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PWS gene expression profiling of obese and non-obese patients

ABSTRACT: We aimed to characterize genetic alterations in PWS using whole genome microarrays. We performed mRNA expression microarray analysis using RNA isolated from whole blood of 25 PWS patients and 25 age-matched controls.. After preprocessing the data to reduce heterogeneity, differentially expressed genes (DEGs) between groups were identified using a linear regression model package. Reactome pathway analysis was performed for upregulated and downregulated genes using EnrichR. Correlations between gene expression levels and clinical factors were estimated using Spearman’s rank correlation coefficient. Of 21,488 probes examined in the microarray analysis, 4,156 were detected. Fifty-two genes had different expression levels in children with PWS compared with healthy controls (36 genes upregulated and 16 downregulated). Twelve genes were upregulated and 13 were downregulated in obese PWS patients compared with normal-weight PWS (NW-PWS) patients. The C-Type Lectin Domain Family 4 Member D (CLEC4D) was upregulated in both PWS (vs. control) and obese-PWS (vs. NW-PWS) patients, and CLEC4D expression was also correlated with body mass index-standard deviation score in PWS patients. Among the genes upregulated in obese PWS vs. NW-PWS, Annexin A3 (ANXA3), Potassium Inwardly Rectifying Channel Subfamily J Member 15 (KCNJ15), and Selenium Binding Protein 1 (SELENBP1) were upregulated in obese-control vs. NW-control. Gene Ontology analysis revealed that upregulated DEGs were significantly enriched in biological processes, including pathways involved in myeloid dendritic cell activation associated with CLEC4D.This study revealed differences in gene expression between obese and NW-PWS patients. The regulation of macrophage infiltration by CLEC4D suggests a possible mechanism associated with obesity-related complications in PWS.

ORGANISM(S): Homo sapiens

PROVIDER: GSE285348 | GEO | 2025/05/01

REPOSITORIES: GEO

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Project description:Rationale. Obesity is a risk factor for atherothrombosis and various cancers. However, the mechanisms are not completely uncovered. Objectives. We aimed to verify whether the microparticles (MPs) released from thrombin-activated platelets differed in obese and nonobese women for number, size, and proteomics cargo and the capacity to modulate in vitro the expression of genes related to the epithelial to mesenchymal transition (EMT) and the endothelial to mesenchymal transition (EndMT), and COX-2, a pro-angiogenic pathway. Methods and Results. MPs were obtained from thrombin activated platelets of four obese women and their matched, lean controls . MPs were analyzed by cytofluorimeter and protein content by liquid chromatography-mass spectrometry. Obese MPs were not different in number but were characterized by increased heterogeneity in size. In obese individuals, MPs containing mitochondria (mitoMPs) expressed lower CD41 levels and increased phosphatidylserine associated with enhanced Factor V representing a signature of a prothrombotic state. Proteomics analysis identified 44 proteins downregulated and 3 upregulated in obese versus nonobese MPs . A reduction in the proteins involved in mitophagy and antioxidant defenses, and of the -granular membrane was detected in the MPs of obese individuals. MPs released from platelets of obese individuals were more prone to induce the expression of marker genes of EMT and EndMT when incubated with HT29 cells and human cardiac microvascular endothelial cells(HCMEC), respectively. A protein, highly enhanced in obese MPs, was the pro-platelet basic protein with pro-inflammatory and tumorigenic actions. MPs from obese, but not nonobese, women induced COX-2 in HCMEC. Conclusions. Platelet-derived MPs of obese women showed higher heterogeneity in size and contained different levels of proteins relevant to thrombosis and tumorigenesis. Obese MPs presented enhanced capacity to induce changes in the expression of EMT and EndMT markers and COX-2. These effects might contribute to the increased risk for the development of thrombosis and multiple malignancies in obesity.

Project description:Purpose: To identify, using RNA-sequencing, differentially expressed genes in the white adipose tissue in obesity and in response to lipid intervention in both normal weight and obese individuals. Methods: White adipose tissue mRNA profiles of normal weight and obses humans at baseline (0-weeks) and 12-weeks after fish oil (3d/day of which 1.1g EPA and 0.8g DHA) or corn oil (3g/day) supplementation were generated by deep sequencing using RNA sequencing. The sequence reads that passed quality filters were aligned to the human genome using TopHat and analyzed at the gene level using DESeq2. qRT–PCR validation was performed using Taqman probe assays Results: Using an optimized data analysis workflow, we mapped reads to the human genome (hg38.0) and identified 789 genes differentially expressed between normal weight and obese individuals at baseline (week-0) (adjusted p value <0.05 and fold change >2). 623 of these were upregulated and 175 were downregulated. Geneset enrichment analysis identified several enriched pathways, including regulation of immune and inflammatory response, tissue growth and glucose metabolism in obese indvidiuals in comparison to normal weight. We identified 26 genes differentially expressed in normal weight individuals in response to fish oil intervention (week-12) (adjusted p value <0.05 and fold change >1). 14 of these were upregulated and 12 were downregulated. We identified 8 genes differentially expressed in obese individuals in response to fish oil intervention (week-12) (adjusted p value <0.05 and fold change >1). 3 of these were upregulated and 5 were downregulated. Geneset enrichment analysis identified several enriched pathways, including regulation of immune and inflammatory response in both normal weight and obese individuals in response to fish oil intervention with greater effects in normal weight individuals. Conclusions: Our study provides novel insights into the association of obesity and changes to the human white adipose tissue transcriptome, in addition to the effects of fish oil (EPA and DHA) on the transcriptome of normal weight and obese individuals and differences in response between these BMI subgroups. Our study further identifies putative gene targets and molecular pathways that help to understand how obesity results in adipose tissue dysfunction and how EPA and DHA may modulate the long term expression of gene networks and disease pathways related to onset of obesity associated inflammation.

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PWS gene expression profiling of obese and non-obese patients

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