Gene Expression Changes in Therapeutic Ultrasound-Treated Human Chronic Wound Tissue
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA922220 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23030753.fastq.gz | Fastqsanger.gz | |||
| SRR23030754.fastq.gz | Fastqsanger.gz | |||
| SRR23030755.fastq.gz | Fastqsanger.gz | |||
| SRR23030756.fastq.gz | Fastqsanger.gz | |||
| SRR23030757.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:The purpose of this study was to evaluate gene expression differences in debrided human venous ulcer tissue from patients treated with low-frequency (20 kHz), low-intensity (100 mW/cm2) ultrasound compared to a sham treatment in an effort to better understand the potential biological mechanisms.
2023-02-01 | GSE222503 | GEO
Project description:Adalimumab is the only FDA- and EMA-approved treatment for moderate-to-severe hidradenitis suppurativa (HS), suggesting that the mechanism of action of adalimumab is distinct in HS and may contribute to improved wound healing. We have demonstrated that adalimumab, but neither etanercept nor certolizumab-pegol, induces a wound healing profile in vitro, which may underlie the differences in efficacy between various anti-TNF agents. To examine and compare the efficacy of therapeutic TNF inhibitors in chronic cutaneous wound healing in vivo, a human TNF knock-in Leprdb/db mouse model was established. The vehicle group exhibited severe impairments in cutaneous wound healing. In contrast, adalimumab significantly accelerated healing, confirmed by both histologic assessment and a unique healing transcriptional profile. Moreover, adalimumab and infliximab showed similar levels of efficacy, but golimumab was less effective, along with etanercept and certolizumab-pegol. In line with histologic assessments, proteomics analyses from healing wounds exposed to various TNF inhibitors revealed distinct and differential wound healing signatures that may underlie the differential efficacy of therapeutic inhibitors in accelerating chronic wound healing.
2023-09-11 | PXD040275 | Pride
Project description:Impaired skin wound healing is a significant global health issue, especially among the elderly. Wound healing is a well-orchestrated process involving the sequential phases of inflammation, proliferation, and tissue remodeling. Although wound healing is a highly dynamic and energy-requiring process, the role of metabolism remains largely unexplored. By combining transcriptomics and metabolomics of human skin biopsy samples, we mapped the core bioenergetic and metabolic changes in normal acute as well as chronic wounds in elderly subjects. We found upregulation of glycolysis, the tricarboxylic acid cycle, glutaminolysis, and β-oxidation in the later stages of acute wound healing and in chronic wounds. To ascertain the role of these metabolic pathways on wound healing, we targeted each pathway in a wound healing assay as well as in a human skin explant model using metabolic inhibitors and stimulants. Enhancement or inhibition of glycolysis and, to a lesser extent, glutaminolysis had a far greater impact on wound healing than similar manipulations of oxidative phosphorylation and fatty acid β-oxidation. These findings increase the understanding of wound metabolism and identify glycolysis and glutaminolysis as potential targets for therapeutic intervention.
2024-07-02 | MTBLS3315 | MetaboLights
Project description:Echo-contrast agents enhance the echogenicity of ultrasound and have been clinically used for diagonosis in current medical fields. Here, the combined effects of Sonazoid, an echo-contrast agent, and ultrasound on the gene expression in human lymphoma U937 cells were investigated using an Affymetrix GeneChip system. The cells were treated with Sonazoid (0.05%; Sonazoid only), ultrasound (0.3 W/cm2 for 1 min; ultrasound only) and the combination of Sonazoid and ultrasound (0.05% Sonazoid plus ultrasound 0.3 W/cm2 for 1 min; Sonazoid + Ultrasound) and followed by incubation for 3 h at 37°C. The percentage of DNA fragmentation 6 h after treatment was 5.8 ± 1.0 (mean ± SD, n = 3), 6.0 ± 0.4, 13.5 ± 1.0, and 18.3 ± 2.3 in cells treated with control, Sonazoid only, ultrasound only and Sonazoid + Ultrasound, respectively. Of approximately 47,000 probe sets analyzed, probe sets that were differentially expressed by a factor 2.0 or greater were 40, 184 and 144 in cells treated with Sonazoid only, ultrasound only and Sonazoid + Ultrasound, respectively. Experiment Overall Design: U937 cells, a human lymphoma cell line, were treated with Sonazoid (0.05%), ultrasound (0.3 W/cm2 for 1 min) and the combination of Sonazoid and ultrasound (0.05% Sonazoid plus ultrasound 0.3 W/cm2 for 1 min) and followed by incubation for 3 h at 37°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturerâ??s instructions.
2009-05-27 | E-GEOD-16118 | biostudies-arrayexpress
Project description:This study aimed to explore the therapeutic potential of cyano-phycocyanin (C-PC) to improve the efficiency of chronic refractory wound healing processes. The hormone induced chronic refractory skin ulcer model were established on the backs of mice. Assessment of wound-healing efficiency of C-PC was evaluated by analyzing total wound closure, recovery percentage and epidermal thickness of wounds. Hematoxylin-eosin, Masson trichrome and immunohistochemical analysis were performed to evaluate the re-epithelialization, inflammatory response, granulation tissue formation and fibrotic tissue formation. Differentially expressed genes were identified through RNA-seq, polymerase chain reaction (PCR) array and confirmed by quantitative PCR (qPCR). Cell viability was determined using a cell counting kit-8 (CCK-8) assay, migration and angiogenesis were detected by wound healing and tube formation assays. The related protein expression was analyzed by Western blot. The results demonstrated a significantly higher wound-healing rate in C-PC group compared to the control group at 3, 7, 14, and 21 days (p< 0.05). The mechanism may involve increased collagen accumulation, promotion of angiogenesis and reduction in the infiltration of inflammatory cells. Additionally, VEGFR-2 was highly likely to be the target for C-PC. Thus, C-PC may hold potential for the treatment of wound healing and ischemic/ reperfusion injuries.
2025-06-01 | GSE296266 | GEO
Project description:Chronic kidney disease (CKD) is a disease characterized by normal or reduced proteinuria, glomerular filtration rate, progressive damage to glomeruli, tubules, and interstitium. In this study, we performed RNA-seq reveals ultrasound-guided renal parenchymal infusion of mesenchymal stem cells in SD rats animal model in chronic kidney disease. Our results indicate that differential genes in the normal group(n=3) VS CKD group(n=3) and normal group(n=3) VS MSCs treatment group(n=3).
2024-10-03 | GSE275449 | GEO
Project description:Focused ultrasound of the spleen is an emerging therapeutic modality and recent reports have shown efficacy in reducing inflammation. We used scRNA seq to identify the gene expression changes in lungs of healthy animals, animals with pulmonary hypertension treated with focused ultrasound of the spleen or sham stimulation.
2023-12-01 | GSE247625 | GEO
Project description:The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were identified. Further investigation revealed that alternative TLN2 and ZNF521 genotypes explained significant inter-patient variation in relative abundance of two key pathogens, Pseudomonas aeruginosa and Staphylococcus epidermidis. Wound diversity was lowest in Pseudomonas aeruginosa infected wounds, and decreasing wound diversity had a significant negative linear relationship with healing rate. In addition to microbiome characteristics, age, diabetic status, and genetic ancestry all significantly influenced healing. Using structural equation modeling to identify common variance among SNPs, six loci were sufficient to explain 53% of variation in wound microbiome diversity, which was a 10% increase over traditional multiple regression. Focusing on TLN2, genotype at rs8031916 explained expression differences of alternative transcripts that differ in inclusion of important focal adhesion binding domains. Such differences are hypothesized to relate to wound microbiomes and healing through effects on bacterial exploitation of focal adhesions and/or cellular migration. Related, other associated loci were functionally enriched, often with roles in cytoskeletal dynamics. This study, being the first to identify patient genetic determinants for wound microbiomes and healing, implicates genetic variation determining cellular adhesion phenotypes as important drivers of infection type. The identification of predictive biomarkers for chronic wound microbiomes may serve as risk factors and guide treatment by informing patient-specific tendencies of infection.
2020-04-25 | GSE149314 | GEO
Project description:IntroductionLow-frequency, low-intensity ultrasound has been previously shown to promote healing of chronic wounds in humans, but mechanisms behind these effects are poorly understood. The purpose of this study was to evaluate gene expression differences in debrided human venous ulcer tissue from patients treated with low-frequency (20 kHz), low-intensity (100 mW/cm2) ultrasound compared to a sham treatment in an effort to better understand the potential biological mechanisms.MethodsDebrided venous ulcer tissue was collected from 32 subjects one week after sham treatment or low-frequency, low-intensity ultrasound treatment. Of these samples, 7 samples (3 ultrasound treated and 4 sham treated) yielded sufficient quality total RNA for analysis by ultra-high multiplexed PCR (Ampliseq) and expression of more than 24,000 genes was analyzed. 477 genes were found to be significantly differentially expressed between the ultrasound and sham groups using cut-off values of p < 0.05 and fold change of 2.Results and discussionThe top differentially expressed genes included those involved in regulation of cell metabolism, proliferation, and immune cell signaling. Gene set enrichment analysis identified 20 significantly enriched gene sets from upregulated genes and 4 significantly enriched gene sets from downregulated genes. Most of the enriched gene sets from upregulated genes were related to cell-cell signaling pathways. The most significantly enriched gene set from downregulated genes was the inflammatory response gene set. These findings show that therapeutic ultrasound influences cellular behavior in chronic wounds as early as 1 week after application. Considering the well-known role of chronic inflammation in impairing wound healing in chronic wounds, these results suggest that a downregulation of inflammatory genes is a possible biological mechanism of ultrasound-mediated venous chronic wound healing. Such increased understanding may ultimately lead to the enhancement of ultrasound devices to accelerate chronic wound healing and increase patient quality of life.
| S-EPMC10098114 | biostudies-literature
Project description:The primary purpose of the trial is to determine the preliminary efficacy of therapeutic ultrasound in the treatment of pain and sensory disturbance related to chemotherapy induced peripheral neuropathy.
| 2194292 | ecrin-mdr-crc