Three-panels showing proximity ligation assay (PLA) signaling in human regulatory T (Treg) cell microscopy FOXP3 and EZH2 binding in human T-regulatory cells

Human T-regulatory (Treg) cells depicting binding of enhancer of zeste homolog 2 (EZH2) and forkhead box protein 3 (FOXP3) via phospholipase A signaling in a proximity ligation assay (PLA) (pink dots). Source: Bamidele AO, et al. Cellular and Molecular Gastroenterology and Hepatology. 2019; doi:10.1016/j.jcmgh.2018.08.009.

Focus Areas

The Immuno-Epigenetics Lab team has several projects studying the pathophysiology of inflammatory bowel disease (IBD) and how the immune system contributes to intestinal inflammation. These projects aim to characterize the immuno-epigenetics phenotype of IBD. During the inflammatory response in IBD, the lab's investigators seek to uncover the mechanisms by which the anti-inflammatory function becomes dysregulated.

The network of genes orchestrated by immune cell transcription factors and epigenetic mechanisms can become dysregulated from the inflammatory cytokines and other environmental signals during the onset of intestinal inflammation. This dysregulation results in the loss of suppression and increase of proinflammatory cytokines perpetuating intestinal inflammation and tissue damage.

With the following projects, Dr. Faubion's team aims to discover the immune cell profile and the respective epigenetic and molecular mechanisms critical for maintaining inflammatory suppressive function and intestinal homeostasis. Furthermore, with collaboration of people with IBD, the group intends to generate a biobank of tissue and blood samples to use in discovery platforms. Translating these discoveries into novel cellular therapeutics can provide a more precise and individualized treatment to patients leading to an improved, sustainable prognosis.

Characterization of the immune phenotype of IBD

To characterize the immune phenotype and understand the pathophysiology of IBD, our goal is to use unbiased approaches through high-throughput sequencing techniques, such as single-cell RNA sequencing and RNA sequencing, on blood and tissue patient samples. These techniques will enable us to generate an immune cellular profile during the onset and chronic manifestations of IBD inflammation. This cellular profile will aid in the discovery of novel IBD markers for patient diagnostic assays as well as individualized cellular therapies.

Projects include:

  • Isolating cells from patient blood samples, tissue biopsies and resections, which are analyzed by a comprehensive mass cytometry (CyTOF) panel for protein expression measurement and RNA sequencing (RNA-seq) for gene transcription measurement.
  • In vitro cell culture and naive T-cell differentiation for mechanistic studies.

Dissecting epigenetic mechanisms of development and function of immune cells

PRC1 and PRC2 complexes have been found to be important regulators of structural architecture of DNA, and thus regulating the expression of gene transcription. Dr. Faubion's lab is using ATAC-seq and ChIP-seq to understand how these complexes regulate gene expression through chromatin remodeling. Understanding these mechanisms can lead to development of drug-therapy targets to revert aberrant gene transcription.

Projects include:

  • BMI1-PRC1 and EZH2-PRC2 mechanisms in naive T-cell development, T-effector and T-regulatory cell functions.
  • Histone ubiquitination, acetylation and methylation dynamics regulating pro-inflammatory gene expression.

Ex vivo optimization of immune cells for adoptive cell therapy

Dr. Faubion's lab has several projects regarding cellular therapy, which uses epigenetic histone modifiers or genetic modifications using CRISPR-Cas9 molecular biology techniques. Using several mouse colitis models of inflammation, lab investigators can test genetically modified immune cells to determine their efficacy in maintaining resistance toward inflammatory cytokine production and preventing intestinal inflammation. These projects can help develop novel therapies for people with IBD.

Projects include:

  • Applying genome editing for immunologic receptors.
  • Using epigenetic drugs to modify histone marks regulating T cell gene networks.
  • Creating a vaccine therapy using modified autologous T cells.

Discovery of novel molecular mechanisms of IBD through integration of high-dimensional data sets

Systems biology is understanding the many ways biochemical and molecular interactions influence cellular and tissue physiology. The series of biochemical and molecular interactions can create a complex network influencing each other's activity, which subsequently orchestrates gene expression and results in impacting the overall homeostasis of cellular physiology.

The lab is using discoveries about the biochemical and molecular interactions from the Immuno-Epigenetics Lab projects to integrate into a systems biology model to identify an immuno-epigenetics profile manifested in intestinal inflammation. This approach can provide a comprehensive description of the molecular heterogenicity of IBD conditions, help pinpoint drug-targetable molecular signatures and provide better information about potential off-target effects from the treatments.

Through this forward-thinking integrative approach, the group's research can advance the field of translational medicine toward individualized therapies for IBD and other autoimmune conditions.