Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide expression analysis of human white blood cells in patients with stroke and/or obesity compared with healthy individuals

ABSTRACT: Obesity is well recognized as a risk factor for coronary heart disease and mortality. The relationship between abdominal obesity and ischemic stroke remains less clear. Previous publication showed the obesity is an independent, potent risk factor for ischemic stroke in all race-ethnic groups. It is a stronger risk factor than BMI and has a greater effect among younger persons. The goal of this experiment was to compare the global transcriptional profile, and its regulation, of white blood cells of healthy normals, patients with obesity and/or stroke in order to understand the transcriptional differences behind the different phenotypes. There were 6 subjects in each group. RNA was purified from white blood cells using a TRIZOL RNA Isolation Protocol (Life technologies) and 500 ng of starting material were used as input for the Illumina TotalPrep Amplification Kit. Next, the Array Studio (OmicSoft Corporation) was used to generate a list of genes that are expressed at a significantly higher/lower level using the two-way ANOVA in order to analyze the 2x2 factorial design.

ORGANISM(S): Homo sapiens

SUBMITTER: Javier Campion

PROVIDER: E-MTAB-2312 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:1. Rationale: Stroke is still a major cause of death and disability worldwide. A better comprehension of stroke pathophysiology is fundamental to reduce its dramatic outcome. The use of high-throughput unbiased omics approaches, such as proteomics and transcriptomics, might aid to deepen the knowledge of stroke at the molecular level. Moreover, the integration of omics data is needed to depict the existing interaction between different molecular units and interpret the results in a global biological context. 2. Objective: Our aim was to identify and verify protein and gene expression changes that occur in the human brain after ischemia through an integrative approach to join and combine the information of both omics analyses. The translational potential of our results was explored in a pilot study with blood samples from ischemic stroke patients. 3. Methods and results: Proteomics and transcriptomics discovery studies were performed in human brain samples from deceased stroke patients, unveiling 128 proteins and 2716 genes significantly dysregulated after cerebral ischemia. Afterwards, integrative bioinformatics analyses joining both datasets exposed several canonical pathways altered in the ischemic area, such as neurotransmitters release or matrisome regulation, highlighting the most influential molecules in these pathways. To conduct the verification phase, 28 genes and 9 proteins were selected to be validated in independent human brain samples by means of orthogonal techniques. Our results were confirmed for NCDN, RAB3C, ST4A1, DNM1L, A1AG1, A1AT, JAM3, VTDB, ANXA1, ANXA2 and IL8. Finally, the blood circulating levels of the validated protein candidates were explored in ischemic stroke patients over the acute phase of the disease. Protein fluctuations along the first week after onset were detected for A1AG1 and A1AT. 4. Conclusion: The results presented here expand the knowledge of stroke pathology, revealing new key molecules that can be further explored as biomarkers and/or therapeutic targets of ischemic stroke.

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Genome-wide expression analysis of human white blood cells in patients with stroke and/or obesity compared with healthy individuals

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