Epigenomic analysis of primary human T cells reveals enhancers associated with TH2

memory cell differentiation and asthma susceptibility

Seumois G, Chavez L, Gerasimova A, et al. Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and

asthma susceptibility. Nat Immunol. 2014;15(8):777-788. doi:10.1038/ni.2937.

Biological BackgroundImmunological 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, 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 study 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.

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Article Background and Summary • Its understood that a feature of asthma is the accumulation,

differentiation, and function of memory CD4+T cells that produce type 2 cytokines. The goal of this study was to develop methods to profile the active and poised enhancers in naive and memory CD4+T cells from healthy individuals and asthmatic patients.

• In this article, the researchers isolated naïve and memory CD4 T cells from peripheral blood of 24 subjects (12 healthy and 12 asthma). After isolation, the CD4 memory T cells were divided by their surface expression of CCR4 (chemokine receptor). These cells were then sequenced for both RNA-seq and ChIP-seq to identify the DNA regions associated with H3K4me2. A total of 120 high-throughput whole genome ChIP-seq assays were completed.

Data Information• All done on AB 5500 Genetic Analyzer• ChIP-Seq: 146 Hs biosamples, Single Ended GSE53646

• 619 ccr4+ t cells, 529 ccr4- t cells, 640 naïve cells runs

• ChIP-Seq: 26 Mm biosamples, Single Ended GSE53644• 24 1k cells, 18 10k cells, 72 100k cells, 42 2m

cells runs• cell type:D10.G4.1 cells, ATCC• chip antibody:H3K4me2 (clone Y47,

lot#YH041501C; Abcam)• source name: mouse derived lymphoblastic cell

line (D10.G4.1 cells, ATCC)• RNA-Seq: 49 Hs biosamples, Single Ended GSE55320

• Healthy patients: 88 ccr4+ t cells, 33 ccr4- t cells, 77 naïve t cells runs

• Asthmatic patients: 121 ccr4+ t cells, 99 ccr4- t cells runs, 121 naïve t cells runs

This study developed methods to profile the active and poised enhancers in naive and memory CD4+T cells.

T-Bioinfo Analysis Steps Machine Learning

Unsupervised BiAssociation and clustering approach allowed identification of some specific samples.

RNA-seq Data Analysis (mapping reads and generation of RSEM table)

ChIP-seq Data Analysis(Mapping of reads and BS analysis)

Gene and Isoform expression profiles in Th0, Th1, and Th2 cells of healthy individual and asthma patients

H3K4me2 enrichment map for 500 bp-long in Th0, Th1, and Th2 cells of healthy individual and asthma patients

Unsupervised BiAssociation and clustering approach allowed identification of some specific samples. As well as Batch Effect Correction was used in this project.

Preliminary Conclusions ● Factor Regression Analysis: identified genes that produce

joined effects of cell type and health conditions, those genes that accounted for the occurrence of asthma.

● Cluster of H3K4me2 Regulated Genes: associations between RNA-seq and ChIP-seq data via shared effects of gene expression and epigenetic marks allowed for identification of clusters for both Th1 and Th2 cells.

● Unsupervised Analysis: Th-cells involvement in inflammation may lie in the capacity to release distinct types of Matrix Metalloproteases

● More updates soon!