scholarly journals Ly6Chi monocytes are metabolically reprogrammed in the blood during inflammatory stimulation allowing for macrophage lineage commitment

2021 ◽  
Author(s):  
Gareth Purvis ◽  
Eileen McNeill ◽  
Benjamin Wright ◽  
Santiago Revale ◽  
Helen Lockstone ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Tracking ◽  
Acute Inflammation ◽  
Human Monocyte ◽  
Cell Types ◽  
Phenotypic Change ◽  
Significant Heterogeneity ◽  
Transcriptional Reprogramming ◽  
New Findings ◽  
Monocytes And Macrophages

Acute inflammation is a rapid and dynamic process involving the recruitment and activation of multiple cell types in a co-ordinated and precise manner. Using cell tracking, linage tracing and single cell transcriptomics we investigated the origin and transcriptional reprogramming of monocytes and macrophages in acute inflammation. Monocyte trafficking and adoptive transfer experiments revealed that monocytes undergo rapid phenotypic change as they exit the blood and give rise to monocyte-derived macrophages that persist during the resolution of inflammation. Single cell transcriptomics revealed significant heterogeneity within the surface marker defined CD11b+Ly6G-Ly6Chi monocyte population within the blood and at the site of inflammation. Lineage trajectory analysis revealed that Ly6Chi monocytes in the blood are re-programmed into a defined differentiation pathway following inflammatory stimulus. We show that two major transcriptional reprogramming events occur during the initial 6h of Ly6Chi monocyte mobilisation, one in the blood priming monocytes for migration and a second at the site of inflammation. Pathway analysis revealed an important role for oxidative phosphorylation (OxPhos) during both these reprogramming events in a subset of M2-like cells. Experimentally we also demonstrate that OxPhos is essential for murine and human monocyte chemotaxis. These new findings opening up the possibility that altering monocyte metabolic capacity towards OxPhos could facilitate enhanced macrophage M2-like polarisation to aid inflammation resolution and tissue repair.

scholarly journals Single-cell RNA-Aequencing Reveals Novel Myofibroblasts with Epithelial Cell-Like Features in the Mammary Gland of Dairy Cattle

2020 ◽  
Author(s):  
Fengfei Gu ◽  
Jiajin Wu ◽  
Senlin Zhu ◽  
Teresa G. Valencak ◽  
Jian-Xin Liu ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Epithelial Cell ◽  
Epithelial Cells ◽  
Dairy Cattle ◽  
Single Cell ◽  
Dairy Product ◽  
Cell Types ◽  
Marker Genes ◽  
New Findings ◽  
Luminal Cells

Abstract Background: Cow’s milk is a highly-nutritious dairy product that is widely consumed worldwide. It is secreted by the developed mammary gland (MG) of dairy cattle. However, a comprehensive understanding of cell-type diversity and cell function within bovine MG is lacking. In the current study, we used single-cell RNA sequencing to investigate the transcriptome of 24,472 high-quality MG cells isolated from newborn and adult cows. Results: Unbiased clustering analysis revealed the existence of 24 cell types, which could be divided into four categories: 9 immune, 3 epithelial, 9 fibroblast, and 3 endothelial cell types. Other cell subtypes were further identified based on re-clustering and pseudotemporal reconstruction of epithelial cells that included 3 mature luminal epithelial, 1 intermediate, and 2 progenitor cell subtypes. The individual top marker genes of these 3 mature luminal epithelial cell subtypes (L0, L1, and L5) were APOA1, STC2, and PTX3, which were further validated using immunofluorescence. Based on functional analysis, the L0, L1, and L5 cell subtypes were all involved in the upregulation of lipid metabolism, protein and hormone metabolism, and the immune response, respectively. Furthermore, we discovered a novel myofibroblast that expresses COL1A1 and CSN3, has visible epithelial-like characteristics, and shows the potential to differentiate into luminal epithelial cells, especially immune-sensing luminal cells (L5). Conclusions: We constructed the first single-cell atlas of the dairy cow MG, and our new findings of epithelial-like myofibroblast cells and their differentiation trajectories into luminal cells may provide novel insights into the development and lactogenesis in dairy cattle MGs.

scholarly journals Dose-dependent spatiotemporal responses of mammalian cells to an alkylating agent

2017 ◽  
Author(s):  
Ann Rancourt ◽  
Sachiko Sato ◽  
Masahiko S. Satoh
Keyword(s):  
Cell Death ◽  
Single Cell ◽  
Cell Lines ◽  
Hela Cells ◽  
Cell Tracking ◽  
Cell Lineage ◽  
Cellular Responses ◽  
Spatiotemporal Data ◽  
Significant Heterogeneity ◽  
Lineage Tracking

AbstractCultured cell populations are composed of heterogeneous cells, and previous single-cell lineage tracking analysis of individual HeLa cells provided empirical evidence for significant heterogeneity of cell fates. Nevertheless, such cell lines have been used for investigations of cellular responses to various substances, resulting in incomplete characterizations. This problem caused by heterogeneity within cell lines could be overcome by analyzing the spatiotemporal responses of individual cells to a substance. However, no approach to investigate the responses using spatiotemporal data is currently available. Thus, the current study aimed to analyze the spatiotemporal responses of individual HeLa cells to cytotoxic, sub-cytotoxic, and non-cytotoxic doses of the well-characterized carcinogen, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Although cytotoxic doses of MNNG are known to induce cell death, the single-cell tracking approach revealed that cell death occurred following at least four different cellular events, suggesting that cell death is induced via multiple processes. We also found that HeLa cells exposed to sub-cytotoxic doses of MNNG were in a state of equilibrium between cell proliferation and cell death, with cell death again induced through different processes. However, exposure of cells to non-cytotoxic doses of MNNG promoted growth by reducing the cell doubling time, thus promoting the growth of a sub-population of cells previously recognized as putative cancer stem cells. These results demonstrate that the responses of cells to MNNG can be analyzed precisely using spatiotemporal data, regardless of the presence of heterogeneity among cultured cells, suggesting that single-cell lineage tracking analysis can be used as a novel and accurate analytical method to investigate cellular responses to various substances.

scholarly journals Interrogation of human hematopoiesis at single-cell and single-variant resolution

2018 ◽  
Author(s):  
Caleb A. Lareau ◽  
Jacob C. Ulirsch ◽  
Erik L. Bao ◽  
Leif S. Ludwig ◽  
Michael H. Guo ◽  
...  
Keyword(s):  
Single Cell ◽  
Target Genes ◽  
Cell Types ◽  
Core Gene ◽  
Chromatin Accessibility ◽  
Significant Heterogeneity ◽  
Analytic Framework ◽  
Causal Variants ◽  
Using Data ◽  
The Uk

AbstractIncomplete annotation of cell-to-cell state variance and widespread linkage disequilibrium in the human genome represent significant challenges to elucidating mechanisms of trait-associated genetic variation. Here, using data from the UK Biobank, we perform genetic fine-mapping for 16 blood cell traits to quantify posterior probabilities of association while allowing for multiple independent signals per region. We observe an enrichment of fine-mapped variants in accessible chromatin of lineage-committed hematopoietic progenitor cells. Further, we develop a novel analytic framework that identifies “core gene” cell type enrichments and show that this approach uniquely resolves relevant cell types within closely related populations. Applying our approach to single cell chromatin accessibility data, we discover significant heterogeneity within classically defined multipotential progenitor populations. Finally, using several lines of empirical evidence, we identify relevant cell types, predict target genes, and propose putative causal mechanisms for fine-mapped variants. In total, our study provides an analytic framework for single-variant and single-cell analyses to elucidate putative causal variants and cell types from GWAS and high-resolution epigenomic assays.

scholarly journals Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity

2021 ◽  
Author(s):  
Caitriona M McEvoy ◽  
Julia M Murphy ◽  
Lin Zhang ◽  
Sergi Clotet-Freixas ◽  
Jessica A Mathews ◽  
...  
Keyword(s):  
Single Cell ◽  
Human Kidney ◽  
Cell Types ◽  
Significant Heterogeneity ◽  
Proximal Tubular Cells ◽  
Healthy Human ◽  
Fresh Tissue ◽  
Tubular Cells ◽  
Distinct Cell ◽  
Proximal Tubular

Maintaining organ homeostasis requires complex functional synergy between distinct cell types, a snapshot of which is glimpsed through the simultaneously broad and granular analysis provided by single-cell atlases. Knowledge of the transcriptional programs underpinning the complex and specialized functions of human kidney cell populations at homeostasis is limited by difficulty accessing healthy, fresh tissue. Here, we present a single-cell perspective of healthy human kidney from 19 living donors, with equal contribution from males and females, profiling the transcriptome of 27677 high-quality cells to map healthy kidney at high resolution. Our sex-balanced dataset revealed sex-based differences in gene expression within proximal tubular cells, specifically, increased anti-oxidant metallothionein genes in females and the predominance of aerobic metabolism-related genes in males. Functional differences in metabolism were confirmed between male and female proximal tubular cells, with male cells exhibiting higher oxidative phosphorylation and higher levels of energy precursor metabolites. Within the immune niche, we identified kidney-specific lymphocyte populations with unique transcriptional profiles indicative of kidney-adapted functions and validated findings by flow cytometry. We observed significant heterogeneity in resident myeloid populations and identified an MRC1+ LYVE1+ FOLR2+ C1QC+ population as the predominant myeloid population in healthy kidney. This study provides a detailed cellular map of healthy human kidney, revealing novel insights into the complexity of renal parenchymal cells and kidney-resident immune populations.

scholarly journals Single-Cell RNAseq analysis of infiltrating neoplastic cells at the migrating front of human glioblastoma

2017 ◽  
Author(s):  
Spyros Darmanis ◽  
Steven A. Sloan ◽  
Derek Croote ◽  
Marco Mignardi ◽  
Sophia Chernikova ◽  
...  
Keyword(s):  
Single Cell ◽  
Immunological Response ◽  
Myeloid Cell ◽  
Cell Types ◽  
Gene Signature ◽  
Tumor Formation ◽  
Common Mechanism ◽  
Significant Heterogeneity ◽  
Neoplastic Cells ◽  
And Migration

SummaryGlioblastoma is the most common primary brain cancer in adults and is notoriously difficult to treat due to its diffuse nature. We performed single-cell RNAseq on 3589 cells in a cohort of four patients. We obtained cells from the tumor core as well as surrounding peripheral tissue. Our analysis revealed cellular variation in the tumor’s genome and transcriptome, We were able to identify infiltrating neoplastic cells in regions peripheral to the core lesions. Despite the existence of significant heterogeneity among neoplastic cells, we found that infiltrating GBM cells share a consistent gene signature between patients, suggesting a common mechanism of infiltration. Additionally, in investigating the immunological response to the tumors, we found transcriptionally distinct myeloid cell populations residing in the tumor core and the surrounding peritumoral space. Our data provide a detailed dissection of GBM cell types, revealing an abundance of novel information about tumor formation and migration.

scholarly journals Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

2021 ◽  
Vol 17 (1) ◽  
pp. e1009292 ◽  
Author(s):  
Jessica K. Fiege ◽  
Joshua M. Thiede ◽  
Hezkiel Arya Nanda ◽  
William E. Matchett ◽  
Patrick J. Moore ◽  
...  
Keyword(s):  
Single Cell ◽  
Airway Epithelium ◽  
Cell Types ◽  
Secretory Cells ◽  
Significant Heterogeneity ◽  
Antiviral Responses ◽  
Human Airway ◽  
Human Airway Epithelium ◽  
Infected Cells ◽  
Interferon Responses

The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNA-sequencing to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of epithelial cell types are susceptible to infection, ciliated cells are the predominant cell target of SARS-CoV-2. The host protease TMPRSS2 was required for infection of these cells. Importantly, remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. Induction of interferon responses within infected cells was rare and there was significant heterogeneity in the antiviral gene signatures, varying with the burden of infection in each cell. We also found that heavily infected secretory cells expressed abundant IL-6, a potential mediator of COVID-19 pathogenesis.

scholarly journals Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

2020 ◽  
Author(s):  
Jessica K. Fiege ◽  
Joshua M. Thiede ◽  
Hezkiel Nanda ◽  
William E. Matchett ◽  
Patrick J. Moore ◽  
...  
Keyword(s):  
Single Cell ◽  
Airway Epithelium ◽  
Cell Types ◽  
Secretory Cells ◽  
Significant Heterogeneity ◽  
Antiviral Responses ◽  
Human Airway ◽  
Human Airway Epithelium ◽  
Infected Cells ◽  
Interferon Responses

AbstractThe human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNA-sequencing to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of epithelial cell types are susceptible to infection, ciliated cells are the predominant cell target of SARS-CoV-2. The host protease TMPRSS2 was required for infection of these cells. Importantly, remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. Induction of interferon responses within infected cells was rare and there was significant heterogeneity in the antiviral gene signatures, varying with the burden of infection in each cell. We also found that heavily infected secretory cells expressed abundant IL-6, a potential mediator of COVID-19 pathogenesis.

scholarly journals Sequential fate-switches in stem-like cells drive the tumorigenic trajectory from human neural stem cells to malignant glioma

Cell Research ◽  
2021 ◽  
Author(s):  
Xiaofei Wang ◽  
Ran Zhou ◽  
Yanzhen Xiong ◽  
Lingling Zhou ◽  
Xiang Yan ◽  
...  
Keyword(s):  
Malignant Glioma ◽  
Single Cell ◽  
De Novo ◽  
Early Stage ◽  
Lineage Tracing ◽  
Human Neural Stem Cells ◽  
Transcriptional Reprogramming ◽  
Neural Stem Progenitor Cells ◽  
Human Gbm ◽  
End Stage

AbstractGlioblastoma (GBM) is an incurable and highly heterogeneous brain tumor, originating from human neural stem/progenitor cells (hNSCs/hNPCs) years ahead of diagnosis. Despite extensive efforts to characterize hNSCs and end-stage GBM at bulk and single-cell levels, the de novo gliomagenic path from hNSCs is largely unknown due to technical difficulties in early-stage sampling and preclinical modeling. Here, we established two highly penetrant hNSC-derived malignant glioma models, which resemble the histopathology and transcriptional heterogeneity of human GBM. Integrating time-series analyses of whole-exome sequencing, bulk and single-cell RNA-seq, we reconstructed gliomagenic trajectories, and identified a persistent NSC-like population at all stages of tumorigenesis. Through trajectory analyses and lineage tracing, we showed that tumor progression is primarily driven by multi-step transcriptional reprogramming and fate-switches in the NSC-like cells, which sequentially generate malignant heterogeneity and induce tumor phenotype transitions. We further uncovered stage-specific oncogenic cascades, and among the candidate genes we functionally validated C1QL1 as a new glioma-promoting factor. Importantly, the neurogenic-to-gliogenic switch in NSC-like cells marks an early stage characterized by a burst of oncogenic alterations, during which transient AP-1 inhibition is sufficient to inhibit gliomagenesis. Together, our results reveal previously undercharacterized molecular dynamics and fate choices driving de novo gliomagenesis from hNSCs, and provide a blueprint for potential early-stage treatment/diagnosis for GBM.

Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

2021 ◽  
Author(s):  
Jordan W. Squair ◽  
Michael A. Skinnider ◽  
Matthieu Gautier ◽  
Leonard J. Foster ◽  
Grégoire Courtine
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Cell Data
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