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Lineage tracing meets single-cell omics: opportunities and challenges

Abstract

A fundamental goal of developmental and stem cell biology is to map the developmental history (ontogeny) of differentiated cell types. Recent advances in high-throughput single-cell sequencing technologies have enabled the construction of comprehensive transcriptional atlases of adult tissues and of developing embryos from measurements of up to millions of individual cells. Parallel advances in sequencing-based lineage-tracing methods now facilitate the mapping of clonal relationships onto these landscapes and enable detailed comparisons between molecular and mitotic histories. Here we review recent progress and challenges, as well as the opportunities that emerge when these two complementary representations of cellular history are synthesized into integrated models of cell differentiation.

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Fig. 1: Inferring cell histories from state manifolds.
Fig. 2: Limitations of cell state manifolds.
Fig. 3: Methods and logic for lineage barcoding experiments.
Fig. 4: Reading and writing transgenic DNA barcodes.
Fig. 5: Applications and pitfalls of lineage tracing on state manifolds.
Fig. 6: Developmental paradigms that shape state–lineage relationships.

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Acknowledgements

The authors thank R. Ward and S. Mekhoubad for critical reading of the manuscript. D.E.W. is supported by grant R00GM121852.

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The authors contributed equally to all aspects of the article.

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Correspondence to Daniel E. Wagner or Allon M. Klein.

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A.M.K. is a founder of 1CellBio, Inc. D.E.W. declares no competing interests.

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Nature Reviews Genetics thanks J. P. Junker and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Glossary

Cell differentiation

The process by which uncommitted progenitor cells are specified and transform into functional (and typically postmitotic) cells that carry out the specialized tasks of a particular tissue or organ.

Landscape

An informal term for a state manifold, typically used in developmental biology to represent the ensemble of cell states during their differentiation.

State manifolds

Approximate representations of high-dimensional cell states (for example, the whole-animal embryonic cell state atlas Tabula Muris) as lower-dimensional shapes.

State trajectories

The paths taken by individual cells or clones of cells through a state manifold.

Prospective lineage tracing

A lineage-tracing experiment that introduces a label for marking cells in a specified state.

Barcodes

Units of DNA with a large number of sequence possibilities, such as those used to uniquely label cells and their progeny.

Cell lineage

A representation of a series of mitotic events that trace back to a single founder cell.

Cell state

A designation of cell identity (defined with respect to a particular measurement) that can be used to classify or quantify physical or molecular differences between cells (for example, ‘basophilic’, ‘KRT4+’, ‘columnar’, ‘RNA-Seq cluster 4’).

RNA velocity

The rate of change in mRNA transcript abundance — more specifically, a set of computational techniques for calculating these rates across all genes from measurements of spliced and unspliced transcript abundances.

Clonal analysis

A lineage-tracing experiment that involves marking an individual cell, followed by state analysis of that founder cell’s clonal descendants.

Retrospective lineage tracing

A lineage-tracing experiment based on phylogenetic reconstruction of endogenous genetic polymorphisms (that is, no experimental intervention).

Hidden variables

Molecular or environmental properties of a cell that correlate with — or could be used to predict — a cell fate decision, which are obscured from a state manifold.

Direct observations

Lineage-tracing experiments that rely on in vivo live imaging of cells as they divide.

Determinate

In the context of developmental processes, when the relationship between lineage and molecular state is tightly controlled at each cell division event and is invariant between individuals.

Indeterminate

In the context of developmental processes, when the relationship between lineage and molecular state can vary greatly between individuals and between cell clones.

Lineage phylogenies

Trees of lineage relationships constructed from end point measurements.

Drop-outs

Type II errors that are common in single-cell omics experiments in which transcripts, lineage barcodes or other features present in cells fail to be detected.

Barcode homoplasy

A type I error in which identical DNA sequence barcodes are randomly recovered from cells with no close lineage relationship.

Cell ontogeny

The developmental history of a cell.

State convergence

A differentiation scenario in which cells with distinct origins converge onto the same end point on a state manifold.

Mitotic coupling

A class of developmental fate regulation mechanisms that specify states to the daughter cells of a mitotic division, either symmetrically or asymmetrically.

Population coupling

A class of developmental fate regulation mechanisms in which the cell state specification is uncoupled from cell division but the proportion of cells specified to each state is controlled.

State divergence

A scenario in which the asymmetric partitioning of cellular components between two daughters of a single cell division differentiates them rapidly or instantaneously into distinct states.

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Wagner, D.E., Klein, A.M. Lineage tracing meets single-cell omics: opportunities and challenges. Nat Rev Genet 21, 410–427 (2020). https://doi.org/10.1038/s41576-020-0223-2

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