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Single cell RNA-seq data comparing lesional (papules) and non-lesional skin biopsies of acne patients

ABSTRACT: Single cell RNA-seq data comparing lesional (papules) and non-lesional skin biopsies of acne patients

PROVIDER: PRJNA733809 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14691809_1.fastq.gz	Fastqsanger.gz
	SRR14691809_2.fastq.gz	Fastqsanger.gz
	SRR14691810_1.fastq.gz	Fastqsanger.gz
	SRR14691810_2.fastq.gz	Fastqsanger.gz
	SRR14691811_1.fastq.gz	Fastqsanger.gz

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Single cell RNA-seq data comparing lesional (papules) and non-lesional skin biopsies of acne patients

Project description:We performed single-cell RNA seq analysis on skin biopsies from six acne patients with a total of 32,966 cells from lesional skin and 29,202 cells from non-lesional skin using 10X Genomics. Gene expression data derived from cells in both lesional and non-lesional skin were aligned and projected onto a two-dimensional space using UMAP (Uniform Manifold Approximation and Projection). Unsupervised clustering revealed eight major clusters corresponding to seven different cell types lymphocytes, myeloid cells, keratinocytes, fibroblasts, endothelial cells, smooth muscle cells, and melanocytes.

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Spatial RNA-seq data comparing lesional (papules) and non-lesional skin biopsies of acne patients

Project description:Spatial RNA-seq data comparing lesional (papules) and non-lesional skin biopsies of acne patients

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Transcription profiling of human acne lesion vs. normal skin from acne and non acne patients

Project description:The pathogenesis of acne has been linked to multiple factors such as increased sebum production, inflammation, follicular hyperkeratinization, and the action of Propionibacterium acnes within the follicle. In an attempt to understand the specific genes involved in inflammatory acne, we performed gene expression profiling in acne patients. Skin biopsies were obtained from an inflammatory papule and from normal skin in six patients with acne. Biopsies were also taken from normal skin of six subjects without acne. Gene array expression profiling was conducted using Affymetrix HG-U133A 2.0 arrays comparing lesional to nonlesional skin in acne patients and comparing nonlesional skin from acne patients to skin from normal subjects. Within the acne patients, 211 genes are upregulated in lesional skin compared to nonlesional skin. A significant proportion of these genes are involved in pathways that regulate inflammation and extracellular matrix remodeling, and they include matrix metalloproteinases 1 and 3, IL-8, human beta-defensin 4, and granzyme B. These data indicate a prominent role of matrix metalloproteinases, inflammatory cytokines, and antimicrobial peptides in acne lesions. These studies are the first describing the comprehensive changes in gene expression in inflammatory acne lesions and are valuable in identifying potential therapeutic targets in inflammatory acne. Experiment Overall Design: total 18 chips. 6 for acne lesion samples, 6 for normal skin samples, 6 for non-acne patient normal skin samples

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Acne lesion vs. normal skin. Also includes non-acne patients' normal skin samples.

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Transcription profiling of lesional and non-lesional skin from acne patients to study the role of inflammation in early acne lesions

Project description:The mechanisms of inflammation in acne are not well understood. This study performed in two separate patient populations focused on the activation of adaptive and innate immunity in early inflamed acne. Biopsies were collected from lesional and non-lesional skin of acne patients. Psoriasis patients and healthy volunteers were included in the study for comparison (not included in the records). Using Affymetrix Genechips, we observed significant elevation of the signature cytokines of the Th17 lineage in acne lesions compared to non-lesional skin. The increased expression of IL-17 was confirmed with real-time qPCR (RT-PCR) in two separate patient populations. Cytokines involved in Th17 lineage differentiation (IL-1beta, IL-6, TGF-beta; IL23p19) were remarkably induced at the RNA level. In addition, pro-inflammatory cytokines (IL-8, TNF-α), Th1 markers (IL12p40, CXCR3, T-bet, IFN-gamma), T regulatory cell markers (Foxp3, IL-10, TGF-β) and antimicrobial peptides (S100A7, S100A9, LNC2, hBD2, hBD3, hCAP18) were induced. Importantly, immunohistochemistry revealed significantly increased numbers of IL-17A positive T cells and CD83 dendritic cells in the acne lesions. In summary our results demonstrate the presence of IL17A positive T cells and the activation of Th17-related cytokines in acne lesions, indicating that the Th17 pathway may play a pivotal role in the disease process, offering new targets of therapy. Total of 24 chips. 12 patients : 2 biospies per patient: 1 lesional and 1 non lesional.

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Project description:We collected RNA from a 20µm thick frozen section of an acne lesion into 55µm wells containing spatially-barcoded capture oligonucleotides and performed transcriptome analysis. We detected 394 spatially defined spots with an average of 1,349 genes and 2,950 transcripts per spot.

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