scholarly journals Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics

2022 ◽  
Vol 12 ◽  
Author(s):  
Livius Penter ◽  
Satyen H. Gohil ◽  
Catherine J. Wu

Blood malignancies provide unique opportunities for longitudinal tracking of disease evolution following therapeutic bottlenecks and for the monitoring of changes in anti-tumor immunity. The expanding development of multi-modal single-cell sequencing technologies affords newer platforms to elucidate the mechanisms underlying these processes at unprecedented resolution. Furthermore, the identification of molecular events that can serve as in-vivo barcodes now facilitate the tracking of the trajectories of malignant and of immune cell populations over time within primary human samples, as these permit unambiguous identification of the clonal lineage of cell populations within heterogeneous phenotypes. Here, we provide an overview of the potential for chromosomal copy number changes, somatic nuclear and mitochondrial DNA mutations, single nucleotide polymorphisms, and T and B cell receptor sequences to serve as personal natural barcodes and review technical implementations in single-cell analysis workflows. Applications of these methodologies include the study of acquired therapeutic resistance and the dissection of donor- and host cellular interactions in the context of allogeneic hematopoietic stem cell transplantation.

2015 ◽  
Vol 26 (22) ◽  
pp. 3940-3945 ◽  
Author(s):  
Laura Lande-Diner ◽  
Jacob Stewart-Ornstein ◽  
Charles J. Weitz ◽  
Galit Lahav

Tracking molecular dynamics in single cells in vivo is instrumental to understanding how cells act and interact in tissues. Current tissue imaging approaches focus on short-term observation and typically nonendogenous or implanted samples. Here we develop an experimental and computational setup that allows for single-cell tracking of a transcriptional reporter over a period of >1 wk in the context of an intact tissue. We focus on the peripheral circadian clock as a model system and measure the circadian signaling of hundreds of cells from two tissues. The circadian clock is an autonomous oscillator whose behavior is well described in isolated cells, but in situ analysis of circadian signaling in single cells of peripheral tissues is as-yet uncharacterized. Our approach allowed us to investigate the oscillatory properties of individual clocks, determine how these properties are maintained among different cells, and assess how they compare to the population rhythm. These experiments, using a wide-field microscope, a previously generated reporter mouse, and custom software to track cells over days, suggest how many signaling pathways might be quantitatively characterized in explant models.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 566-566
Author(s):  
Arnav Mehta ◽  
Mati Mann ◽  
Monika Kowalczyk ◽  
Carl de Boer ◽  
Jun Wang ◽  
...  

Abstract Hematopoietic stem cells (HSCs) have the unique responsibility to produce balanced immune cell output throughout an organism's life. Importantly, they must do so robustly despite a plethora of external stress, including frequent inflammatory challenge. With age, the accumulation of these stresses leads to impaired HSC function and myeloid-biased output. Aged HSCs are also more prone to pathological hematopoiesis, such as myeloproliferative disorder, leukemia and autoimmune diseases. However, little is known about the subcellular mechanisms that govern the inflammatory response of HSCs with age, which in turn might contribute to pathologic transformation. We show that young hematopoietic stem and progenitor cells (HSPCs) demonstrate a robust transcriptional response to toll-like receptor (TLR) ligands. Interestingly, this response is similar to that of mature immune cell types such as dendritic cells. Using single-cell proteomic assays, we found that young HSPCs secrete a diverse array of myeloid and lymphoid cytokines. However, when challenged with TLR ligands in vivo, young mice acutely increase myeloid-biased output but return rapidly to baseline hematopoietic output of both lymphoid and myeloid cells. Moreover, inflammatory challenge of young long-term HSCs in vitro did not perturb the function and output of these cells in bone marrow reconstitution experiments. In contrast to their counterparts from young mice, we found HSPCs obtained from aged mice have a diminished ability to secrete cytokines in response to TLR ligands. Furthermore, they secrete a homogenous subset of myeloid-biased cytokines. When challenged with TLR ligands in vivo, aged mice acutely increased myeloid output and maintain elevated myeloid output for several months implying memory of the inflammatory challenge. Consistent with this, we also found that pre-stimulation of aged HSCs prior to bone marrow transplant results in a sustained increase in myeloid output compared to unstimulated aged HSCs. To elucidate the differential heterogeneity between young and aged HSPCs in response to TLR signaling, we next performed single-cell RNA sequencing (RNA-seq) experiments. We found that the sustained myeloid output in aged mice after TLR stimulation is largely due to expansion of a myeloid-biased HSC subset in the aged HSC pool. By characterizing the gene expression networks that define these myeloid-biased HSCs under stimulation conditions, we were then able to identify a myeloid-biased HSC subset in both the unperturbed young and aged HSC pools. Moreover, we found that these cells are more abundant in aged mice at steady-state, and that these HSCs demonstrate a unique response to inflammatory challenge. We further identify putative transcriptional regulators, including Klf4, Klf5, Ikzf1 and Stat3, among others, that define gene expression in these myeloid-biased HSCs. We further show that loss of function of these factors can differentially alter myeloid output in young and aged mice both in vitro and in vivo. Our results demonstrate that there is a differential response of young and aged HSCs to inflammatory signals. Using single-cell RNA-seq and protein secretion studies, we elucidate the molecular heterogeneity of the HSC pool at steady state and with TLR stimulation. By resolving heterogeneous subsets of cells in both the young and aged HSC pool, and by uncovering the transcriptional regulators that influence their function, we thus propose a new model of inflammatory hematopoiesis that may have implications to understanding age-related defects in immune development. Disclosures No relevant conflicts of interest to declare.


Blood ◽  
2021 ◽  
Author(s):  
Shu Sun ◽  
Chen Jin ◽  
Jia Si ◽  
Ying Lei ◽  
Kunying Chen ◽  
...  

Megakaryocytes (MKs), the platelet progenitor cell, play important roles in hematopoietic stem cell (HSC) maintenance and immunity. However, it is not known whether these diverse programs are executed by a single population or by distinct subsets of cells. Here, we manually-isolated primary CD41+ MKs from the bone marrow (BM) of mice and human donors based on ploidy (2N-32N), performed single-cell RNA sequencing analysis. We found that cellular heterogeneity existed within three distinct subpopulations possessing gene signatures related to platelet-generation, HSC niche interaction, and inflammatory responses, respectively. In situ immunostaining of mouse BM demonstrated that platelet-generation and HSC-niche related MKs were physically in close proximity to blood vessels and HSCs, respectively. Proplatelets, which could give rise to platelets under the blood shear forces, were predominantly formed on platelet-generation subset. Remarkably, the inflammatory responses subpopulation, consisting generally of low-ploidy LSP1+ and CD53+ MKs (≤8N), represented approximately 5% of total MKs in the BM. These MKs could specifically respond to pathogen infections in mice. Rapid expansion of this population was accompanied by strong upregulation of a pre-existing PU.1 and IRF-8-associated monocytic-like transcriptional program involved in pathogen recognition and clearance, as well as antigen presentation. Consistently, isolated primary CD53+ cells were capable to engulf and digest bacteria and to stimulate T cells in vitro. Together, our findings uncover new molecular, spatial, and functional heterogeneity within MKs in vivo and demonstrate the existence of a specialized MK subpopulation that may act as a new type of immune cell.


2020 ◽  
Author(s):  
Bertram Bengsch ◽  
Marius Schwabenland ◽  
Henrike Salié ◽  
Jovan Tanevski ◽  
Saskia Killmer ◽  
...  

Abstract COVID-19 causes neurological symptoms that can be potentially life-threatening in up to 67 % of the patients. The underlying pathophysiological mechanisms of COVID-19 associated encephalopathy, the involved immune cells, their spatial distribution and their cellular interactions during disease remain largely unclear. In this study, we performed a 38-biomarker imaging mass cytometry analysis of the brain stem from 25 patients and additional controls to understand the local immune response during SARS-CoV-2 infection at a spatially resolved, high-dimensional single-cell level. Importantly, utilizing an unbiased image segmentation and cell classification pipeline, we observed a significant immune activation in the central nervous system (CNS) and identified novel context-specific CD8 T cell and microglial clusters. Spatially resolved single-cell analysis identified distinct phenotypes of T cells and microglial clusters, their presence in specific anatomical regions and their cellular interactions. Our analysis further highlights microglial nodules and perivascular immune cell clusters as key sites of the local immune response. It also demonstrates that disease-associated neuroinflammation is associated with severe axonal damage as a structural basis for the neurologic deficits. Finally, we identified compartment- and cluster-specific immune checkpoints that can be used for future therapeutic interventions.


2021 ◽  
Vol 12 ◽  
Author(s):  
Gráinne Jameson ◽  
Mark W. Robinson

Diverse populations of natural killer (NK) cells have been identified in circulating peripheral blood and a wide variety of different tissues and organs. These tissue-resident NK cell populations are phenotypically distinct from circulating NK cells, however, functional descriptions of their roles within tissues are lacking. Recent advances in single cell RNA sequencing (scRNA-seq) have enabled detailed transcriptional profiling of tissues at the level of single cells and provide the opportunity to explore NK cell diversity within tissues. This review explores potential novel functions of human liver-resident (lr)NK cells identified in human liver scRNA-seq studies. By comparing these datasets we identified up-regulated and down-regulated genes associated with lrNK cells clusters. These genes encode a number of activating and inhibiting receptors, as well as signal transduction molecules, which highlight potential unique pathways that lrNK cells utilize to respond to stimuli within the human liver. This unique receptor repertoire of lrNK cells may confer the ability to regulate a number of immune cell populations, such as circulating monocytes and T cells, while avoiding activation by liver hepatocytes and Kupffer cells. Validating the expression of these receptors on lrNK cells and the proposed cellular interactions within the human liver will expand our understanding of the liver-specific homeostatic roles of this tissue-resident immune cell population.


2021 ◽  
Vol 358 ◽  
pp. 109192
Author(s):  
Yajie Liang ◽  
Liset M. de la Prida

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Łukasz Kiraga ◽  
Paulina Kucharzewska ◽  
Damian Strzemecki ◽  
Tomasz P. Rygiel ◽  
Magdalena Król

Abstract In vivo tracking of administered cells chosen for specific disease treatment may be conducted by diagnostic imaging techniques preceded by cell labeling with special contrast agents. The most commonly used agents are those with radioactive properties, however their use in research is often impossible. This review paper focuses on the essential aspect of cell tracking with the exclusion of radioisotope tracers, therefore we compare application of different types of non-radioactive contrast agents (cell tracers), methods of cell labeling and application of various techniques for cell tracking, which are commonly used in preclinical or clinical studies. We discuss diagnostic imaging methods belonging to three groups: (1) Contrast-enhanced X-ray imaging, (2) Magnetic resonance imaging, and (3) Optical imaging. In addition, we present some interesting data from our own research on tracking immune cell with the use of discussed methods. Finally, we introduce an algorithm which may be useful for researchers planning leukocyte targeting studies, which may help to choose the appropriate cell type, contrast agent and diagnostic technique for particular disease study.


2000 ◽  
Vol 164 (6) ◽  
pp. 3047-3055 ◽  
Author(s):  
Dragana Jankovic ◽  
Marika C. Kullberg ◽  
Nancy Noben-Trauth ◽  
Patricia Caspar ◽  
William E. Paul ◽  
...  

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tracy M. Yamawaki ◽  
Daniel R. Lu ◽  
Daniel C. Ellwanger ◽  
Dev Bhatt ◽  
Paolo Manzanillo ◽  
...  

Abstract Background Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete transcriptomes due to the prevalence of cellular and transcriptional dropout events. This issue is often compounded by limited sample availability and limited prior knowledge of heterogeneity, which can confound data interpretation. Results Here, we systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluated methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5′ v1 and 3′ v3 methods. We demonstrate that these methods have fewer dropout events, which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures. Conclusion Overall, our characterization of immune cell mixtures provides useful metrics, which can guide selection of a high-throughput single-cell RNA-seq method for profiling more complex immune-cell heterogeneity usually found in vivo.


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