Single-cell analysis reveals IGF-1 potentiation of inhibition of the TGF-β/Smad pathway of fibrosis in human keratocytes in vitro

AbstractHIV-1 cDNA pre-integration complexes have been shown to persist for weeks in macrophages and to be transcriptionally active. Early and late gene transcripts are produced, along with some viral proteins, yet whole virus is not. While previous work has focused on the transcription and translation of HIV-1 genes; our understanding of cellular milieu that accompanies viral production is incomplete. We have used an in vitro system to model HIV-1 infection of macrophages, and single cell RNA sequencing (scRNA-seq) to compare the transcriptomes of uninfected cells, cells harboring pre-integration HIV-1 complexes (PIC) and those containing integrated provirus and actively making late HIV proteins. These are also compared to control cells, not exposed to virus.Several observations provide new perspective on the effects of HIV-1 transcription from pre-integrated cDNA versus from integrated provirus. First, HIV-1 transcript levels do not necessarily correlate with virus production, cells harboring PIC cDNA have transcript loads comparable to cells transcribing from provirus and making p24, mCherry, and vpu proteins. Second, all HIV-1 transcripts are easily detectable in abundance from PIC cDNA transcription, as is the case with cells transcribing from provirus, although the frequency of PIC cells with detectable gag-pol, tat, env, and nef transcripts is higher than the corresponding frequencies observed for “Provirus cells”. Third, the background transcriptomes of cells harboring pre- integrated HIV-1 cDNA are not otherwise detectably altered from cells not containing any HIV- 1 transcript. Fourth, integration and production of p24, mCherry, and Vpu proteins is accompanied by a switch from transcriptomes characterized by NFkB and AP-1 promoted transcription to a transcriptome characterized by E2F family transcription products. While some of these observations may seem heretical, single cell analysis provides a more nuanced understanding of PIC cDNA transcription and the transcriptomic changes that support HIV-1 protein production from integrated provirus.Author SummarySingle cell analysis is able to distinguish between HIV-1 infected macrophage cells that are transcribing pre-integrated HIV-1 cDNA and those transcribing HIV-1 provirus. Only cells transcribing HIV-1 provirus are making p24, marker mCherry and Vpu proteins, which corresponds with a change in the host cell’s background transcriptome from one expressing viral restriction and immunological response genes to one that is expressing genes associated with cell replication and oxidative phosphorylation.

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Single-cell analysis of T-cell responses in vitro and in vivo: role of costimulatory signals

Transplantation Proceedings ◽

10.1016/s0041-1345(98)01784-9 ◽

1999 ◽

Vol 31 (1-2) ◽

pp. 814-815 ◽

Cited By ~ 8

Author(s):

A Wells ◽

H Gudmundsdottir ◽

M Walsh ◽

L.A Turka

Keyword(s):

T Cell ◽

Single Cell ◽

Single Cell Analysis ◽

T Cell Responses ◽

Cell Analysis ◽

Cell Responses ◽

Costimulatory Signals

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Single-cell analysis reveals a nestin+ tendon stem/progenitor cell population with strong tenogenic potentiality

Science Advances ◽

10.1126/sciadv.1600874 ◽

2016 ◽

Vol 2 (11) ◽

pp. e1600874 ◽

Cited By ~ 42

Author(s):

Zi Yin ◽

Jia-jie Hu ◽

Long Yang ◽

Ze-Feng Zheng ◽

Cheng-rui An ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Cell Population ◽

Single Cell Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cell Analysis ◽

Nestin Expression

The repair of injured tendons remains a formidable clinical challenge because of our limited understanding of tendon stem cells and the regulation of tenogenesis. With single-cell analysis to characterize the gene expression profiles of individual cells isolated from tendon tissue, a subpopulation of nestin+ tendon stem/progenitor cells (TSPCs) was identified within the tendon cell population. Using Gene Expression Omnibus datasets and immunofluorescence assays, we found that nestin expression was activated at specific stages of tendon development. Moreover, isolated nestin+ TSPCs exhibited superior tenogenic capacity compared to nestin− TSPCs. Knockdown of nestin expression in TSPCs suppressed their clonogenic capacity and reduced their tenogenic potential significantly both in vitro and in vivo. Hence, these findings provide new insights into the identification of subpopulations of TSPCs and illustrate the crucial roles of nestin in TSPC fate decisions and phenotype maintenance, which may assist in future therapeutic strategies to treat tendon disease.

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Single-cell analysis identifies EpCAM+/CDH6+/TROP-2− cells as human liver progenitors

10.1101/294272 ◽

2018 ◽

Cited By ~ 1

Author(s):

Joe M Segal ◽

Daniel J Wesche ◽

Maria Paola Serra ◽

Bénédicte Oulès ◽

Deniz Kent ◽

...

Keyword(s):

Single Cell ◽

Progenitor Cell ◽

Healthy Adult ◽

Single Cell Analysis ◽

Cell Analysis ◽

Adult Tissue ◽

Adult Liver ◽

Lineage Differentiation ◽

Liver Progenitor Cell

AbstractThe liver is largely composed of hepatocytes and bile duct epithelial cells (BECs). Controversy exists as to whether a liver stem/progenitor cell capable of renewing both hepatocytes and BECs exists. Single cell RNA sequencing of freshly isolated human foetal and healthy adult liver identified hepatocyte, hepatoblast and liver progenitor cell (hLPC) populations. hLPCs, found at the interface between hepatocytes and bile ducts in both foetal and adult tissue, were distinguishable from BECs by their negative expression of TROP-2. Prospective isolation followed by in vitro culture demonstrated their potential for expansion and bi-lineage differentiation. The hLPC expression signature was also conserved within expanded cell populations specific to certain cases of liver injury and cancer. These data support the idea of a true progenitor existing within healthy adult liver that can be activated upon injury. Further work to define the mechanisms regulating hLPC behaviour could advance understanding of human development and disease.

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The Trends of Single-Cell Analysis: A Global Study

BioMed Research International ◽

10.1155/2020/7425397 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Hua Tian ◽

Haifeng Liu ◽

Yuanyuan Zhu ◽

Dan Xing ◽

Bin Wang

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Bibliographic Coupling ◽

In Vivo Studies ◽

Cell Analysis ◽

The Usa ◽

Visualization Of Data ◽

Number Of Publications

Objective. The field of single-cell analysis has rapidly grown worldwide, and a bibliometric analysis and visualization of data and publications pertaining to such single-cell research has the potential to offer insights into the development of this field over the past two decades while also highlighting future avenues of research. Methods. Single-cell analysis-related studies published from 2000-2019 were identified through searches of the Web of Science, Scopus, and PubMed databases, and corresponding bibliometric data were systematically compiled. Extracted data from each study included author names, country of origin, and affiliations. GraphPad Prism was used to analyze these data, while VOSviewer was used to perform global analyses of bibliographic coupling, coauthorship, cocitation, and co-occurrence. Results. In total, 4,071 relevant studies were included in this analysis. The number of publications increased substantially with time, suggesting that single-cell analyses are becoming increasingly more prevalent in recent years. Studies from the USA had the greatest impact in this field, with higher H -index values and numbers of citations relative to other countries, whereas Israel exhibited the highest average number of citations per publication. Bibliographic coupling, coauthorship, cocitation, and co-occurrence analyses revealed that Analytical Chemistry was associated with the highest number of publications in this field, and the University of Stanford contributed the most to this field. The most cited study included in this analysis was published by Macosko et al. in 2015 in Cell. Co-occurrence analyses revealed that the most common single-cell research topics included “mechanistic studies,” “in vitro studies,” “in vivo studies,” and “fabrication studies.” Conclusions. Single-cell analyses are a rapidly growing area of scientific interest, and higher volumes of publications in this field are expected in the coming years, particularly for studies conducting fabrication and in vivo single-cell analyses.

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Abstract P353: Adipose-derived Stem Cells Contribute To Vascular Remodeling Via Clec11a + Subpopulation

Circulation Research ◽

10.1161/res.129.suppl_1.p353 ◽

2021 ◽

Vol 129 (Suppl_1) ◽

Author(s):

Yongli Ji ◽

Yunrui Lu ◽

Jian Shen ◽

Meixiang Xiang ◽

Yao Xie

Keyword(s):

Stem Cells ◽

Single Cell ◽

Vascular Remodeling ◽

Single Cell Analysis ◽

Gene Set Enrichment Analysis ◽

Adipose Derived Stem Cells ◽

Cell Analysis ◽

Tgf Β1

Introduction: Recent researches identified the existence of perivascular adipose-derived stem cells (ADSCs) which could differentiate into vascular lineages and participate in vascular remodeling. Single-cell mRNA analysis revealed cellular heterogeneity of subcutaneous ADSCs in respect to cell clustering and cell differentiation. However, such analysis of perivascular ADSCs has not been investigated at a single-cell level. Hypothesis: There is a significant difference among perivascular ADSCs subpopulations in respect to vascular-lineage differentiation. Methods: We performed droplet-based single-cell profiling of subcutaneous and perivascular adipose stromal cells and compared ADSCs regarding their heterogeneity, gene ontology, and cell fate trajectory by applying single-cell analysis as well as in vitro and in vivo assays. Results: Single-cell analysis uncovered 4 perivascular ADSCs subpopulations including Dpp4+ , Col4a2+ / Icam1+ , Clec11a+ / Cpe+ and Sult1e1+ cells. Notably, the Clec11a + subpopulation comprised the bulk of perivascular ADSCs, while was hardly presented in subcutaneous ADSCs. Further gene-set enrichment analysis suggested Clec11a + ADSCs were potentially involved with TGF-β signaling pathways and pseudotemporal analysis predicted that Clec11a + subpopulation lay at the end of the differential trajectory towards smooth muscle cells (SMCs). In vitro assays displayed that perivascular ADSCs could differentiate into SMCs via CLEC11A regulation when treated by TGF-β1. To further elucidate the role of the Clec11a + subpopulation in SMCs differentiation, we labeled CLEC11A+ and CLEC11A- perivascular ADSCs by lentivirus transfection and isolated them by FACS assay. CLEC11A+ cells showed the greater capability of SMCs differentiation in response to TGF-β1 in vitro and enhanced neointima formation when transplanted to the adventitial side of guidewire injured arteries. Conclusions: The present study depicted the unique heterogeneity of perivascular ADSCs and the novel role of the Clec11a + subpopulation, providing a supplement for the relationship between perivascular ADSCs and vascular SMCs.

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Assessing the Heterogeneity of Cardiac Non-myocytes and the Effect of Cell Culture with Integrative Single Cell Analysis

10.1101/2020.03.04.975177 ◽

2020 ◽

Author(s):

Brian S. Iskra ◽

Logan Davis ◽

Henry E. Miller ◽

Yu-Chiao Chiu ◽

Alexander R. Bishop ◽

...

Keyword(s):

Cell Culture ◽

Single Cell ◽

Single Cell Analysis ◽

Cell Types ◽

Cell Analysis ◽

Mass Cytometry ◽

Single Cell Rna Sequencing ◽

High Depth

AbstractCardiac non-myocytes comprise a diverse and crucial cell population in the heart that plays dynamic roles in cardiac wound healing and growth. Non-myocytes broadly fall into four cell types: endothelium, fibroblasts, leukocytes, and pericytes. Here we characterize the diversity of the non-myocytes in vivo and in vitro using mass cytometry. By leveraging single-cell RNA sequencing we inform the design of a mass cytometry panel. To aid in annotation of the mass cytometry datasets, we utilize data integration with a neural network. We introduce approximately 460,000∼ single cell proteomes of non-myocytes as well as 5,000∼ CD31 negative single cell transcriptomes. Using our data, as well as previously reported datasets, we characterize cardiac non-myocytes with high depth in six mice, characterizing novel surface markers (CD9, CD200, Notch3, and FolR2). Further, we find that extended cell culture promotes the proliferation of CD45+CD11b+FolR2+IAIE- myeloid cells in addition to fibroblasts.

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Longitudinal single-cell analysis of a myeloma mouse model identifies subclonal molecular programs associated with progression

Nature Communications ◽

10.1038/s41467-021-26598-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Danielle C. Croucher ◽

Laura M. Richards ◽

Serges P. Tsofack ◽

Daniel Waller ◽

Zhihua Li ◽

...

Keyword(s):

Mouse Model ◽

Single Cell ◽

Single Cell Analysis ◽

Copy Number Variations ◽

Adaptive Mechanism ◽

Cell Analysis ◽

Early Disease ◽

Disease Spectrum ◽

Intratumoural Heterogeneity

AbstractMolecular programs that underlie precursor progression in multiple myeloma are incompletely understood. Here, we report a disease spectrum-spanning, single-cell analysis of the Vκ*MYC myeloma mouse model. Using samples obtained from mice with serologically undetectable disease, we identify malignant cells as early as 30 weeks of age and show that these tumours contain subclonal copy number variations that persist throughout progression. We detect intratumoural heterogeneity driven by transcriptional variability during active disease and show that subclonal expression programs are enriched at different times throughout early disease. We then show how one subclonal program related to GCN2 stress response is progressively activated during progression in myeloma patients. Finally, we use chemical and genetic perturbation of GCN2 in vitro to support this pathway as a therapeutic target in myeloma. These findings therefore present a model of precursor progression in Vκ*MYC mice, nominate an adaptive mechanism important for myeloma survival, and highlight the need for single-cell analyses to understand the biological underpinnings of disease progression.

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