Explore the vast range of titles available.

Cell fate determination is a fundamental process in multicellular development. In multicellular organisms, cells display plasticity in their fate, allowing them to revert to prior states or adopt alternative differentiation pathways, thereby altering their identity and functional specialization in response to specific stimuli. Investigating cell fate determination and its plasticity enhances our understanding of organ development, tissue homeostasis, and disease pathogenesis and progression, providing novel insights into regenerative medicine strategies. Lineage tracing technologies have fundamentally revolutionized this understanding of cell fate dynamics by enabling the identification and tracking of cells and their progeny in vivo. These technologies have progressed significantly, from the direct observation and manual annotation of cell lineage trees to complex recombinase‐mediated genetic labeling techniques. With the advent of sequencing technologies, the resolution and scale of lineage tracing have also developed toward the single‐cell level in individual organisms. Furthermore, lineage tracing is increasingly expanding to investigate how the tissue microenvironment influences cell fate decisions. Here, the evolution of lineage tracing technologies is introduced and their applications in cell fate determinations across development, regeneration, and diseases contexts. This figure is a candidate for the cover image. It shows a whole‐mount fluorescent image of lymphatic vessels (red) in the heart of an adult Cdh5‐Dre; Prox1‐RSR‐CreER; Rosa26‐tdT mouse. Image courtesy of Ximeng Han.

Idiopathic pulmonary fibrosis (IPF) is an age‐associated disease characterized by the irreversible accumulation of excessive extracellular matrix components by activated myofibroblasts (aMYFs). Following bleomycin administration in young mice, fibrosis formation associated with efficient resolution takes place limiting the clinical relevance of this model for IPF. In this study, we used aged mice in combination with bleomycin administration to trigger enhanced fibrosis formation and delayed resolution as a more relevant model for IPF. Alveolosphere assays were carried out to compare the alveolar resident mesenchymal niche activity for AT2 stem cells in young versus old mice. Lineage tracing of the Acta2+ aMYFs in old mice exposed to bleomycin followed by scRNAseq of the lineage‐traced cells isolated during fibrosis formation and resolution was performed to delineate the heterogeneity of aMYFs during fibrosis formation and their fate during resolution. Integration of previously published similar scRNAseq results using young mice was carried out. Our results show that alveolar resident mesenchymal cells from old mice display decreased supporting activity for AT2 stem cells. Our findings suggest that the cellular and molecular mechanisms underlying the aMYFs formation and differentiation towards the Lipofibroblast phenotype are mostly conserved between young and old mice. In addition to persistent fibrotic signaling in aMYF from old mice during resolution, we also identified differences linked to interleukin signaling in old versus young alveolar fibroblast populations before and during bleomycin injury. Importantly, our work confirms the relevance of a subcluster of aMYFs in old mice that is potentially relevant for future management of IPF. Model of LIF‐to‐aMYF reversible switch during fibrosis formation and resolution in old mice. The main contributors during fibrosis formation to Cthrc1+ aMYF are Acta2+ LIFhigh alveolar fibroblasts. During fibrosis resolution, Cthrc1+ aMYF differentiate back to the LIFhigh (please write \"high\" in superscript) alveolar fibroblasts cluster.

Tumor cell heterogeneity is a crucial characteristic of malignant brain tumors and underpins phenomena such as therapy resistance and tumor recurrence. Advances in single‐cell analysis have enabled the delineation of distinct cellular states of brain tumor cells, but the time‐dependent changes in such states remain poorly understood. Here, we construct quantitative models of the time‐dependent transcriptional variation of patient‐derived glioblastoma (GBM) cells. We build the models by sampling and profiling barcoded GBM cells and their progeny over the course of 3 weeks and by fitting a mathematical model to estimate changes in GBM cell states and their growth rates. Our model suggests a hierarchical yet plastic organization of GBM, where the rates and patterns of cell state switching are partly patient‐specific. Therapeutic interventions produce complex dynamic effects, including inhibition of specific states and altered differentiation. Our method provides a general strategy to uncover time‐dependent changes in cancer cells and offers a way to evaluate and predict how therapy affects cell state composition. Synopsis A single cell‐based strategy that tracks and models time‐dependent changes in brain tumor cells indicates that patient‐derived glioblastoma cells follow a near‐hierarchical organisation that can be altered by therapeutic agents. A general method is developed for de novo construction of quantitative network models of cancer cell State Transitions and Growth (STAG) from single‐cell measurements. Patient‐derived glioblastoma cells transit between transcriptional states, recapitulating normal neural cell types, in a hierarchical fashion. The STAG model can identify patient differences in cell state dynamics and define how therapeutic agents can alter the transition network. The long‐term cell population growth and cell state composition can be predicted by a mathematical eigendecomposition of the STAG network. Graphical Abstract A single cell‐based strategy that tracks and models time‐dependent changes in brain tumor cells indicates that patient‐derived glioblastoma cells follow a near‐hierarchical organisation that can be altered by therapeutic agents.

Lineage tracing is a valuable technique that has greatly facilitated the exploration of cell origins and behavior. With the continuous development of single-cell sequencing technology, lineage tracing technology based on the single-cell level has become an important method to study biological development. Single-cell Lineage tracing technology plays an important role in the hematological system. It can help to answer many important questions, such as the heterogeneity of hematopoietic stem cell function and structure, and the heterogeneity of malignant tumor cells in the hematological system. Many studies have been conducted to explore the field of hematology by applying this technology. This review focuses on the superiority of the emerging single-cell lineage tracing technologies of Integration barcodes, CRISPR barcoding, and base editors, and summarizes their applications in the hematology system. These studies have suggested the vast potential in unraveling complex cellular behaviors and lineage dynamics in both normal and pathological contexts.

Elucidating the chromatin dynamics that orchestrate embryogenesis is a fundamental question in developmental biology. Here, we exploit position effects on expression as an indicator of chromatin activity and infer the chromatin activity landscape in every lineaged cell during Caenorhabditis elegans early embryogenesis. Systems‐level analyses reveal that chromatin activity distinguishes cellular states and correlates with fate patterning in the early embryos. As cell lineage unfolds, chromatin activity diversifies in a lineage‐dependent manner, with switch‐like changes accompanying anterior–posterior fate asymmetry and characteristic landscapes being established in different cell lineages. Upon tissue differentiation, cellular chromatin from distinct lineages converges according to tissue types but retains stable memories of lineage history, contributing to intra‐tissue cell heterogeneity. However, the chromatin landscapes of cells organized in a left–right symmetric pattern are predetermined to be analogous in early progenitors so as to pre‐set equivalent states. Finally, genome‐wide analysis identifies many regions exhibiting concordant chromatin activity changes that mediate the co‐regulation of functionally related genes during differentiation. Collectively, our study reveals the developmental and genomic dynamics of chromatin activity at the single‐cell level. SYNOPSIS This study investigates the influence of local chromatin environment on reporter gene expression during Caenorhabditis elegans embryogenesis, based on single‐cell lineage tracing and live‐cell imaging. The chromatin activity landscape is inferred in lineage‐resolved single cells during C. elegans early embryogenesis. Chromatin activity diversifies in a lineage‐dependent manner, accompanying lineage fate commitment and anterior‐posterior fate asymmetry. Chromatin activity converges on tissue‐specific states but retains memories of lineage origins that contribute to cell heterogeneity within tissues. Predetermination of analogous chromatin activity occurs in early progenitor cells during left‐right symmetry establishment. Graphical Abstract This study investigates the influence of local chromatin environment on reporter gene expression during Caenorhabditis elegans embryogenesis, based on single‐cell lineage tracing and live‐cell imaging.

Basic mechanism of spine development is poorly understood. Type II collagen positive (Col2+) cells have been reported to encompass early mesenchymal progenitors that continue to become chondrocytes, osteoblasts, stromal cells, and adipocytes in long bone. However, the function of Col2+ cells in spine and intervertebral disc (IVD) development is largely unknown. To further elucidate the function of Col2+ progenitors in spine, we generated the mice with ablation of Col2+ cells either at embryonic or at postnatal stage. Embryonic ablation of Col2+ progenitors caused the mouse die at newborn with the absence of all spine and IVD. Moreover, postnatal deletion Col2+ cells in spine resulted in a shorter growth plate and endplate cartilage, defected inner annulus fibrosus, a less compact and markedly decreased gel‐like matrix in the nucleus pulposus and disorganized cell alignment in each compartment of IVD. Genetic lineage tracing IVD cell populations by using inducible Col2‐creERT;tdTomato reporter mice and non‐inducible Col2‐cre;tdTomato reporter mice revealed that the numbers and differentiation ability of Col2+ progenitors decreased with age. Moreover, immunofluorescence staining showed type II collagen expression changed from extracellular matrix to cytoplasm in nucleus pulposus between 6 month and 1‐year‐old mice. Finally, fate‐mapping studies revealed that Col2+ progenitors are essential for IVD repair in IVD injured model. In summary, embryonic Col2+ cells are the major source of spine development and Col2+ progenitors are the important contributors for IVD repair and regeneration. Type II collagen‐positive embryonic progenitors are the major contributors to spine and intervertebral disc development and repair.

The liver and pancreas are closely associated organs that share a common embryological origin. They display amphicrine properties and have similar exocrine organization with parenchymal cells, namely, hepatocytes and acinar cells, secreting bile and pancreatic juice into the duodenum via a converging network of bile ducts and pancreatic ducts. Here we compare and highlight the similarities of molecular mechanisms leading to liver and pancreatic cancer development. We suggest that unraveling tumor development in an organ may provide insight into our understanding of carcinogenesis in the other organ.

The site‐specific excision of a target DNA sequence for genetic knockout or lineage tracing is a powerful tool for investigating biological systems. Currently, site‐specific recombinases (SSRs), such as Cre or Flp recombination target cassettes, have been successfully excised or inverted by a single SSR to regulate transgene expression. However, the use of a single SSR might restrict the complex control of gene expression. This study investigated the potential for expanding the multiple regulation of transgenes using three different integrase systems (TP901‐1, R4, and Bxb1). We designed three excision cassettes that expressed luciferase, where the luciferase expression could be exchanged to a fluorescent protein by site‐specific recombination. Individual cassettes that could be regulated independently by a different integrase were connected in tandem and inserted into a mouse artificial chromosome (MAC) vector in Chinese hamster ovary cells. The transient expression of an integrase caused the targeted luciferase activity to be lost and fluorescence was activated. Additionally, the integrase system enabled the specific excision of targeted DNA sequences without cross‐reaction with the other recombination targets. These results suggest that the combined use of these integrase systems in a defined locus on a MAC vector permits the multiple regulation of transgene expression and might contribute to genomic or cell engineering. We generated a reporter system to evaluate the precise target DNA excision for three distinct integrases, TP901‐1, R4, and Bxb1. Using this reporter system, we marked cells with up to eight different expression patterns of fluorescent proteins after the transient expression of specific integrases. The reporter system was inserted into a mouse artificial chromosome vector for the stable expression of reporters.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia—a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia .