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FOXP3 Panel

FoxP3 Panel

EpigenDx FoxP3 Methylation Panel

FOXP3 Methylation Panel

Quantify DNA methylation levels in genes relevant to regulatory T-cell characterization and the FOXP3 transcriptional network. The human FOXP3 Panel analyzes up to 20 genes, 29 regions, and 141 CpG sites. The mouse Foxp3 panel covers up to 8 genes, 14 regions, and 125 CpG sites. The genes being analyzed include the regulatory regions of FOXP3, PDL1, CTLA4, IL2RA, RUNX1, IKZF2, IKZF4, and more.

Sample Submission Guidelines

EpigenDx accepts various kinds of starting material, including blood serum, FFPE prepared samples, gDNA and more. Download the Sample Submission Form to find out more.

Full List of Human FOXP3 Methylation Panel Assays

The Relevance of FOXP3

Regulatory T-cells (Tregs) prevent autoimmune disease by inhibiting self-reactive T-cells. FOXP3 (forkhead box P3) is a transcription factor that is found in Tregs. It controls the expression of genes involved in regulating the immune system, making FOXP3 the master regulator that controls the development and function of Tregs. The methylation status of the FOXP3 gene can be used to measure the proportion of Tregs in a larger population of leukocytes. EpigenDx’s FOXP3 panel is a set of validated DNA methylation assays studying the methylation status of the FOXP3 gene and the regulation of genes (such as CTLA4 and CD25) important to Treg function.

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FOXP3 Panel: Quick Overview

All parts of our methylation services are customizable and modular. Pick and choose the service plan that is appropriate and ideal for your needs.

Human FOXP3 Methylation Panel
Platform: Targeted Next-Gen Bisulfite Sequencing
Pyrosequencing for analyzing a selected gene and a target region within this panel
Species: Human (Homo sapiens)
Stats: Greater than 120 CpG sites over 18 genes and 25 amplicons
Full Gene List: CD274, CD3D_CD3G, CDKN1C, CTLA4, ETS1, FOXP3, IKZF2, IKZF4, IL2, IL2RA, IL2RB, IL4, PDCD1, PDL2, RUNX1, S100A6, TNFa, TNFRSF18, TNFRSF25, TOLLIP
Mouse Foxp3 Methylation Panel
Platform: Targeted Next-Gen Bisulfite Sequencing
Pyrosequencing for analyzing a selected gene and a target region within this panel
Species: Mouse (Mus musculus)
Stats: Greater than 100 CpG sites over 7 genes and 12 amplicons
Full Gene List: Foxp3, Ctla4, Helios (Ikzf2), Eos (Ikzf4), Il2ra (Cd25), Tnfrsf18 (Gitr), Cd274, and Irf4

Selected Genes of the FOXP3 Panel

Forkhead-box protein P3 (Foxp3) is a major transcription factor that is necessary for induction of the immunosuppressive function of regulatory T cells (Tregs). It is considered to be the most specific marker for Tregs in tumors, with its expression leading to poor survival rates in some types of cancer and improved survival rates in other types. Studies have shown that epigenetic modifications contribute to the stable expression of FOXP3 and other molecules associated with Treg cell function. These modifications include demethylation of CpG sites in the conserved non-coding sequence 2 (CNS2), Treg specific demethylated region (TSDR), proximal promoter, and upstream enhancer regions of the gene. Understanding the epigenetic regulation of FOXP3 and associated genes is critical in developing new approaches to autoimmune disease and cancer treatment.

Human FOXP3 Methylation Analysis: Product Contents
  • 3 Methylation Assays across the promoter and intron 1 (TSDR and CNS2 region) of Human FOXP3
  • Total coverage of 19 CpG sites
Mouse Foxp3 Methylation Analysis: Product Contents
  • 10 Methylation Assays across the distal promoter, proximal promoter, intron 1 (TSDR and CNS2 region), and 3′ downstream trailer of Mouse Foxp3.
  • Total Coverage of 102 CpG sites
Rhesus Monkey Foxp3 Methylation Analysis: Product Contents
  • 1 Methylation Assays across the homologous TSDR region
  • Total Coverage of 10 CpG sites

 

CTLA4 is an inhibitory receptor protein found on the surface of FOXP3+ Tregs. The interaction between CTLA4 and receptors on antigen-presenting cells is known to turn off the immune response. While FOXP3 and CTLA4 are usually demethylated and expressed in Tregs, hypermethylation of the CTLA4 promoter has been found to result in dysfunctional FOXP3+ Tregs and autoimmune diseases such as rheumatoid arthritis. Assays covering SNPs in the gene have also been used to study the expression of CTLA4 in T-cells.

Human CTLA4 Methylation Analysis: Product Contents
  • 1 Methylation Assay across intron 1 and exon 2 of Human CTLA4
  • Total coverage of 7 CpG sites
Mouse Ctla4 Methylation Analysis: Product Contents
  • 1 Methylation Assay across intron 1 and exon 2 of Mouse Ctla4
  • Total Coverage of 4 CpG sites

 

PD-1, or programmed cell death protein 1, is a receptor on T-cells that causes T-cell death or inhibition when bound with its ligand PDL1 (CD274), or programmed cell death ligand 1. High PDL1 expression has been associated with the reduction of conventional T-cell populations and the induction of FOXP3-expressing Tregs, downregulating the immune response. Thus, PD-1 and PD-L1 inhibitors are useful as cancer immunotherapy treatments.

EpigenDx has designed and validated DNA methylation assays covering the promoter region of PDL1.

Human PDL1 Methylation Analysis: Product Contents
  • 2 Methylation Assays across the promoter region of Human PDCD1
  • Total coverage of 10 CpG sites
Mouse Pdl1 Methylation Analysis: Product Contents
  • 1 Methylation Assay across the promoter region of Mouse Pdl1
  • Total coverage of 14 CpG sites

 

Helios (IKZF2) and Eos (IKZF4) are two members of the Ikaros transcription factor family that are demethylated and expressed along with FOXP3 in Tregs. While Eos interacts directly with FOXP3 to silence certain genes (encoding T effector cytokines for instance), Helios binds to the FOXP3 promoter to upregulate FOXP3 expression. Both Eos and Helios are important biomarkers, essential for the proper function of CD4+ FOXP3+ Tregs. EpigenDx has designed and validated DNA methylation assays covering the intronic, non-coding regions of these two genes.

Mouse Ikzf2 Methylation Analysis: Product Contents
  • 1 Methylation Assay across intron 3 of Mouse Ikzf2
  • Total coverage of 6 CpG sites
Mouse Ikzf4 Methylation Analysis: Product Contents
  • 1 Methylation Assay across intron 1 of Mouse Ikzf4
  • Total Coverage of 4 CpG sites

 

Helios (IKZF2) and Eos (IKZF4) are two members of the Ikaros transcription factor family that are demethylated and expressed along with FOXP3 in Tregs. While Eos interacts directly with FOXP3 to silence certain genes (encoding T effector cytokines for instance), Helios binds to the FOXP3 promoter to upregulate FOXP3 expression. Both Eos and Helios are important biomarkers, essential for the proper function of CD4+ FOXP3+ Tregs. EpigenDx has designed and validated DNA methylation assays covering the intronic, non-coding regions of these two genes.

Mouse Ikzf2 Methylation Analysis: Product Contents
  • 1 Methylation Assay across intron 3 of Mouse Ikzf2
  • Total coverage of 6 CpG sites
Mouse Ikzf4 Methylation Analysis: Product Contents
  • 1 Methylation Assay across intron 1 of Mouse Ikzf4
  • Total Coverage of 4 CpG sites

 

TNFRSF18, or GITR (glucocorticoid-induced TNF tumor-necrosis factor-related receptor), is another protein that is demethylated and expressed in high levels in Tregs and activated T cells. Because the engagement of GITR with anti-GITR antibodies can inhibit Treg function and deplete Treg population, drugs blocking GITR/TNFRSF18 have been proposed as cancer immunotherapy treatments and allergy medication.

Mouse Tnfrsf18 Methylation Analysis: Product Contents
  • 1 Methylation Assay across exon 4 of Mouse Tnfrsf18
  • Total Coverage of 4 CpG sites

 

Why EpigenDx?

  • Worldwide experts in the field of FOXP3 epigenetics
  • Experienced bisulfite sequencing technicians
  • Personalized, flexible project plans designed around your needs
  • Quantitative techniques to analyze DNA methylation
  • High-throughput, high-quality data: 100-5000x read coverage per CpG site

Workflow

Project Consultation
Examination of regulatory elements of target genes. Target amplicon selection. If the amplicon is new, we design and optimize new primers.

Assay Optimization
Testing of optimal experimental conditions on project-specific samples. Bisulfite treatment, PCR and library prep.

Sequencing
Depending on the project, we perform either Pyrosequencing or (ion semiconductor) Next-Generation Sequencing on the bisulfite-converted gDNA.

Data Analysis
Calculation of % methylation for each individual CpG site.

TURNAROUND TIME: 3-8 WEEKS DEPENDING ON A CUSTOM PANEL

How to Order:

EpigenDx how to order visual

The Results

ONE

An Excel spreadsheet containing all CpG sites, their % methylation and read coverage. See Example

TWO

A PDF project report containing the experimental design, all quality control results and final data.

THREE

Raw data, FASTQ files and any other bioinformatics files available on request.

Now Offering GLP and GCP Compliant Laboratory Services

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EpigenDx Offers Many Customized Services
YOU DON'T WANT TO MISS THIS!Epigenetics In The A.M. 2021 Event
Are you interested in DNA methylation, gene expression & gene regulation? Then this online event is for you! Let’s share our expertise on how to generate meaningful methylation data for publications, clinical research, biomarker discoveries & much more.

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