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Heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by scRNA-seq analysis and trajectory inference

ABSTRACT: Heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by scRNA-seq analysis and trajectory inference

PROVIDER: PRJNA820742 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18505125.fastq.gz	Fastqsanger.gz
	SRR18505126.fastq.gz	Fastqsanger.gz

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Heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by scRNA-seq analysis and trajectory inference

Project description:We subdivided circulating CD4+CD8+ double positive T cells, known to be associated with various disease environments, into several subtypes through single-cell RNA sequencing, and analyzed transition in transcriptome using trajectory analysis.

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Heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by scRNA-seq analysis and trajectory inference.

Project description:The frequency of CD4+CD8+ double-positive (DP) T cells is highly associated with a variety of diseases. Recently, we used high-throughput single-cell RNA sequencing to show that circulating DP T cells in cynomolgus monkeys comprise nine heterogeneous populations. To better understand the characteristics of DP T cells, we analyzed 7601 cells from a rhesus monkey and detected 14,459 genes. Rhesus monkey DP T cells comprised heterogeneous populations (naïve, Treg-, Tfh-, CCR9+ Th-, Th17-, Th2-, Eomes+ Tr1-, CTL-, PLZF+ innate- and Eomes+ innate-like cells) with multiple potential functions. We also identified two new subsets using aggregated scRNA-seq datasets from the rhesus and the cynomolgus monkey: CCR9+ Th-like cells expressing ICAM2 and ITGA1, and PLZF+ innate-like cells that display innate-associated gene signatures such as ZBTB16, TYROBP, MAP3K8, and KLRB1. Trajectory inference of cell differentiation status showed that most DP T cells in the rhesus monkey were found in the mid-to-late pseudotime, whereas DP T cells from the cynomolgus monkey were found in early pseudotime. This suggests that DP T cells in rhesus monkeys may exhibit more diverse differentiation states than those in cynomolgus monkeys. Thus, scRNA-seq and trajectory inference identified a more diverse subset of the circulating DP T cells than originally thought.

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scEGOT: single-cell trajectory inference framework by entropic Gaussian mixture optimal transport

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Cellular heterogeneity of circulating CD4+CD8+ double positive T cells characterized by single-cell RNA sequencing

Project description:Cellular heterogeneity of circulating CD4+CD8+ double positive T cells characterized by single-cell RNA sequencing

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scEGOT: single-cell trajectory inference framework by entropic Gaussian mixture optimal transport

Project description:Time-series single-cell RNA sequencing (scRNA-seq) data in biology has opened the door to elucidate cell differentiation processes. In this context, the optimal transport theory has attracted attention to interpolate scRNA-seq data in adjacent times and infer the trajec- tories of cell differentiation. This paper presents scEGOT, a novel comprehensive single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport (EGOT). The method- ology facilitates the inference of cell differentiation pathways and dynamics from time-series scRNA-seq data. The scEGOT frame- work provides comprehensive outputs, including cell state graphs, velocity fields of cell differentiation, time interpolations of scRNA- seq data, space-time continuous videos of cell differentiation with gene expressions, gene regulatory networks, and reconstructions of Waddington’s epigenetic landscape. These outputs allow us to un- derstand the dynamics of the cell differentiation process from mul- tiple perspectives. To demonstrate that scEGOT is a powerful and versatile tool for single-cell biology, it was applied to time-series scRNA-seq data of the human primordial germ cell-like cell (human PGCLC) induction system. This application provided new insights into the mechanism of PGCLC/somatic cell segregation. In particu- lar, we identified the PGCLC progenitor population and the time point of the segregation. In addition, we found novel key genes that may be critical for human PGCLC differentiation.

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Time trajectory analysis reveals age-modulated small RNA cargo of circulating extracellular vesicles

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Project description:Endothelial cell (EC) metabolism regulates angiogenesis and is an emerging target for anti-angiogenic therapy in tumor and choroidal neovascularization (CNV). In contrast to tumor ECs (TECs), CNV-ECs cannot be isolated for unbiased metabolic target discovery. Here we used scRNA-sequencing to profile 28,337 choroidal ECs (CECs) from mice to in silico distinguish healthy CECs from CNV-ECs. Trajectory inference suggested that CNV-ECs plastically upregulate genes in central carbon metabolism and collagen biosynthesis during differentiation from quiescent postcapillary venous ECs. CEC-tailored genome scale metabolic modeling predicted essentiality of SQLE and ALDH18A1 for proliferation and collagen production, respectively. Comparative analysis in TECs revealed more outspoken metabolic transcriptome heterogeneity in subtypes and consistent upregulation of SQLE and ALDH18A1 across tumor types. Inhibition of SQLE and ALDH18A1 reduced sprouting angiogenesis in vitro. These findings demonstrate the potential of integrated scRNA-seq analysis to identify angiogenic metabolic targets in disease ECs.

2020-06-25 | E-MTAB-8119 | biostudies-arrayexpress

Endothelial cell heterogeneity in pathological angiogenesis characterized by metabolic transcriptome diversity

Project description:Endothelial cell (EC) metabolism is an emerging target for anti-angiogenic therapy in tumor and choroidal neovascularization (CNV), but little is known about individual EC metabolic transcrip-tomes. Here, by scRNA-sequencing 28,337 murine choroidal ECs (CECs) and sprouting CNV-ECs, we constructed a taxonomy to characterize their heterogeneity. Comparison with murine lung tumor ECs (TECs) revealed congruent marker gene expression by distinct EC phenotypes across tissues and diseases, suggesting similar angiogenic mechanisms. Trajectory inference of CNV-ECs revealed that differentiation of venous to angiogenic ECs was accompanied by metabolic transcriptome plasticity. EC phenotypes displayed metabolic transcriptome heterogeneity. Hypothesizing that conserved genes are more important, we used an integrated analysis, based on congruent transcriptome analysis, CEC-tailored genome scale metabolic modeling, and gene expression me-ta-analysis in multiple cross-species datasets, followed by functional validation, to identify the top-ranking metabolic targets SQLE and ALDH18A1, involved in EC proliferation and collagen production, respectively, as novel angiogenic targets.

2020-03-31 | E-MTAB-8604 | biostudies-arrayexpress

Cellular heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by single-cell RNA sequencing.

Project description:Circulating CD4+CD8+ double-positive (DP) T cells are associated with a variety of disease states. However, unlike conventional T cells, the composition of this population is poorly understood. Here, we used single-cell RNA sequencing (scRNA-seq) to analyze the composition and characteristics of the DP T cell population circulating in the peripheral blood of cynomolgus monkeys. We found that circulating DP T cells not only contain a large number of naïve cells, but also comprise a heterogeneous population (CD4 CTL-, Eomes+ Tr1-, Th2-, Th17-, Tfh-, Treg-, CD8 CTL-, and innate-like cells) with multiple potential functions. Flow cytometry analysis revealed that a substantial number of the naïve DP T cells expressed CD8αβ, as well as CD8αα, along with high expression of CD31. Moreover, the CD4hiCD8lo and CD4hiCD8hi populations, which express high levels of the CD4 coreceptor, comprised subsets characterized by helper and regulatory functions, some of which also exhibited cytotoxic functions. By contrast, the CD4loCD8hi population with high CD8 coreceptor expression comprised a subset characterized by CD8 CTL- and innate-like properties. Taken together, the data show that scRNA-seq analysis identified a more diverse subset of the circulating DP cells than is currently known, despite this population being very small.

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