Single-cell RNA transcriptome defines the signaling networks stimulated by alkali burn
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1152563 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30401360_1.fastq.gz | Fastqsanger.gz | |||
| SRR30401360_2.fastq.gz | Fastqsanger.gz | |||
| SRR30401361_1.fastq.gz | Fastqsanger.gz | |||
| SRR30401361_2.fastq.gz | Fastqsanger.gz |
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Project description:To understand the pathological mechanisms of alkali burn, mouse corneal epithelium was exposed to 1M NaOH for 30s . Corneas were processed for scRNA-seq using 10X genomics and data was analyzed using R with a Seurat package.
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Project description:Alkali stress is an important means of inactivating undesirable pathogens in a wide range of situations, ranging from environmental cleaning of food processing environments, to the phagolysosomal killing of cells engulfed by mammalian phagocytes. Unfortunately, L. monocytogenes can launch an alkaline tolerance response (AlTR), significantly increasing persistence of the pathogen in such environments. This study compared the transcriptome patterns of alkali stressed and non alkali stressed L. monocytogenes 10403S cells, to elucidate the mechanisms by which this important pathogen adapts and/or grows during short or long-term alkali stress. Transcription profiles associated with alkali shock (AS) responses were obtained by DNA microarray analysis of mid-exponential cells suspended in pH 9 media for 15, 30 or 60 min. Transcription profiles associated with alkali adaptation (AA) were obtained by DNA microarray analysis of cells grown to mid-exponential phase in pH 9 media . Comparison of AS and AA transcription profiles with profiles from control (pH 7.0) cells identified over 2,000 genes that were differentially expressed under alkaline conditions. Rapid (15min) changes in expression included upregulation of genes encoding for multiple metabolic pathways, (including those associated with Na+/H+ antiporters), ABC transporters of functional compatible solutes such as carnitine, motility and virulence-associated genes as well as the σB controlled stress resistance network. Slower (30min and more) responses to AS and adaptation during growth in alkaline conditions (AA), included modest changes in mRNA concentrations, and genes involved in proton export. Keywords: Time course study of gene expression response to alkaline shock and adaptation
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Project description:#G017 Burn/Trauma Study. This is a Glue Grant Study comparison between gene expression analyses performed in eight trauma/burn subjects using either a buffy coat isolation of whole blood or using the PAXgene system Keywords: other
2004-04-24 | GSE1343 | GEO
Project description:To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88. Seven-day-old uniform-sized seedlings grown in hydroponic medium were transferred to fresh hydroponic medium alone or containing 50 mM alkali salts. Shoots were harvested 24 h after transfer and 10 shoots were pooled for microarray analysis.
2014-05-16 | E-GEOD-45724 | biostudies-arrayexpress
Project description:Animal experiments were performed with male Sprague-Dawley rats (Charles River Laboratories, Boston, MA) weighing 150 ? 200 grams. All experimental protocols used in this study were approved by the Subcommittee on Research Animal Care, Massachusetts General Hospital. Rats were individually housed in a temperature-controlled (25oC) and light-controlled room (12h light-dark cycle) and allowed to adjust to their new surroundings for at least 5 days prior to the experiment. Water and rat chow were provided ad libitum to the animals. On the day of the treatment, the animals were randomly divided into two groups, burned and sham-burned. The burn injury consisted of a full-skin-thickness scald burn of the dorsum, calculated to be ~ 20% of the rat?s total body surface area (TBSA), induced by immersing the designated area in boiling water for 10 s (45). Rats were resuscitated with an intra-peritoneal injection of sterile saline solution (1.5 mL/Kg body weight/% TBSA) immediately after burn. The mortality rate of this treatment was negligible. At each time point (1, 2, 4, and 7d), three animals belonging to each group were sacrificed, the liver and serum collected, and stored at ?80oC after being inflicted with 20% TBSA burn injury. Sham-burn rats (n=3) considered as the control were treated identically except that they were immersed into a 37oC water bath and immediately sacrificed to collect the livers. Keywords = Burn Liver microarray genechip time course Keywords: time-course
2005-10-11 | GSE1860 | GEO
Project description:Neutrophils accumulate early in burn wounds, and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However, we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here, we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single-cell transcriptional (scRNA-Seq) mapping of myeloid cells during a 3-day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions, we found subtype-specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils, with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality, suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore, we characterized the transcriptional dynamics of cell-cell interactions in both conditions by time. Among burn-induced signaling pathways, we found il6-il6r signaling as a time-point-specific macrophage-neutrophil interaction, suggesting the importance of timing in innate immune response in burn. Finally, to test the translational value of our fish model, we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area (TBSA) in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single-cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients.
2024-07-26 | GSE250610 | GEO
Project description:Purpose Corneal neovascularization (CNV) impairs corneal transparency and visual acuity. The study aims to deepen our understanding of the molecules involved in CNV induced by alkali burns, facilitate a better grasp of CNV mechanisms, and uncover potential therapeutic targets. Methods Mice were selected for establishing CNV models via alkali burns. On days 3, 7, and 14 after the burns, corneal observations and histological investigations were conducted. An integrated analysis of RNA sequencing (RNA-seq)-based transcriptomics and label-free quantitative proteomics was performed in both normal and burned corneas. Bioinformatics approaches, encompassing GO and KEGG analysis, were applied to discern differentially expressed genes (DEGs) and crucial signaling pathways. Four potentially CNV-related genes were validated using qRT-PCR and Western blot. Results Significant CNV was observed on the seventh day. Forty-one genes were differentially expressed in neovascularized corneas, with 15 upregulated and 26 downregulated at both mRNA and protein levels. Bioinformatics analysis revealed that these DEGs participated in diverse biological processes, encompassing retinol and retinoic acid metabolism, neutrophil chemotaxis, and actin filament assembly, along with significant enrichment pathways like cytochrome P450, tyrosine, and phenylalanine metabolism. The upregulation of lymphocyte cytosolic protein 1 (LCP1) and cysteine and glycine-rich protein 2 (CSRP2) genes and the downregulation of transglutaminase 2 (TGM2) and transforming growth factor-beta-induced (TGFBI) genes were confirmed. Conclusions We analyzed gene expression differences in mouse corneas seven days after alkali burns, finding 41 genes with altered expression. The exact role of these genes in CNV is not fully understood, but exploring angiogenesis-related molecules offers potential for CNV treatment or prevention.
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Project description:Burn injury remains a major clinical challenge to both survival and to quality of life. Its progressive, aberrant inflammation underlies the lethal dysfunction of various organs and the pain it induces is excruciating and notoriously difficult to manage. While it is known that burn injury’s complex local and disseminating pathology is orchestrated from the burned tissue, few studies have sought to characterise the local signalling environment. An enhanced understanding of the local and acutely temporally-dynamic processes defining burn injury and its progression is required for the development of novel therapeutic interventions. Microdialysis was used as an interstitial sampling technique, conducted over three hours post-burn. Samples were analysed by metabolomics and a multiplex cytokine immunoassay. Next-Generation sequencing libraries of the burn and control microdialysis sites were prepared to measure transcriptional changes potentially underlying the interstitial profile characterising burn injury.
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Project description:Burn wound blister fluid is a valuable matrix for understanding the biological pathways associated with burn injury. In this study, 152 blister fluid samples collected from paediatric burn wounds at two different hospitals were analysed using mass spectrometry proteomic techniques. The protein abundance profile at different days post-burn indicated that there were more proteins associated with cellular damage/repair in the first 24 hours, whereas after this point there were more proteins associated with antimicrobial defence and inflammation. The inflammatory proteins persisted at a high level in the blister fluid for more than 7 days. This may indicate that removal of burn blisters prior to two days post-burn is optimal to prevent excessive or prolonged inflammation in the wound environment. Additionally, many proteins associated with the neutrophil extracellular trap (NET) pathway were increased post-burn, further implicating NETs in the post-burn inflammatory response. NET inhibitors may therefore be a potential treatment to reduce post-burn inflammation and coagulation pathology and enhance burn wound healing outcomes.
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