Gene expression changes in lymphoblastoid cell lines and primary B cells by dexamethasone

Cellular expression profiles of Epstein-Barr virus-transformed B-lymphoblastoid cell lines

Epstein-Barr virus (EBV) can infect human B cells and is associated with various types of B cell lymphomas. Studies on the global alterations of the cellular pathways mediated by EBV-induced B cell transformation are limited. In the present study, microarray analysis was performed following generation of two EBV-infected B-lymphoblastoid cell lines (BLCL), in which normal B cells obtained from two healthy Thai individuals and transcriptomic profiles were compared with their respective normal B cells. The two EBV-transformed BLCL datasets exhibited a high degree of similarity between their RNA expression profiles, whereas the two normal B-cell datasets did not exhibit the same degree of similarity in their RNA expression profiles. Differential gene expression analysis was performed, and the results showed that EBV infection was able to dysregulate several cellular pathways in the human B-cell genes involved in cancer and cell activation, such as the MAPK, WNT and PI3K-Akt signaling pathways, which were upregulated in the BLCL and were associated with increased cellular proliferation and immortalization of EBV-infected B cells. Expression of proteins located in the plasma membrane, which initiate a biological response to ligand binding, were also notably upregulated. Expression of genes involved in cell cycle control, the p53 signaling pathway and cellular senescence were downregulated. In conclusion, genes that were markedly upregulated by EBV included those involved in the acquisition of a tumorigenic phenotype of BLCL, which was positively correlated with several hallmarks of cancer.

Understanding the Molecular Mechanisms of Asthma through Transcriptomics

The transcriptome represents the complete set of RNA transcripts that are produced by the genome under a specific circumstance or in a specific cell. High-throughput methods, including microarray and bulk RNA sequencing, as well as recent advances in biostatistics based on machine learning approaches provides a quick and effective way of identifying novel genes and pathways related to asthma, which is a heterogeneous disease with diverse pathophysiological mechanisms. In this manuscript, we briefly review how to analyze transcriptome data and then provide a summary of recent transcriptome studies focusing on asthma pathogenesis and asthma drug responses. Studies reviewed here are classified into 2 classes based on the tissues utilized: blood and airway cells.

Genetic Signatures of Acute Asthma Exacerbation Related With Ineffective Response to Corticosteroid

Purpose

Acute exacerbation (AE) is an important domain of asthma management and may be related with ineffective response to corticosteroid. This study aimed to find mechanisms of AE using genome-wide gene expression profiles of blood cells from asthmatics and its perturbation by in vitro dexamethasone (Dex)-treatment.

Methods

We utilized lymphoblastoid B cells from 107 childhood asthmatics and peripheral blood mononuclear cells from 29 adult asthmatics who were treated with inhaled corticosteroids. We searched for a preserved co-expression gene module significantly associated with the AE rate in both cohorts and measured expression changes of genes belong to this module after Dex-treatment.

Results

We identified a preserved module composed of 77 genes. Among them, expressions of 2 genes (EIF2AK2 and NOL11) decreased significantly after Dex-treatment in both cohorts. EIF2AK2, a key gene acting antiviral defense mechanism, showed significantly higher expressions in asthmatics with AE. The protein repair pathway was enriched significantly in 64 genes which belong to the preserved module but showed no expression differences after Dex-treatment in both cohorts. Among them, MSRA and MSRB2 may play key roles by controlling oxidative stress.

Conclusions

Many genes belong to the AE rate-associated and preserved module identified in blood cells from childhood and adults asthmatics showed no expression changes after in vitro Dex-treatment. These findings suggest that we may need alternative treatment options to corticosteroids to prevent AE. EIF2AK2, MSRA and MSRB2 expressions on blood cells may help us select AE-susceptible asthmatics and adjust treatments to prevent AE.