Dataset Information

Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin.

ABSTRACT: Human skin consists of multiple cell types, including epithelial, immune, and stromal cells. Transcriptomic analyses have previously been performed from bulk skin samples or from epithelial and immune cells expanded in cell culture. However, transcriptomic analysis of bulk skin tends to drown out expression signals from relatively rare cells while cell culture methods may significantly alter cellular phenotypes and gene expression profiles. To identify distinct transcriptomic profiles of multiple cell populations without substantially altering cell phenotypes, we employed a fluorescence activated cell sorting method to isolate keratinocytes, dendritic cells, CD4+ T effector cells, and CD8+ T effector cells from healthy skin samples, followed by RNA-seq of each cell population. Principal components analysis revealed distinct clustering of cell types across samples, while differential expression and coexpression network analyses revealed transcriptional profiles of individual cell populations distinct from bulk skin, most strikingly in the least abundant CD8+ T effector population. Our work provides a high resolution view of cutaneous cellular gene expression and suggests that transcriptomic profiling of bulk skin may inadequately capture the contribution of less abundant cell types.

SUBMITTER: Ahn RS

PROVIDER: S-EPMC5430950 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin.

Ahn Richard S RS Taravati Keyon K Lai Kevin K Lee Kristina M KM Nititham Joanne J Gupta Rashmi R Chang David S DS Arron Sarah T ST Rosenblum Michael M Liao Wilson W

Scientific reports 20170502 1

Human skin consists of multiple cell types, including epithelial, immune, and stromal cells. Transcriptomic analyses have previously been performed from bulk skin samples or from epithelial and immune cells expanded in cell culture. However, transcriptomic analysis of bulk skin tends to drown out expression signals from relatively rare cells while cell culture methods may significantly alter cellular phenotypes and gene expression profiles. To identify distinct transcriptomic profiles of multipl ...[more]

PMID: 28465541

Similar Datasets

Project description:Triple-negative breast cancer (TNBC) resistance to neoadjuvant chemotherapy (NAC) represents a major clinical challenge; therefore, delineating tumor heterogeneity can provide novel insight into resistance mechanisms and potential therapeutic targets. Herein, we identified the transcriptional landscape associated with TNBC resistance to NAC at the single-cell level by analyzing publicly available transcriptome data from more than 5,000 single cells derived from four extinction (responders) and four persistence (non-responders) patients, revealing remarkable tumor heterogeneity. Employing iterative clustering and guide-gene selection (ICGS) and uniform manifold approximation and projection (UMAP), we classified TNBC single cells into several clusters based on their distinct gene signatures. The presence of clusters indicative of immune cell activation was a hallmark of the extinction group pre-NAC, while post NAC, the extinction tissue consisted mostly of breast, omental fat, and fibroblasts. The persistent gene signatures of pre-NAC resembled the gene signature of lung epithelial, mammary, and salivary glands and acute myeloid leukemia blast cells, which were associated with enhanced cellular movement and activation of FOXM1, NOTCH1, and MYC and suppression of tumor necrosis factor (TNF) and IFNG mechanistic networks. Multivariate survival analysis identified persistence-derived three-gene signature (KIF5BhighHLA-ClowIGHG2low) predictive of relapse-free survival (hazard ratio [HR]: 2.2 [1.6-3.2, p < 0.0001]) in a second cohort of 360 TNBC patients. Mechanistically, loss of function of several upregulated genes in the persistent group (BYSL, FDPS, ENO1, MED20, MRPL9, MRPL37, NDUFB11, PMVK, MYC, and GSTP1) inhibited MDA-MB-231 and BT-549 TNBC models' colony-forming unit (CFU) potential and enhanced their sensitivity to paclitaxel. Our data unraveled the transcriptional portrait associated with NAC resistance, identified several key genes, and suggested their potential utilization as prognostic markers and therapeutic targets in TNBC.

Project description:Rationale: V-domain immunoglobulin suppressor of T cell activation (VISTA) is a novel inhibitory immune checkpoint molecule. Vsir-/- mice have exacerbated psoriasis-like skin inflammation. The immune cell subsets involved in inflammation in Vsir-/- psoriatic mice are largely unknown. We have used scRNA-seq as an unbiased profiling strategy to study the heterogeneity of immune cells at a single cell level in the skin of Vsir-/- psoriatic mice. Methods: In the present study, the right ear and shaved back skin of wild type and Vsir-/- mice were treated with IMQ for 5 consecutive days to induce psoriasis-like dermatitis. Then, the single-cell RNA sequencing analysis of mouse back skin lesions was performed using 10 × Genomics technique. Results: We identified 12 major cell subtypes among 23,258 cells. The major populations of the skin cells included macrophages, dendritic cells and fibroblasts. Macrophages constituted the main immune cell population in the WT (61.29%) and Vsir-/- groups (77.7%). It should be noted that DCs and fibroblasts were expanded in the Vsir-/- psoriatic mice. Furthermore, the gene expression signatures were assessed. We observed that Hspb1 and Cebpb were significantly upregulated in the Vsir-/- psoriatic mice. Differential gene expression and gene ontology enrichment analyses revealed specific gene expression patterns distinguishing these subsets and uncovered putative functions of each cell type. Date analysis resulted in the discovery of a number of novel psoriasis-associated genes in Vsir-/- mice. Conclusion: We present a comprehensive single-cell landscape of the skin immune cells in Vsir-/- psoriatic mice. These unprecedented data uncovered the transcriptional landscape and phenotypic heterogeneity of skin macrophages in psoriasis and identified their gene expression signature suggesting specialized functions in Vsir-/- mice. Our findings will open novel opportunities to investigate the role of VISTA in driving psoriasis.

Project description:G protein-coupled receptors (GPCRs), the largest family of cell receptors, act as important regulators of diverse signaling pathways. Our understanding of the impact of GPCRs in tumors is emerging, yet there is no therapeutic platform based on GPCR driver genes. As cancer progresses, it disrupts normal epithelial organization and maintains the cells outside their normal niche. The dynamic and flexible microenvironment of a tumor contains both soluble and matrix-immobilized proteases that contribute to the process of cancer advancement. An example is the activation of cell surface protease-activated receptors (PARs). Mammalian PARs are a subgroup of GPCRs that form a family of four members, PAR1⁻4, which are uniquely activated by proteases found in the microenvironment. PAR₁ and PAR₂ play central roles in tumor biology, and PAR₃ acts as a coreceptor. The significance of PAR₄ in neoplasia is just beginning to emerge. PAR₁ has been shown to be overexpressed in malignant epithelia, in direct correlation with tumor aggressiveness, but there is no expression in normal epithelium. In this review, the involvement of key transcription factors such as Egr1, p53, Twist, AP2, and Sp1 that control PAR₁ expression levels specifically, as well as hormone transcriptional regulation by both estrogen receptors (ER) and androgen receptors (AR) are discussed. The cloning of the human protease-activated receptor 2; Par2 (hPar2) promoter region and transcriptional regulation of estrogen (E₂) via binding of the E₂⁻ER complex to estrogen response elements (ERE) are shown. In addition, evidence that TEA domain 4 (TEAD₄) motifs are present within the hPar2 promoter is presented since the YAP oncogene, which plays a central part in tumor etiology, acts via the TEAD₄ transcription factor. As of now, no information is available on regulation of the hPar3 promoter. With regard to hPar4, only data showing CpG methylation promoter regulation is available. Characterization of the PAR transcriptional landscape may identify powerful targets for cancer therapies.

Project description:BackgroundCardiac involvement is an important determinant of mortality among sarcoidosis patients. Although granulomatous inflammation is a hallmark finding in cardiac sarcoidosis, the precise immune cell populations that comprise the granuloma remain unresolved. Furthermore, it is unclear how the cellular and transcriptomic landscape of cardiac sarcoidosis differs from other inflammatory heart diseases.MethodsWe leveraged spatial transcriptomics (GeoMx digital spatial profiler) and single-nucleus RNA sequencing to elucidate the cellular and transcriptional landscape of cardiac sarcoidosis. Using GeoMX digital spatial profiler technology, we compared the transcriptomal profile of CD68+ rich immune cell infiltrates in human cardiac sarcoidosis, giant cell myocarditis, and lymphocytic myocarditis. We performed single-nucleus RNA sequencing of human cardiac sarcoidosis to identify immune cell types and examined their transcriptomic landscape and regulation. Using multichannel immunofluorescence staining, we validated immune cell populations identified by single-nucleus RNA sequencing, determined their spatial relationship, and devised an immunostaining approach to distinguish cardiac sarcoidosis from other inflammatory heart diseases.ResultsDespite overlapping histological features, spatial transcriptomics identified transcriptional signatures and associated pathways that robustly differentiated cardiac sarcoidosis from giant cell myocarditis and lymphocytic myocarditis. Single-nucleus RNA sequencing revealed the presence of diverse populations of myeloid cells in cardiac sarcoidosis with distinct molecular features. We identified GPNMB (transmembrane glycoprotein NMB) as a novel marker of multinucleated giant cells and predicted that the MITF (microphthalmia-associated transcription factor) family of transcription factors regulated this cell type. We also detected additional macrophage populations in cardiac sarcoidosis including HLA-DR (human leukocyte antigen-DR)+ macrophages, SYTL3 (synaptotagmin-like protein 3)+ macrophages and CD163+ resident macrophages. HLA-DR+ macrophages were found immediately adjacent to GPMMB+ giant cells, a distinct feature compared with other inflammatory cardiac diseases. SYTL3+ macrophages were located scattered throughout the granuloma and CD163+ macrophages, CD1c+ dendritic cells, nonclassical monocytes, and T cells were located at the periphery and outside of the granuloma. Finally, we demonstrate mTOR (mammalian target of rapamycin) pathway activation is associated with proliferation and is selectively found in HLA-DR+ and SYLT3+ macrophages.ConclusionsIn this study, we identified diverse populations of immune cells with distinct molecular signatures that comprise the sarcoid granuloma. These findings provide new insights into the pathology of cardiac sarcoidosis and highlight opportunities to improve diagnostic testing.

Dataset Information

Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin.

Publications

Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets