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Integrative Analysis of Genome-Wide Epigenetic and Transcriptomic Alterations Reveals Molecular Markers for Diagnosing Pediatric Obstructive Sleep Apnea in Black Females [WGBS]

ABSTRACT: Integrative Analysis of Genome-Wide Epigenetic and Transcriptomic Alterations Reveals Molecular Markers for Diagnosing Pediatric Obstructive Sleep Apnea in Black Females [WGBS]

PROVIDER: PRJNA994520 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25267800_1.fastq.gz	Fastqsanger.gz
	SRR25267800_2.fastq.gz	Fastqsanger.gz
	SRR25267900_1.fastq.gz	Fastqsanger.gz
	SRR25267900_2.fastq.gz	Fastqsanger.gz
	SRR25268000_1.fastq.gz	Fastqsanger.gz

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Integrative Analysis of Genome-Wide Epigenetic and Transcriptomic Alterations Reveals Molecular Markers for Diagnosing Pediatric Obstructive Sleep Apnea in Black Females [WGBS]

Project description:This study explores the epigentic and transcriptomic changes associated with pediatric obstructive sleep apnea in Black female patients. By analyzing saliva samples, the study identifies dysregulated pathways and specific molecular markers, emphasizing the need for accessible diagnostic tools and addressing healthcare disparities in underrepresented population. The non-invasive approach using saliva samples offers potential for future research and improved diagnostics for pediatric OSA.

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Integrative Analysis of Genome-Wide Epigenetic and Transcriptomic Alterations Reveals Molecular Markers for Diagnosing Pediatric Obstructive Sleep Apnea in Black Females

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Epigenome analysis of peripheral blood mononuclear cell (PBMC) samples from obstructive sleep apnea patients and healthy subjects

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Epigenome analysis of peripheral blood mononuclear cell (PBMC) samples from obstructive sleep apnea patients and healthy subjects

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Integrative Analysis of Genome-Wide Epigenetic and Transcriptomic Alterations Reveals Molecular Markers for Diagnosing Pediatric Obstructive Sleep Apnea in Black Females [RNA-Seq]

Project description:Integrative Analysis of Genome-Wide Epigenetic and Transcriptomic Alterations Reveals Molecular Markers for Diagnosing Pediatric Obstructive Sleep Apnea in Black Females [RNA-Seq]

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Serum proteomic analysis by tandem mass tags-based quantitative proteomics in pediatric obstructive sleep apnea

Project description:Pediatric obstructive sleep apnea (OSA) is a frequent respiratory disorder with an estimated prevalence of 3–6% in the general population. However, the underlying pathophysiology of OSA remains unclear. Recently, proteomic analysis using high-resolution and high-throughput mass spectrometry has been widely used in the field of medical sciences. In the present study, tandem mass tags (TMT)-based proteomic analysis was performed in the serum of patients with OSA.

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Visceral fat trancriptome in obstructive sleep apnea

Project description:Rationale: Obstructive sleep apnea (OSA) has been associated with metabolic dysregulation and systemic inflammation. This may be due to pathophysiologic effects of OSA on visceral adipose tissue. We sought to assess the transcriptional consequences of OSA on adipocytes by utilizing pathway-focused analyses. Methods: Patients scheduled to undergo ventral hernia repair surgery were recruited to wear a portable home sleep monitor for two nights prior to surgery. Visceral fat biopsies were obtained intra-operatively. RNA was extracted and whole-genome expression profiling was performed. Gene Set Enrichment Analysis (GSEA) was used to identify curated gene sets that were differentially enriched in OSA subjects. Network analysis was applied to a select set of highly enriched pathways. Results: 10 patients with OSA and 8 control subjects were recruited. There were no differences in age, gender, body mass index between the two groups, but the OSA subjects had a significantly higher respiratory disturbance index (19.2 vs. 0.6, P-value 0.05) and worse hypoxemia (minimum oxygen saturation 79.7% vs. 87.8%, P-value < 0.001). GSEA identified a number of gene sets up-regulated in adipose tissue of OSA patients including the pro-inflammatory NF-M-NM-:B pathway and the proteolytic ubiquitin/proteasome module. A critical metabolic pathway, the peroxisome proliferator-activated receptor (PPAR), was down-regulated in subjects with OSA. Network analysis linked members of these modules together and identified regulatory hubs. Conclusions: OSA is associated with alterations in visceral fat gene expression. Pathway-based network analysis highlighted perturbations in several key pathways whose coordinated interactions may contribute to the metabolic dysregulation observed in this complex disorder. Total RNA from visceral fat of 18 subjects (10 OSA, 8 Control) was hybridized to 18 Affymetrix Genechip Human Gene 1.0 ST microarrays.

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Project description:Obstructive sleep apnea (OSA) has been linked to dysregulated metabolic states and treatment of sleep apnea may improve these conditions. Subcutaneous adipose tissue is a readily samplable fat depot that plays an important role in regulating metabolism. However, neither the pathophysiologic consequences of OSA nor the effects of continuous positive airway pressure (CPAP) in altering this compartment’s molecular pathways are understood. This study aimed to systematically identify subcutaneous adipose tissue transcriptional programs modulated in OSA and in response to its effective treatment with CPAP. Two subject groups were investigated: Study Group 1 was comprised of 10 OSA and 8 controls; Study Group 2 included 24 individuals with OSA studied at baseline and following CPAP. For each subject, genome-wide gene expression measurement of subcutaneous fat was performed. Differentially activated pathways elicited by OSA (Group 1) and in response to its treatment (Group 2) were determined using network and Gene Set Enrichment Analysis (GSEA). In Group 2, treatment of OSA with CPAP improved apnea hypopnea index, daytime sleepiness, and blood pressure, but not anthropometric measures. In Group 1, GSEA revealed many up-regulated gene sets in OSA subjects, most of which were involved in immuno-inflammatory (e.g., interferon-γ signaling), transcription, and metabolic processes such as adipogenesis. Unexpectedly, CPAP therapy in Group 2 subjects was also associated with up-regulation of several immune pathways as well as cholesterol biosynthesis. Collectively, our findings demonstrate that OSA alters distinct inflammatory and metabolic programs in subcutaneous fat, but these transcriptional signatures are not reversed with short-term effective therapy.

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Visceral fat trancriptome in obstructive sleep apnea

Project description:Rationale: Obstructive sleep apnea (OSA) has been associated with metabolic dysregulation and systemic inflammation. This may be due to pathophysiologic effects of OSA on visceral adipose tissue. We sought to assess the transcriptional consequences of OSA on adipocytes by utilizing pathway-focused analyses. Methods: Patients scheduled to undergo ventral hernia repair surgery were recruited to wear a portable home sleep monitor for two nights prior to surgery. Visceral fat biopsies were obtained intra-operatively. RNA was extracted and whole-genome expression profiling was performed. Gene Set Enrichment Analysis (GSEA) was used to identify curated gene sets that were differentially enriched in OSA subjects. Network analysis was applied to a select set of highly enriched pathways. Results: 10 patients with OSA and 8 control subjects were recruited. There were no differences in age, gender, body mass index between the two groups, but the OSA subjects had a significantly higher respiratory disturbance index (19.2 vs. 0.6, P-value 0.05) and worse hypoxemia (minimum oxygen saturation 79.7% vs. 87.8%, P-value < 0.001). GSEA identified a number of gene sets up-regulated in adipose tissue of OSA patients including the pro-inflammatory NF-κB pathway and the proteolytic ubiquitin/proteasome module. A critical metabolic pathway, the peroxisome proliferator-activated receptor (PPAR), was down-regulated in subjects with OSA. Network analysis linked members of these modules together and identified regulatory hubs. Conclusions: OSA is associated with alterations in visceral fat gene expression. Pathway-based network analysis highlighted perturbations in several key pathways whose coordinated interactions may contribute to the metabolic dysregulation observed in this complex disorder.

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