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Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer

ABSTRACT: Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer

PROVIDER: PRJNA929216 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23266465.fastq.gz	Fastqsanger.gz
	SRR23266466.fastq.gz	Fastqsanger.gz
	SRR23266467.fastq.gz	Fastqsanger.gz
	SRR23266468.fastq.gz	Fastqsanger.gz
	SRR23266469.fastq.gz	Fastqsanger.gz

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Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer

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Single Cell Analysis of Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer Foot Wounds

Project description:We investigate the changes between diabetic and non-diabetic wound healing process in chronic foot ulcer.

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Spatial transcriptomics of healing and non-healing diabetic foot ulcers

Project description:Diabetic foot ulcers (DFUs) are a devastating complication of diabetes. To better understand the molecular mechanisms and cell types implicated in DFU healing, we used NanoString’s GeoMx Digital Spatial profiling platform on DFU tissue sections and compared gene expression of areas within the same ulcer as well as between patients who in 12 weeks following surgery healed their DFU (Healers, N=2) vs those who did not (Non-Healers, N=2).

2021-10-28 | GSE166120 | GEO

Single Cell Analysis of Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer Foot Wounds

Project description:Single Cell Analysis of Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer Foot Wounds

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Single Cell Transcriptomic Landscape of Diabetic Foot Ulcers

Project description:Diabetic foot ulcers (DFUs) are a devastating complication of diabetes. In order to identify systemic and local factors associated with DFU healing, we examined the cellular landscape of DFUs by single-cell RNA-seq analysis of foot and forearm skin specimens, as well as PBMC samples, from 10 non-diabetic subjects, and 17 diabetic patients, 11 with, and 6 without DFU. Our analysis shows enrichment of a unique inflammatory fibroblast population in DFU patients with healing wounds. The patients with healing DFUs also depicted enrichment of macrophages with M1 polarization, as opposed to more M2 macrophages in non-healing wounds. These findings were verified using Immunohistochemistry and Spatial Transcriptomics.

2021-11-01 | GSE165816 | GEO

Circular RNA expression profiling in diabetic foot ulcers and human normal acute wounds

Project description:Circular RNA (circRNA) microarray analysis was performed to examine the expression profiles of circRNAs in diabetic foot ulcers (DFU) and in human excisional skin wounds 7 days after injury.

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Diabetic foot ulcer mycobiome

Project description:Phylogeny of the diabetic foot ulcer mycobiome of an Afro-Caribbean population

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Diabetic foot ulcer microbiome

Project description:Phylogenetic profiling of the diabetic foot ulcer microbiome of an Afro-Caribbean population

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The Role of Fibroblasts in Diabetic Ulcer Healing and the Therapeutic Potential of Platelet-Rich Plasma (PRP): Insights from Single-Cell Sequencing and Animal Models

Project description:Objective: This study aims to investigate the diversity of fibroblasts present in diabetic ulcers and their impact on the wound healing process, as well as to evaluate the effectiveness of Platelet-Rich Plasma (PRP) therapy in the management of diabetic ulcers. Methodology: The single-cell dataset GSE165816 from the GEO database was utilized to analyze DFU-healer and DFU-nonhealer samples in order to evaluate variations in fibroblasts. Functional characteristics of fibroblasts were investigated through analyses of cell communication, transcription factors, and pseudotime analysis. Additionally, a diabetic ulcer rat model was established to compare the therapeutic effects of PRP, followed by histological and transcriptomic sequencing analyses. Result: Single-cell sequencing analysis identified a greater abundance of fibroblasts in the group of diabetic foot ulcer (DFU) patients who exhibited healing. The findings from biological informatics analysis emphasized the critical role of fibroblasts in the wound healing process. Treatment with PRP notably enhanced wound healing in diabetic ulcers in rats, and transcriptomic analysis indicated that gene expression levels post-PRP treatment resembled those of the non-diabetic ulcer group, with a strong association to fibroblasts. Conclusion: Fibroblasts are essential in the process of healing diabetic ulcers, as certain transcription factors have the potential to facilitate wound closure. PRP therapy has been shown to enhance the healing process in diabetic ulcer rat models, possibly through the modulation of gene expression and the promotion of extracellular matrix arrangement. This research offers novel insights and potential therapeutic approaches for managing diabetic ulcers.

2024-11-11 | GSE280992 | GEO

Characterization of Diabetic and Non-Diabetic Foot Ulcers Using Single-Cell RNA-Sequencing

Project description:We examined the feasibility of single cell RNA sequencing (scRNA-seq) analysis to evaluate human chronic wound samples acquired in the clinic, subjected to prolonged cold ischemia time, and processed without FACS sorting. Wound tissue from human diabetic and non-diabetic plantar foot ulcers were evaluated using an optimized 10X Genomics scRNA-seq platform and analyzed using a modified data pipeline designed for low-yield specimens. Cell subtypes were identified informatically and their distributions and transcriptional programs were compared between diabetic and non-diabetic tissue. 139,000 diabetic and non-diabetic wound cells were delivered for 10X capture after either 90 or 180 min of cold ischemia time. cDNA library concentrations were 858.7 and 364.7 pg/µL, respectively, prior to sequencing. Among all barcoded fragments, we found that 83.5% successfully aligned to the human transcriptome and 68% met the minimum cell viability threshold. The average mitochondrial mRNA fraction was 8.5% for diabetic cells and 6.6% for non-diabetic cells, correlating with differences in cold ischemia time. A total of 384 individual cells were of sufficient quality for subsequent analyses; from this cell pool, we identified transcriptionally-distinct cell clusters whose gene expression profiles corresponded to fibroblasts, keratinocytes, neutrophils, monocytes, and endothelial cells. Fibroblast subpopulations with differing fibrotic potentials were identified, and their distributions were found to be altered in diabetic vs. non-diabetic cells.

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