Building a lineage from single cells: genetic techniques for cell lineage tracking

Abstract

Resolving lineage relationships between cells in an organism is a fundamental interest of developmental biology. Furthermore, investigating lineage can drive understanding of pathological states, including cancer, as well as understanding of developmental pathways that are amenable to manipulation by directed differentiation. Although lineage tracking through the injection of retroviral libraries has long been the state of the art, a recent explosion of methodological advances in exogenous labelling and single-cell sequencing have enabled lineage tracking at larger scales, in more detail, and in a wider range of species than was previously considered possible. In this Review, we discuss these techniques for cell lineage tracking, with attention both to those that trace lineage forwards from experimental labelling, and those that trace backwards across the life history of an organism.

Single-Cell RNA Sequencing: Unraveling the Brain One Cell at a Time

“…The dynamic changes in gene expression patterns at the single cell level in response to environmental or disease conditions may provide important insights into the ongoing cellular responses and mechanisms under relevant physiological and pathological processes. However, one should be cautious in interpreting whether a molecular profile corresponds to a cell type or a cell state [33, 37, 38]. The former refers to a unique, molecular signature that remains stable under different conditions, throughout development and into adulthood, while the latter corresponds to a more dynamic set of genes that shift their expression in response to different signaling stimuli.…”

ESC-Track: A Computer Workflow for 4-D Segmentation, Tracking, Lineage Tracing and Dynamic Context Analysis of ESCs

“…Most of these methods have been applied to Drosophila (1418) and zebrafish (1921) embryogenesis, or plant morphogenesis (22) studies. Of special relevance to the field of stem cell biology is the ability to integrate the cell behavior analysis with information about lineage (parentprogeny) and contextual (neighborhood) cellular relationships (9,11). In the last decade, several generic processing and tracking packages, such as Icy (23), Cell Profiler (24), tTt (25), qTfy (25), or the Fiji plugin TrackMate (26,27) have been reported.…”

“…Moreover, a new generation of fluorescent proteins and dyes allows biochemical characterization of signaling pathways in intact living cells (8). Tagging by fluorescent proteins enables positional tracking of any given cell over time, which is easily achieved when the population of tagged cells is distributed among non-expressing cells by virtue of lineage or in experimental mosaics, but it becomes challenging when a fluorescent protein label is widely expressed (9). The ability to track and analyze live cells in time-lapse 4-D microscopy images is a matter of intense research (10,11) since visual inspection and analysis are insufficient to extract meaningful insights, making automated tracking and quantitative analysis of cells an absolute requirement.…”

Synthetic gene circuits and cellular decision-making in human pluripotent stem cells

“…Traditionally, gene knock-outs, fluorescent labeling of endogenous genes or sensing of transcription factors or signaling pathways have been used to study essential genes that maintain the pluripotent state or lead to cell state transitions [63]. Another focus, that has recently received new attention due to the introduction of CRISPR/Cas9-based approaches [64,65], lies in developing genetic lineage tracking systems to track lineage choices in single live cells [66]. Other genetic methods have been developed to overcome challenges in producing hPSC-derived cells, most common being the defined control of key-transcription factors to manipulate hPSC transitions to differentiated cells.…”