Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1232139 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32576756.fastq.gz | Fastqsanger.gz | |||
| SRR32576757.fastq.gz | Fastqsanger.gz | |||
| SRR32576758.fastq.gz | Fastqsanger.gz | |||
| SRR32576759.fastq.gz | Fastqsanger.gz | |||
| SRR32576760.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Diabetic wound infections have poor healing outcomes due to the presence of numerous pathogens in addition to an impaired immune response. Group B Streptococcus (GBS) is one of the most commonly isolated bacteria from diabetic wound infections, but virulence mechanisms GBS uses during these infections have not been investigated. Here, we developed a new murine model of GBS diabetic wound infection to determine how GBS establishes infection and persists in the wound environment. Using dual RNA sequencing, we demonstrate that GBS infection of diabetic wounds triggers an inflammatory response, leading to increased transcript levels of inflammatory cytokines and chemokines as well as markers of neutrophil degranulation such as myeloperoxidase, calprotectin, and elastase. We then confirm that diabetic wounds infected with GBS have significantly higher abundance of Il-1b, KC (CXCL1), myeloperoxidase, calprotectin and elastase in wound tissues than uninfected controls . When examining how GBS adapts to this hyper-inflammatory environment we find that GBS upregulates numerous virulence factors including the surface plasminogen-binding protein pbsP, the nuclease nucA, the cyl operon which is responsible for hemolysin production and pigmentation as well as numerous effectors of type VII secretion. In addition, we recovered multiple hyper-pigmented/hemolytic GBS colonies from the murine diabetic wound environment which encode mutations in the two-component system covRS. We then go on to demonstrate that a mutant in cylE, which is repressed by CovR, is attenuated in diabetic wound infection. Finally, we examine the most highly upregulated gene pbsP in diabetic wound infection and find that PbsP is necessary for diabetic wound infection via adherence to the skin and promotion of inflammation.
2022-09-30 | GSE201342 | GEO
Project description:MicroRNAs are powerful gene expression regulators, but their corneal repertoire and potential changes in corneal diseases remain unknown. Our purpose was to identify miRNAs altered in the human diabetic cornea by microarray analysis, and to examine their effects on wound healing in cultured telomerase-immortalized human corneal epithelial cells (HCEC) in vitro. Using microarrays, 29 miRNAs were identified as differentially expressed in diabetic samples. Two miRNA candidates showing the highest fold increased in expression in the diabetic cornea were confirmed by Q-PCR and further characterized. HCEC transfection with h-miR-146a or h-miR-424 significantly retarded wound closure, but their respective antagomirs significantly enhanced wound healing vs. controls. Cells treated with h-miR-146a or h-miR-424 had decreased p-p38 and p-EGFR staining, but these increased over control levels close to the wound edge upon antagomir treatment. In conclusion, several miRNAs with increased expression in human diabetic central corneas were found. Two such miRNAs inhibited cultured corneal epithelial cell wound healing. Dysregulation of miRNA expression in human diabetic cornea may be an important mediator of abnormal wound healing.
2013-11-09 | GSE52233 | 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).
2022-09-29 | GSE214338 | GEO
Project description:MicroRNAs are powerful gene expression regulators, but their corneal repertoire and potential changes in corneal diseases remain unknown. Our purpose was to identify miRNAs altered in the human diabetic cornea by microarray analysis, and to examine their effects on wound healing in cultured telomerase-immortalized human corneal epithelial cells (HCEC) in vitro. Using microarrays, 29 miRNAs were identified as differentially expressed in diabetic samples. Two miRNA candidates showing the highest fold increased in expression in the diabetic cornea were confirmed by Q-PCR and further characterized. HCEC transfection with h-miR-146a or h-miR-424 significantly retarded wound closure, but their respective antagomirs significantly enhanced wound healing vs. controls. Cells treated with h-miR-146a or h-miR-424 had decreased p-p38 and p-EGFR staining, but these increased over control levels close to the wound edge upon antagomir treatment. In conclusion, several miRNAs with increased expression in human diabetic central corneas were found. Two such miRNAs inhibited cultured corneal epithelial cell wound healing. Dysregulation of miRNA expression in human diabetic cornea may be an important mediator of abnormal wound healing. Total RNA was extracted from age-matched human autopsy normal (n=6) and diabetic (n=6) central corneas, Flash Tag end-labeled, and hybridized to Affymetrix® GeneChip® miRNA Arrays. Select miRNAs associated with diabetic cornea were validated by quantitative RT-PCR (Q-PCR) and by in situ hybridization (ISH) in independent samples.
2013-11-09 | E-GEOD-52233 | biostudies-arrayexpress
Project description:Impaired healing of diabetic wounds causes significant morbidity and mortality. This study aimed to identify novel mechanisms of diabetic wound healing defects and test a therapeutic intervention using diabetic mouse and pig models. We found Smad7 transgene expression in mouse epidermis promoting wound healing in diabetic db/db mice, with reductions in obesity and blood glucose. To isolate effects of Smad7 on wounds, we created a Smad7-based biologic (Tat-PYC-Smad7) that penetrates wound cells. Topical application of Tat-PYC-Smad7 to diabetic pig and mouse wounds accelerated healing compared to controls. RNAseq analysis of mouse wound samples showed reduced TGFβ/NFκB signaling, leading to faster re-epithelialization and better extracellular matrix remodeling. Tat-PYC-Smad7 also attenuated neutrophil degranulation and NETosis by blocking histone 3 citrullination and inhibiting myeloperoxidase activities. Our study reveals that Tat-PYC-Smad7 promotes diabetic wound healing by targeting keratinocytes and neutrophils, providing insight into cellular mechanisms of diabetic wound healing defects targetable by Smad7-based therapy.
2024-08-13 | GSE274513 | GEO
Project description:<p> Background: Diabetic foot tendon exposures are prone to infection, necrosis, and prolonged treatment cycles, not only hindering wound healing but potentially leading to amputation and life-threatening complications. Shengji ointment combined with bromelain has demonstrated preliminary efficacy in treating these wounds, but its mechanisms of action and impact on wound metabolites require further investigation.</p><p> Methods: Thirty patients with diabetic foot tendon exposure wounds received four-week treatment with Shengji ointment combined with bromelain. Clinical outcomes including granulation tissue coverage and wound healing rates were evaluated. Wound exudates collected pretreatment and posttreatment underwent metabolomics analysis to characterize treatment-induced metabolic changes.</p><p> Results: Following treatment, significant improvements were observed in granulation tissue coverage and wound healing rates compared to pretreatment baseline. Metabolomic profiling identified 4034 differential metabolites (1907 upregulated, 2127 downregulated), revealing significant alterations in key metabolic pathways including phenylpropanoid biosynthesis, tyrosine metabolism, and amino acid biosynthesis pathways.</p><p> Conclusion: Shengji ointment combined with bromelain effectively promotes healing of diabetic foot wounds with tendon exposure through significant modulation of the wound metabolic environment, particularly via regulation of critical metabolic pathways. These metabolomics findings provide mechanistic insights supporting this treatment approach.</p>
2025-07-14 | MTBLS12713 | MetaboLights
Project description:At present, there is no effective treatment for diabetic wounds, and the cost of treatment is high. MicroRNAs (miRNAs) plays an important role in the process of diabetic wound healing. By regulating the expression of target genes, it regulates growth factors, cytokines and signal pathways, thereby affecting various stages of ulcer healing such as hemostasis, anti-inflammatory, proliferation and remodeling. In this study, differential expression of miRNAs in diabetic wound was screened. MiR-206 was selected as the research object to detect the effect of miR-206 on the proliferation of fibroblasts and vascular endothelial cell by regulating HIF-1?. Finally, in vivo studies showed that miR-206 antagomir could promote the expression of HIF-1?, CD34 and VEGF, and further promote wound healing in diabetic rats.
2022-11-10 | GSE188783 | GEO
Project description:This a model from the article:
Modeling the effects of treating diabetic wounds with engineered skin
substitutes.
Waugh HV, Sherratt JA. Wound Repair Regen
2007 Jul-Aug;15(4):556-65 17650100
,
Abstract:
In this paper, a novel mathematical model of wound healing in both normal and
diabetic cases is presented, focusing upon the effects of adding two currently
available commercial engineered skin substitute therapies to the wound
(Apligraf) and Dermagraft). Our work extends a previously developed model, which
considers inflammatory and repair macrophage dynamics in normal and diabetic
wound healing. Here, we extend the model to include equations for
platelet-derived growth factor concentration, fibroblast density, collagen
density, and hyaluronan concentration. This enables us to examine the variation
of these components in both normal and diabetic wound healing cases, and to
model the treatment protocols of these therapies. Within the context of our
model, we find that the key component to successful healing in diabetic wounds
is hyaluronan and that the therapies work by increasing the amount of hyaluronan
available in the wound environment. The time-to-healing results correlate with
those observed in clinical trials and the model goes some way to establishing an
understanding of why diabetic wounds do not heal, and how these treatments
affect the diabetic wound environment to promote wound closure.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Waugh HV, Sherratt JA. (2007) - version=1.0
The original CellML model was created by:
Catherine Lloyd
c.lloyd@auckland.ac.nz
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1006230102 | BioModels