The influence of the PTPN22R619W variant allele on T cell and Neutrophil function

Background

Background: A common mutation in the gene encoding an intracellular tyrosine phosphatase, PTPN22, was identified in a Genome Wide Association Study (GWAS) to predispose humans to developing a number of autoimmune diseases 1. The mutation results in a single amino acid change in the protein PTPN22R620W which is outside the catalytic domain and in a region thought to be involved in protein:protein interactions. In order to understand the role of this phosphatase in immune regulation we have generated mice that: lack the phosphatase entirely, lack the phosphatase in specific lineages only (flox/cre), or contain the disease-associated point mutation. Our previous studies using PTPN22 knockout mice showed that loss of the phosphatase resulted in increased sensitivity of T cells to stimulation through the TCR, particularly in the context of stimulation with weak antigens 2. In contrast, lack of PTPN22 in neutrophils made these cells more resistant to immune complex stimulation3. As both T cells and neutrophils are key orchestrators of autoimmune diseases, comprehending how PTPN22 contributes to their activation and regulation is important in the context of understanding the basics of genetic susceptibility to autoimmune disease.

Aims

The aim of the project is to make a systems-wide comparison between function and regulation of T cells and neutrophils with altered PTPN22 expression to try and understand the function of the phosphatase in these two cell types. As a starting point we will ask whether T cells and neutrophils expressing the variant protein PTPN22R620W behave functionally in the same way as cells containing the wild-type or knockout allele. We have already generated unbiased datasets (RNA-Seq and whole proteome) comparing PTPN22 WT and knockout T cells and these have revealed a number of pathways and functions that are altered in T cells as a consequence of loss of the phosphatase, and similar datasets will be generated for T cells that express the variant allele. We will generate new RNA-Seq datasets for WT, PTPN22KO and

PTPN22R620W neutrophils in order to gain an understanding of how alterations in PTPN22 influences neutrophil differentiation and activation. Comparisons of these datasets will be used to identify pathways that are regulated by the phosphatase and these will be validated in functional assays in vitro and in vivo. Together these data will provide a better understanding of how this phosphatase influences disease susceptibility.

Training Outcomes

The student will undergo training in bioinformatics and the handling of large datasets which will be a key component of the project. A focus will be on methods of comparing datasets in order to pull out similarities and differences in cell population behaviour. Likely candidate pathways that are changed in the mutant cells will be confirmed and interrogated experimentally, so the student will gain experience in a wide variety of in vivo and in vitro immunological assays. In particular competence will be obtained in handling and stimulating both T cells and neutrophils, in performing functional assays and monitoring biochemical changes downstream of receptor engagement.

This MRC programme is joint between the Universities of Edinburgh and Glasgow. You will be registered at the host institution of the primary supervisor detailed in your project selection.

All applications should be made via the University of Edinburgh, irrespective of project location:

http://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=919

Please note, you must apply to one of the projects and you are encouraged to contact the primary supervisor prior to making your application. Additional information on the application process if available from the link above.

For more information about Precision Medicine visit:

http://www.ed.ac.uk/usher/precision-medicine