Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA827133 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18840000.fastq.gz | Fastqsanger.gz | |||
| SRR18840000_1.fastq.gz | Fastqsanger.gz | |||
| SRR18840000_2.fastq.gz | Fastqsanger.gz | |||
| SRR18840100.fastq.gz | Fastqsanger.gz | |||
| SRR18840100_1.fastq.gz | Fastqsanger.gz |
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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
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
Project description:Analysis of ex vivo isolated lymphatic endothelial cells from the dermis of patients to define type 2 diabetes-induced changes. Results preveal aberrant dermal lymphangiogenesis and provide insight into its role in the pathogenesis of persistent skin inflammation in type 2 diabetes. The ex vivo dLEC transcriptome reveals a dramatic influence of the T2D environment on multiple molecular and cellular processes, mirroring the phenotypic changes seen in T2D affected skin. The positively and negatively correlated dLEC transcripts directly cohere to prolonged inflammatory periods and reduced infectious resistance of patients´ skin. Further, lymphatic vessels might be involved in tissue remodeling processes during T2D induced skin alterations associated with impaired wound healing and altered dermal architecture. Hence, dermal lymphatic vessels might be directly associated with T2D disease promotion. Global gene expression profile of normal dermal lymphatic endothelial cells (ndLECs) compared to dermal lymphatic endothelial cells derived from type 2 diabetic patients (dLECs).Quadruplicate biological samples were analyzed from human lymphatic endothelial cells (4 x diabetic; 4 x non-diabetic). subsets: 1 disease state set (dLECs), 1 control set (ndLECs)
2012-06-01 | E-GEOD-38396 | biostudies-arrayexpress
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).
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Project description:Spatial transcriptomics of healing and non-healing diabetic foot ulcers
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Project description:Severe angiopathy is a major driver for diabetes associated secondary complications. Knowledge on underlying mechanisms essential for advanced therapies to attenuate these pathologies is limited. Injection of ABCB5+ stromal precursors (SPs) at the edge of non-healing diabetic wounds in a murine db/db model, closely mirroring human type II diabetes, profoundly accelerates wound closure. Strikingly, enhanced angiogenesis was substantially enforced by the release of the ribonuclease angiogenin from ABCB5+ SPs. This compensates for the profoundly reduced angiogenin expression in non-treated murine and human chronic diabetic wounds. Silencing of angiogenin in ABCB5+ SPs prior to injection significantly reduced angiogenesis, reduced numbers of M2 macrophages and delayed wound closure in diabetic db/db mice implying an unprecedented key role for angiogenin in tissue regeneration in diabetes. These data hold significant promise for further refining SPs-based therapies of non-healing diabetic foot ulcers and other pathologies with impaired angiogenesis.
2021-08-12 | GSE181881 | GEO
Project description:Impaired wound healing is one of the main reasons that leads to diabetic foot ulcerations. However, the exact mechanism of delayed wound healing in diabetes mellitus is not fully understood. Long non-coding RNAs (lncRNAs) are widely involved in a variety of biological processes and diseases, including diabetes and its associated complications. To further identify the roles of LncRNAs in diabetic wound healing, four STZ induced diabetic rat skin tissues and four control rat skin tissues were prepared for a LncRNAs microarray expression profiling by using rat LncRNA Array (4 x 44K, Arraystar).
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Project description:Hsa_circ_0084443 expression level is down-regulated during normal skin wound healing and higher level of hsa_circ_0084443 was found in chronic non-healing diabetic foot ulcers compared to normal wounds. However, the biological function of hsa_circ_0084443 in epidermal keratinocytes during wound repair has not been studied. To study the genes regulated by hsa_circ_0084443, we transfected siRNA targeting hsa_circ_0084443 diagnostic junction into human primary epidermal keratinocytes to knockdown hsa_circ_0084443 expression. We performed a global transcriptome analysis of keratinocytes upon knockdown of hsa_circ_0084443 using Affymetrix arrays.
2019-10-01 | GSE114236 | GEO
Project description:Diabetes Mellitus (DM) is a chronic, severe disease rapidly increasing in incidence and prevalence and is associated with numerous complications. Patients with DM are at high risk of developing diabetic foot ulcers (DFU) that often lead to lower limb amputations, long term disability, and a shortened lifespan. Despite this, the effects of DM on human foot skin biology are largely unknown. Thus, the focus of this study was to determine whether DM changes foot skin biology predisposing it for healing impairment and development of DFU. Foot skin samples were collected from 20 patients receiving corrective foot surgery and, using a combination of multiple molecular and cellular approaches we performed comparative analyses of non-ulcerated non-neuropathic diabetic foot skin (DFS) and healthy non-diabetic foot skin (NFS). MicroRNA (miR) profiling of laser captured epidermis and primary dermal fibroblasts from both DFS and NFS samples identified 5 miRs de-regulated in the epidermis of DFS though none reached statistical significance. MiR-31-5p and miR-31-3p were most profoundly induced. Although none were significantly regulated in diabetic fibroblasts, miR-29c-3p showed a trend of up-regulation, which was confirmed by qPCR in a prospective set of 20 skin samples. Gene expression profiling of full thickness biopsies identified 36 de-regulated genes in DFS (>2 fold-change, unadjusted p-value ≤ 0.05). Of this group, three out of seven tested genes were confirmed by qPCR: SERPINB3 was up-regulated whereas OR2A4 and LGR5 were down-regulated in DFS. However no morphological differences in histology, collagen deposition, and number of blood vessels or lymphocytes were found. No difference in proliferative capacity was observed by quantification of Ki67 positive cells in epidermis. These findings suggest DM causes only subtle changes to foot skin. Since morphology, mRNA and miR levels were not affected in a major way, additional factors, such as neuropathy, vascular complications, or duration of DM, may further compromise tissue’s healing ability leading to development of DFUs.
2015-05-01 | GSE68185 | GEO
Project description:OBJECTIVE: To assess the safety and efficacy as well as determination of the molecular mechanism of action of topical allogeneic ADSC therapy in the treatment of ulcers in patients with neuropathic diabetic foot. RESEARCH DESIGN AND METHODS: We examined a total of 57 patients with neuropathic diabetic foot in grades IA and IIA according to the University of Texas classification. Finally 23 patients received treatment with standard therapy and fibrin glue (fibrin gel group) and 23 received treatment with standard therapy and ADSC suspended in tissue glue (fibrin gel + ADSC group). The primary outcome was determining the time needed to reduce the wound size by 50% from the initial size in both groups by assessing the wound surface, the evaluation of treatment safety, expressed as the occurrence of any adverse events; the evaluation of symptoms improvement (e.g. pain, itching, etc.) assessed by Visual Analogue Scale (VAS) and analysis of the expression of selected pro-angiogenic and immunomodulatory factors in the wounds treated in both study groups. RESULTS:The ADSC group benefited from the use of stem cells in terms of accelerated wound healing and greater likelihood of complete healing of the wound. In a second week after administration of therapy, the difference between the groups was already statistically significant (p = 0,04). The time to the 50% reduction of the size of the wound in the fibrin gel + ADSC group was significantly shorter (18.9 +/- 2.2 days ) than in the group receiving fibrin gel (39.8 +/- 6.9 days ), p = 0.0035. CONCLUSIONS: The results of the preliminary analysis show that the use of allogeneic ADSCs in the treatment of neuropathic diabetic foot ulcers is a safe method of therapy, which allows to improve the effects of wound healing. Our study indicates also the association of higher expression of selected proteins expression intensifying the healing process through a faster transition to the proliferation phase with a faster reduction in wound area, and long-term efficacy of allogeneic ADSC cells.
2023-03-11 | PXD032099 | Pride