Asthma, a disease caused by airway inflammation and is caused by excessive response to an allergen, such as grass. The main molecular feature of asthma is the excessive differentiation of CD4 T cells. The goal of this publication was to develop methods to profile active and poised enhancers in naïve and memory CD4 T cells from healthy individual and asthmatic patients. An enhancer, is a short region of DNA that is bound to proteins and increases the likelihood that transcription of that particular gene will occur. This team generated maps of H3K4me2 marked cis-regulatory regions and identified a large number of cell type specific and disease specific enhancers. Immunological Memory, is how a body is able to maintain a protective immune system, as it can respond to a pathogen more rapidly and effectively if that pathogen has been encountered before.
- Asthma is a disease characterized by airway inflammation that is mediated by excessive memory responses to inhaled allergens, such as grass pollen. At present, there is no cure for asthma, and most patients require long-term, daily nonspecific medication such as corticosteroids to control the underlying inflammation and prevent symptoms and life-threatening asthma attacks
- Our team wanted to repeat this study with the goal to develop methods to profile active and poised enhancers in naive and memory CD4+ T cells from healthy individuals and asthmatic patients. Because we wished to extend these methods eventually to very small cell populations isolated from diseased tissues, we chose to profile cis-regulatory regions using a single histone modification, H3K4me2.
For the analysis of this public data set, these T-Bioinfo Analysis Steps were performed:
The retrieved sequenced data have been mapped on the reference genome by means of Bowtie2 and the result of this mapping was then processed by RSEM. In additon,the result of mapping of ChIP-seq reads was analyzed by an algorithm, BS analysis, was developed in the Tauber Bioinformatics Research Center.
The basic strategy for this research project was to screen for genes whose pattern of transcription and epigenetic modification accounted for a particular T-cell phenotype and the health-condition of the donor.
1) We determined components of PCA that reveal biological meaningful separation of groups (Healthy/Unhealthy, Th1/Th2/Naive).
2) We adopted factor regression analysis, a procedure permitting investigation of relationships between variables to identify those that produce particular outcomes (in our case (Healthy/Unhealthy, Th1/Th2/Naïve).
Both, the analysis of PCA components and factor regression analysis helped to identify genes that produce joined effects of cell type and health condition. In other words it helped us to find genes and epigenetic control regions, which while being distinctly regulated in Naive, Th1 or Th2 cells simultaneously accounted for the occurrence of asthma.
This project is still in progress, we hope to develop an educational course around this project soon!