Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses

Eshghi, Shadi Toghi; Au-Yeung, Amelia; Takahashi, Chikara; Bolen, Christopher R.; Nyachienga, Maclean N.; Lear, Sean; Green, Cherie; Mathews, W. Rodney; O’Gorman, William

doi:10.3389/fimmu.2019.01194

Cited by 55 publications

(33 citation statements)

References 23 publications

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“…After the CyTOF data was normalized, a t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm was run to determine immune cell clusters in an unsupervised manner using FlowSOM by R 3.6.0 programming. viSNE plots were also analyzed in the same manner [ 26 ]. Independent t-test were performed for the endothelial cellular experiments.…”

Section: Methodsmentioning

confidence: 99%

Immune biomarkers link air pollution exposure to blood pressure in adolescents

et al. 2020

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Background Childhood exposure to air pollution contributes to cardiovascular disease in adulthood. Immune and oxidative stress disturbances might mediate the effects of air pollution on the cardiovascular system, but the underlying mechanisms are poorly understood in adolescents. Therefore, we aimed to identify immune biomarkers linking air pollution exposure and blood pressure levels in adolescents. Methods We randomly recruited 100 adolescents (mean age, 16 years) from Fresno, California. Using central-site data, spatial-temporal modeling, and distance weighting exposures to the participant’s home, we estimated average pollutant levels [particulate matter (PM), polyaromatic hydrocarbons (PAH), ozone (O3), carbon monoxide (CO) and nitrogen oxides (NOx)]. We collected blood samples and vital signs on health visits. Using proteomic platforms, we quantitated markers of inflammation, oxidative stress, coagulation, and endothelial function. Immune cellular characterization was performed via mass cytometry (CyTOF). We investigated associations between pollutant levels, cytokines, immune cell types, and blood pressure (BP) using partial least squares (PLS) and linear regression, while adjusting for important confounders. Results Using PLS, biomarkers explaining most of the variance in air pollution exposure included markers of oxidative stress (GDF-15 and myeloperoxidase), acute inflammation (C-reactive protein), hemostasis (ADAMTS, D-dimer) and immune cell types such as monocytes. Most of these biomarkers were independently associated with the air pollution levels in fully adjusted regression models. In CyTOF analyses, monocytes were enriched in participants with the highest versus the lowest PM2.5 exposure. In both PLS and linear regression, diastolic BP was independently associated with PM2.5, NO, NO2, CO and PAH456 pollution levels (P ≤ 0.009). Moreover, monocyte levels were independently related to both air pollution and diastolic BP levels (P ≤ 0.010). In in vitro cell assays, plasma of participants with high PM2.5 exposure induced endothelial dysfunction as evaluated by eNOS and ICAM-1 expression and tube formation. Conclusions For the first time in adolescents, we found that ambient air pollution levels were associated with oxidative stress, acute inflammation, altered hemostasis, endothelial dysfunction, monocyte enrichment and diastolic blood pressure. Our findings provide new insights on pollution-related immunological and cardiovascular disturbances and advocate preventative measures of air pollution exposure.

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Section: Methodsmentioning

confidence: 99%

Immune biomarkers link air pollution exposure to blood pressure in adolescents

et al. 2020

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“…Specific to LSA, k-medoid clustering that produced 9 clusters for downstream analysis was provided. In addition, graph-based clustering and visualization via t-SNE were provided 26 , and the data were normalized to unit norms before performing graph-based clustering and t-SNE projection.…”

Section: Methodsmentioning

confidence: 99%

Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay

Zheng

et al. 2020

Sci Rep

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A detailed understanding of the gene-regulatory network in ankylosing spondylitis (AS) is vital for elucidating the mechanisms of AS pathogenesis. Assaying transposase-accessible chromatin in single cell sequencing (scATAC-seq) is a suitable method for revealing such networks. Thus, scATAC-seq was applied to define the landscape of active regulatory DNA in AS. As a result, there was a significant change in the percent of CD8+ T cells in PBMCs, and 37 differentially accessible transcription factor (TF) motifs were identified. T cells, monocytes-1 and dendritic cells were found to be crucial for the IL-17 signaling pathway and TNF signaling pathway, since they had 73 potential target genes regulated by 8 TF motifs with decreased accessibility in AS. Moreover, natural killer cells were involved in AS by increasing the accessibility to TF motifs TEAD1 and JUN to induce cytokine-cytokine receptor interactions. In addition, CD4+ T cells and CD8+ T cells may be vital for altering host immune functions through increasing the accessibility of TF motifs NR1H4 and OLIG (OLIGI and OLIG2), respectively. These results explain clear gene regulatory variation in PBMCs from AS patients, providing a foundational framework for the study of personal regulomes and delivering insights into epigenetic therapy.

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“…CD3, CD4 and Viability Dye were removed from the t-SNE and Phenograph analysis. In order to choose the analysis parameters for the t-SNE and Phenograph analysis, the data were run with increasing perplexity (from 10 to 10 starting at 30 as the default value) for t-SNE and increasing k value (from 5 to 5, starting at 30) for Phenograph (36). From a perplexity of 80 and above, the clustering did not significantly change anymore.…”

Section: Analysis Of Flow Cytometry Data With T-sne and Phenographmentioning

confidence: 99%

Vitamin D/CD46 Crosstalk in Human T Cells in Multiple Sclerosis

et al. 2020

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Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS), in which T-cell migration into the CNS is key for pathogenesis. Patients with MS exhibit impaired regulatory T cell populations, and both Foxp3+ Tregs and type I regulatory T cells (Tr1) are dysfunctional. MS is a multifactorial disease and vitamin D deficiency is associated with disease. Herein, we examined the impact of 1,25(OH)2D3 on CD4+ T cells coactivated by either CD28 to induce polyclonal activation or by the complement regulator CD46 to promote Tr1 differentiation. Addition of 1,25(OH)2D3 led to a differential expression of adhesion molecules on CD28- and CD46-costimulated T cells isolated from both healthy donors or from patients with MS. 1,25(OH)2D3 favored Tr1 motility though a Vitamin D-CD46 crosstalk highlighted by increased VDR expression as well as increased CYP24A1 and miR-9 in CD46-costimulated T cells. Furthermore, analysis of CD46 expression on T cells from a cohort of patients with MS supplemented by vitamin D showed a negative correlation with the levels of circulating vitamin D. Moreover, t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis allowed the visualization and identification of clusters increased by vitamin D supplementation, but not by placebo, that exhibited similar adhesion phenotype to what was observed in vitro. Overall, our data show a crosstalk between vitamin D and CD46 that allows a preferential effect of Vitamin D on Tr1 cells, providing novel key insights into the role of an important modifiable environmental factor in MS.

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Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses

Cited by 55 publications

References 23 publications

Immune biomarkers link air pollution exposure to blood pressure in adolescents

Immune biomarkers link air pollution exposure to blood pressure in adolescents

Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay

Vitamin D/CD46 Crosstalk in Human T Cells in Multiple Sclerosis

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