Identification of T cell clones without the need for sequencing

Multicolor strategies for investigating clonal expansion and tissue plasticity

Understanding the generation of complexity in living organisms requires the use of lineage tracing tools at a multicellular scale. In this review, we describe the different multicolor strategies focusing on mouse models expressing several fluorescent reporter proteins, generated by classical (MADM, Brainbow and its multiple derivatives) or acute (StarTrack, CLoNe, MAGIC Markers, iOn, viral vectors) transgenesis. After detailing the multi-reporter genetic strategies that serve as a basis for the establishment of these multicolor mouse models, we briefly mention other animal and cellular models (zebrafish, chicken, drosophila, iPSC) that also rely on these constructs. Then, we highlight practical applications of multicolor mouse models to better understand organogenesis at single progenitor scale (clonal analyses) in the brain and briefly in several other tissues (intestine, skin, vascular, hematopoietic and immune systems). In addition, we detail the critical contribution of multicolor fate mapping strategies in apprehending the fine cellular choreography underlying tissue morphogenesis in several models with a particular focus on brain cytoarchitecture in health and diseases. Finally, we present the latest technological advances in multichannel and in-depth imaging, and automated analyses that enable to better exploit the large amount of data generated from multicolored tissues.

Multi-color clonal tracking reveals intra-stage proliferative heterogeneity during mammary tumor progression

Despite major progress in breast cancer research, the functional contribution of distinct cancer cell clones to malignant tumor progression and metastasis remains largely elusive. We have assessed clonal heterogeneity within individual primary tumors and metastases and also during the distinct stages of malignant tumor progression using clonal tracking of cancer cells in the MMTV-PyMT mouse model of metastatic breast cancer. Comparative gene expression analysis of clonal subpopulations reveals a substantial level of heterogeneity across and also within the various stages of breast carcinogenesis. The intra-stage heterogeneity is primarily manifested by differences in cell proliferation, also found within invasive carcinomas of luminal A-, luminal B-, and HER2-enriched human breast cancer. Surprisingly, in the mouse model of clonal tracing of cancer cells, chemotherapy mainly targets the slow-proliferative clonal populations and fails to efficiently repress the fast-proliferative populations. These insights may have considerable impact on therapy selection and response in breast cancer patients.

Seeing the Confetti Colors in a New Light Utilizing Flow Cytometry and Imaging Flow Cytometry

Stochastic multicolor transgenic labeling systems, such as the Brainbow reporters, have emerged as powerful tools in lineage tracing experiments. Originally designed for large-scale mapping of neuronal projections in densely populated tissues, they have been repurposed for diverse uses. The Brainbow 2.1-derived Confetti reporter was used, for example, to define stem cell clonality and dynamics in crypts of the intestinal mucosa, T-cell clonality, microglial heterogeneity, and B-cell clonal evolution in germinal centers. Traditionally, read-outs have relied on imaging in situ, providing information about cellular localization within tissue stroma. However, recent applications of the technique have moved into hematopoietically derived motile cell types, for example, T and B lymphocytes and their progeny, creating an unmet need to survey larger populations of cells ex vivo to determine labeling densities or skews in color representation over time to read-out clonal expansion and selection effects. Originally designed for imaging methods, these reporters encode information in the spectral properties of fluorophores and their subcellular localization, making them poorly suited to traditional flow cytometry analyses. The advent of high-content imaging and imaging flow cytometry have recently closed the gap between flow cytometry and imaging. We analyzed a 10-color biallelic Confetti reporter using flow and imaging flow cytometry. Beyond its use as a high-throughput method for measuring reporter labeling densities and color distributions over time, it also opens the door to new avenues of research relying on similar read-outs, for example, tumor heterogeneity and clonal dynamics. © 2020 International Society for Advancement of Cytometry.

Development of an in vivo model to study clonal lineage relationships in hematopoietic cells using Brainbow2.1/Confetti mice

Hematopoietic stem cells maintain the homeostasis of all blood cell progeny during development and repopulation-demanding events. To study the lineage relationships during hematopoiesis, increasingly complex cell tracing models are being developed. In this study, we describe adaptations to the original R26R-Confetti mouse model, which subsequently offers a relatively easy approach to study low complexity clonality during hematopoiesis, with special focus on B and T lymphocyte development. This protocol employs spatiotemporal Cre expression controlled by gammaretroviral transduction for efficient fluorescent protein cell marking. Transplantation of fluorescently marked Lin- cKit+ hematopoietic progenitor cells into Rag1-/- mice, resulted in the visualization of differentially contributing stem cell clones to various lineages. Our methodology is useful to study questions in fundamental and preclinical hematopoietic research and in vivo B- and T-cell development.

Live-Cell FRET Imaging Reveals a Role of Extracellular Signal-Regulated Kinase Activity Dynamics in Thymocyte Motility

Extracellular signal-regulated kinase (ERK) plays critical roles in T cell development in the thymus. Nevertheless, the dynamics of ERK activity and the role of ERK in regulating thymocyte motility remain largely unknown due to technical limitations. To visualize ERK activity in thymocytes, we here developed knockin reporter mice expressing a Förster/fluorescence resonance energy transfer (FRET)-based biosensor for ERK from the ROSA26 locus. Live imaging of thymocytes isolated from the reporter mice revealed that ERK regulates thymocyte motility in a subtype-specific manner. Negative correlation between ERK activity and motility was observed in CD4/CD8 double-positive thymocytes and CD8 single-positive thymocytes, but not in CD4 single-positive thymocytes. Interestingly, however, the temporal deviations of ERK activity from the average correlate with the motility of CD4 single-positive thymocytes. Thus, live-cell FRET imaging will open a window to understanding the dynamic nature and the diverse functions of ERK signaling in T cell biology.

•

Mice expressing EKAREV from ROSA26 locus enable ERK activity monitoring in T cells

•

ERK activity negatively regulates the motility of thymocytes in the thymus

•

Temporal dynamics of ERK activity regulates cell motility of CD4-SP in the medulla

•

TCR signal from intercellular association induces ERK activity dynamics in CD4-SP

Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development

Haematopoietic stem cells (HSCs) arise in the developing aorta during embryogenesis. The number of HSC clones born has been estimated through transplantation, but experimental approaches to assess the absolute number of forming HSCs in a native setting have remained challenging. Here, we applied single-cell and clonal analysis of HSCs in zebrafish to quantify developing HSCs. Targeting creER^T2 in developing cd41:eGFP⁺ HSCs enabled long-term assessment of their blood contribution. We also applied the Brainbow-based multicolour Zebrabow system with drl:creER^T2 that is active in early haematopoiesis to induce heritable colour barcoding unique to each HSC and its progeny. Our findings reveal that approximately 21 HSC clones exist prior to HSC emergence and 30 clones are present during peak production from aortic endothelium. Our methods further reveal that stress haematopoiesis, including sublethal irradiation and transplantation, reduces clonal diversity. Our findings provide quantitative insights into the early clonal events that regulate haematopoietic development.