;Spanjaard et al, 2018). In principle, atlases can be constructed from samples that are staged using traditional methods (Cao et thus facilitating coarse-grained temporal modeling of inferred transcriptional states.…”

Section: Introductionmentioning

confidence: 99%

A single-embryo, single-cell time-resolved model for mouse gastrulation

Mittnenzweig

Mayshar

Cheng

et al. 2021

Cell

127

153

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Summary Mouse embryonic development is a canonical model system for studying mammalian cell fate acquisition. Recently, single-cell atlases comprehensively charted embryonic transcriptional landscapes, yet inference of the coordinated dynamics of cells over such atlases remains challenging. Here, we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 h of molecular diversification. Using algorithms and precise timing, we infer differentiation flows and lineage specification dynamics over the embryonic transcriptional manifold. Rapid transcriptional bifurcations characterize the commitment of early specialized node and blood cells. However, for most lineages, we observe combinatorial multi-furcation dynamics rather than hierarchical transcriptional transitions. In the mesoderm, dozens of transcription factors combinatorially regulate multifurcations, as we exemplify using time-matched chimeric embryos of Foxc1/Foxc2 mutants. Our study rejects the notion of differentiation being governed by a series of binary choices, providing an alternative quantitative model for cell fate acquisition.

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“…Then, as in retrospective tracing approaches, computational approaches (29)(30)(31)(32)(33)(34) can reconstruct a phylogenetic tree that best models subclonal cellular relationships (e.g., by maximum-parsimony) from the observed shared or distinguishing alleles. Thus far, Cas9-enabled tracing has been successfully applied to study the cellular progenitor landscape in early mammalian embryogenesis (23,35), hematopoiesis (36), and neural development in zebrafish (22). Additionally, resources now exist for studying other phylogenetic processes in murine models (23,35), and analytical tools are available for computationally reconstructing and benchmarking trees from large lineage tracing datasets (33,37).…”

mentioning

confidence: 99%

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

Quinn

Jones

Okimoto

et al. 2021

Science

182

108

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Detailed phylogenies of tumor populations can recount the history and chronology of critical events during cancer progression, such as metastatic dissemination. We applied a Cas9-based, single-cell lineage tracer to study the rates, routes, and drivers of metastasis in a lung cancer xenograft mouse model. We report deeply resolved phylogenies for tens of thousands of cancer cells traced over months of growth and dissemination. This revealed stark heterogeneity in metastatic capacity, arising from pre-existing and heritable differences in gene expression. We demonstrate that these identified genes can drive invasiveness, and uncovered an unanticipated suppressive role for KRT17. We also show that metastases disseminated via multidirectional tissue routes and complex seeding topologies. Overall, we demonstrate the power of tracing cancer progression at subclonal resolution and vast scale.

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An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

Cited by 48 publications

References 0 publications

A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq

A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq

A single-embryo, single-cell time-resolved model for mouse gastrulation

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

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