scholarly journals Dynamic changes in RNA-chromatin interactome promote endothelial dysfunction

2019 ◽  
Author(s):  
Riccardo Calandrelli ◽  
Lixia Xu ◽  
Yingjun Luo ◽  
Weixin Wu ◽  
Xiaochen Fan ◽  
...  
Keyword(s):  
Endothelial Dysfunction ◽  
Single Cell ◽  
High Glucose ◽  
Cell Function ◽  
Strong Increase ◽  
Mesenchymal Transition ◽  
Cell Transcriptome ◽  
Key Aspects ◽  
Single Cell Transcriptome

AbstractChromatins are pervasively attached by RNAs. Here, we asked whether global RNA-chromatin contacts are altered in a given cell type in a disease context, and whether these alterations impact gene expression and cell function. In endothelial cells (ECs) treated by high-glucose and TNFα, we employed single-cell RNA-sequencing and in situ mapping of RNA-genome interaction (iMARGI) assay to delineate temporal changes in transcriptome and RNA-chromatin interactome. ECs displayed dramatic and heterogeneous changes in single cell transcriptome, accompanied by a dynamic and strong increase in inter-chromosomal RNA-DNA interactions, particularly among super enhancers (SEs). These SEs overlap with genes contributing to inflammatory response and endothelial mesenchymal transition (EndoMT), two key aspects of endothelial dysfunction. Perturbation of a high-glucose and TNFα-activated interaction involving SEs overlapping LINC00607 and SERPINE1 attenuated the pro-inflammatory and pro-EndoMT gene induction and EC dysfunction. Our findings highlight RNA-chromatin contacts as a crucial regulatory feature in biological and disease processes, exemplified by endothelial dysfunction, a major mediator of numerous diseases.

scholarly journals The Drosophila Embryo at Single Cell Transcriptome Resolution

2017 ◽  
Author(s):  
Nikos Karaiskos ◽  
Philipp Wahle ◽  
Jonathan Alles ◽  
Anastasiya Boltengagen ◽  
Salah Ayoub ◽  
...  
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Drosophila Embryo ◽  
Evolutionary Changes ◽  
Cell Transcriptome ◽  
Mechanisms Of Development ◽  
In Situ Hybridizations ◽  
Single Cell Transcriptome

ABSTRACTDrosophila is a premier model system for understanding the molecular mechanisms of development. By the onset of morphogenesis, ~6000 cells express distinct gene combinations according to embryonic position. Despite extensive mRNA in situ screens, combinatorial gene expression within individual cells is largely unknown. Therefore, it is difficult to comprehensively identify the coding and non-coding transcripts that drive patterning and to decipher the molecular basis of cellular identity. Here, we single-cell sequence precisely staged embryos, measuring >3100 genes per cell. We produce a ‘transcriptomic blueprint’ of development – a virtual embryo where 3D locations of sequenced cells are confidently identified. Our “Drosophila-Virtual-Expression-eXplorer” performs virtual in situ hybridizations and computes expression gradients. Using DVEX, we predict spatial expression and discover patterned lncRNAs. DEVX is sensitive enough to detect subtle evolutionary changes in expression patterns between Drosophila species. We believe DVEX is a prototype for powerful single cell studies in complex tissues.

scholarly journals Single-cell transcriptome analysis of the immunosuppressive effect of differential expression of tumor PD-L1 on responding TCR-T cells

2020 ◽  
Author(s):  
Renpeng Ding ◽  
Shang Liu ◽  
Shanshan Wang ◽  
Huanyi Chen ◽  
Fei Wang ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Tumor Cells ◽  
Cell Function ◽  
Immune Cell ◽  
Gene Clusters ◽  
Cellular Assays ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractPD-L1 expression levels in tumors do not consistently predict cancer patients’ response to PD-(L)1 inhibitors. We therefore evaluated how tumor PD-L1 levels affect the anti-PD-(L)1 efficacy and T cell function. We used MART-1-specific TCR-T cells (TCR-TMART-1) stimulated with MART-127-35 peptide-loaded MEL-526 tumor cells with different proportions of them expressing PD-L1 to perform cellular assays and high-throughput single-cell RNA sequencing. Compared to control T cells, TCR-TMART-1 were more sensitive to exhaustion and secreted lower pro-inflammatory but higher anti-inflammatory cytokines with increasing proportions of PD-L1+ tumor cells. The colocalization of T cells and tumor cells in gene clusters correlated negatively with the proportion of PD-L1+ tumor cells and positively with immune cell cytotoxicity. Moreover, elevated proportion of PD-L1+ tumor cells increased PD-L1 expression and decreased PD-1 expression on T cells and enhanced T cell death. The expression of PD-1 and PD-L1 in T cells and macrophages also correlated positively with COVID-19 severity.

Dysfunction of VIPR2 leads to myopia in humans and mice

2020 ◽  
pp. jmedgenet-2020-107220
Author(s):  
Fuxin Zhao ◽  
Qihang Li ◽  
Wei Chen ◽  
He Zhu ◽  
Dengke Zhou ◽  
...  
Keyword(s):  
Single Cell ◽  
Bipolar Cell ◽  
Cell Function ◽  
Gene Knockout ◽  
Bipolar Cells ◽  
Signalling Pathway ◽  
Chinese Han ◽  
Novel Target ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

BackgroundMyopia is the leading cause of refractive errors. As its pathogenesis is poorly understood, we determined if the retinal VIP-VIPR2 signalling pathway axis has a role in controlling signalling output that affects myopia development in mice.MethodsAssociation analysis meta-study, single-cell transcriptome, bulk RNA sequencing, pharmacological manipulation and VIPR2 gene knockout studies were used to clarify if changes in the VIP-VIPR2 signalling pathway affect refractive development in mice.ResultsThe SNP rs6979985 of the VIPR2 gene was associated with high myopia in a Chinese Han cohort (randomceffect model: p=0.013). After either 1 or 2 days’ form deprivation (FD) retinal VIP mRNA expression was downregulated. Retinal single-cell transcriptome sequencing showed that VIPR2 was expressed mainly by bipolar cells. Furthermore, the cAMP signalling pathway axis was inhibited in some VIPR2+ clusters after 2 days of FD. The selective VIPR2 antagonist PG99-465 induced relative myopia, whereas the selective VIPR2 agonist Ro25-1553 inhibited this response. In Vipr2 knockout (Vipr2-KO) mice, refraction was significantly shifted towards myopia (p<0.05). The amplitudes of the bipolar cell derived b-waves in 7-week-old Vipr2-KO mice were significantly larger than those in their WT littermates (p<0.05).ConclusionsLoss of VIPR2 function likely compromises bipolar cell function based on presumed changes in signal transduction due to altered signature electrical wave activity output in these mice. As these effects correspond with increases in form deprivation myopia (FDM), the VIP-VIPR2 signalling pathway axis is a viable novel target to control the development of this condition.

scholarly journals Identification of ZEB2 as an Immune-Associated Gene in Endometrial Carcinoma and Associated with Macrophage Infiltration by Bioinformatic Analysis

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Yuanyuan Zhu ◽  
Xinchao Lin ◽  
Yuanlong Zang ◽  
Qiaohui Yang
Keyword(s):  
Endometrial Carcinoma ◽  
Single Cell ◽  
Immune Cells ◽  
Prognostic Significance ◽  
Group Analysis ◽  
Disease Free Survival ◽  
Rna Seq ◽  
Mesenchymal Transition ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Endometrial cancer (EC) is the most common gynecological tumor arising from the endometrium. In this study, we use a published single-cell transcriptome profile of endometrial carcinoma (EC) to reveal the composition of immune cells and found an immunosuppressive environment since the presence of macrophage subtype M2 and exhausted CD8+ T cell markers. We focused on ZEB2 (Zinc finger E-box binding homeobox 2), a well-known player in epithelial to mesenchymal transition process, and we showed that ZEB2 is exclusively expressed in immune cells in single-cell transcriptome and, at the same time, downregulated in TCGA-UCEC (The Cancer Genome Atlas—Uterine Corpus Endometrial Carcinoma) bulk RNA-seq data and negatively associated with tumor purity. Loss of ZEB2 protein in EC in normal endometrium and EC samples was validated in samples using immunohistochemistry (IHC) from HPA (Human Protein Atlas) database. Furthermore, we found ZEB2 was associated with immune infiltrations especially for macrophage using TIMER 2.0. Interestingly, ZEB2 prognostic significance differed under various macrophage and Th2 helper cell content using Kaplan–Meier Plotter analysis. More importantly, we showed that over 11% EC patients have somatic mutations of ZEB2 in EC samples collected from cBioportal and they have a lower body weight, earlier diagnosis age, and better overall survival and disease-free survival status compared with the unaltered group. Analysis in TIMER2.0 suggested that ZEB2 mutation would possibly change the composition of tumor-infiltrating lymphocytes. Taken together, by combining the results from single-cell data, bulk TCGA RNA-seq, and other online bioinformatic tools, we provided evidence that ZEB2 might have a unique role in the immune environment of EC. These results would provide a better insight into the pathogenetic process and ZEB2 might further be used an immunotherapeutic target of EC.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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