The three-dimensional structure of the genome – the epigenome – contributes significantly to the regulation of gene expression and forms the molecular basis for each cell type-specific transcription profile. In contrast to the DNA sequence, however, the epigenome can be modified by external influences and can therefore adapt the gene expression profile of a cell to new circumstances (e.g. in the case of differentiation, aging, environmental influences, infections, inflammation, etc). Our laboratory investigates the epigenetic regulatory mechanisms in immune cells, which have to react particularly flexibly to external influences (differentiation cues, infection, inflammation, microbiota, etc.). We profile genome-wide epigenetic structures to identify key elements that make a decisive contribution to the generation and function of immune cells during health1 and in situations of misguided immune reactions (e.g. chronic inflammation and autoimmunity). These elements will help to clarify the molecular reasons for misregulated immune reactions and might represent promising therapeutic targets. Furthermore, in situation where immune cells serve as therapeutic agents to regain health (advanced therapy medicinal products, ATMPs, such as adoptive cell therapy) epigenetic structures may be used as biomarkers for quality and safety control purposes,2 and also as molecular switches for gene expression (‘epigenetic editing’3), which may equip cell products with desired characteristics.
T lymphocytes are highly motile cells which patrol the body via the lymphatic system and the bloodstream. However, they need to be able to leave the circulation and migrate into their target organs to exert their function wherever needed (e.g. infection site). We have shown in the past that the expression of surface receptors involved in the migration of cells (so-called homing receptors, e.g. chemokine receptors and integrins) are epigenetically imprinted in T cells,4,5 which ensures their correct migration into their target organ in case of re-occurring infections.
In this project, we want to establish a CRISPR-Cas9-based epigenetic editing approach,3 which will facilitate the deliberate imprinting of homing receptor expression patterns on T cells, to guide them to organs of interest (e.g. gut or skin). This technique is of great interest for application in adoptive T cell therapy approaches, as it might allow the deliberate targeting of transferred T cell products to selected organs.
Aim 1: Identification of the most promising target regions for epigenetic editing of homing receptor genes. This will be done on already available as well as newly generated epigenomic data sets.
Aim 2: Design and generation of the CRISPR-Cas9-based epigenetic editor complex, based on our established modular epigenetic editing system.
Aim 3: Assessment of epigenetic editing efficiency and molecular functional consequences (i.e. expression control of regulated gene).
Aim 4: Assessment of cellular functional consequences after epigenetic editing (i.e. migration behavior of edited cells). This project requires the application of various methods from cell biology (e.g. flow cytometry, T cell isolation and culture), molecular biology (e.g. DNA methylation profiling, in vitro mRNA transcription) as well as aspects of bioinformatics (e.g. analysis of array-based genome-wide DNA methylation profiles), all of which are established in our lab and can be learned by the doctoral student.