Garth Burn

Why is PTPN22 a good candidate susceptibility gene for autoimmune disease

The PTPN22 locus is one of the strongest risk factors outside of the major histocompatability complex that associates with autoimmune diseases. PTPN22 encodes lymphoid protein tyrosine phosphatase (Lyp) which is expressed exclusively in immune cells. A single base change in the coding region of this gene resulting in an arginine to tryptophan amino acid substitution within a polyproline binding motif associates with type 1 diabetes, rheumatoid arthritis, systemic lupus erythematosis, Hashimotos thyroiditis, Graves disease, Addisons disease, Myasthenia Gravis, vitiligo, systemic sclerosis juvenile idiopathic arthritis and psoriatic arthritis. Here, we review the current understanding of the PTPN22 locus from a genetic, geographical, biochemical and functional perspective.

Bayesian cluster identification in single-molecule localization microscopy data.

Single-molecule localization-based super-resolution microscopy techniques such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) produce pointillist data sets of molecular coordinates. Although many algorithms exist for the identification and localization of molecules from raw image data, methods for analyzing the resulting point patterns for properties such as clustering have remained relatively under-studied. Here we present a model-based Bayesian approach to evaluate molecular cluster assignment proposals, generated in this study by analysis based on Ripleys K function. The method takes full account of the individual localization precisions calculated for each emitter. We validate the approach using simulated data, as well as experimental data on the clustering behavior of CD3ζ, a subunit of the CD3 T cell receptor complex, in resting and activated primary human T cells.

Superresolution imaging of the cytoplasmic phosphatase PTPN22 links integrin-mediated T cell adhesion with autoimmunity

The tyrosine phosphatase PTPN22 redistributes from clusters to the leading edge in migrating T cells to inhibit integrin-mediated adhesion. Release the phosphatase! T cells need to move through the circulation, attach to endothelial cells, transmigrate into tissues, and stably interact with target cells. The phosphatase PTPN22 targets phosphorylated tyrosines in Src and Syk family kinases, many of which are phosphorylated and activated in migrating T cells in response to the binding of the integrin LFA-1 to its ligand ICAM-1. Burn et al. used superresolution microscopy to show that PTPN22 formed clusters in nonmigrating T cells, which were dispersed in T cells that migrated on surfaces coated with ICAM-1. Freed from these complexes, PTPN22 interacted with its targets near the front of the migrating T cell, which inhibited LFA-1 signaling. In contrast, clusters containing the PTPN22 R620W mutant, a variant that is associated with autoimmune diseases, failed to disaggregate in migrating T cells, and thus, LFA-1 clustering and signaling were not inhibited. Together, these data suggest how a mutation associated with autoimmunity dysregulates T cell adhesion and migration. Integrins are heterodimeric transmembrane proteins that play a fundamental role in the migration of leukocytes to sites of infection or injury. We found that protein tyrosine phosphatase nonreceptor type 22 (PTPN22) inhibits signaling by the integrin lymphocyte function-associated antigen–1 (LFA-1) in effector T cells. PTPN22 colocalized with its substrates at the leading edge of cells migrating on surfaces coated with the LFA-1 ligand intercellular adhesion molecule–1 (ICAM-1). Knockout or knockdown of PTPN22 or expression of the autoimmune disease–associated PTPN22-R620W variant resulted in the enhanced phosphorylation of signaling molecules downstream of integrins. Superresolution imaging revealed that PTPN22-R620 (wild-type PTPN22) was present as large clusters in unstimulated T cells and that these disaggregated upon stimulation of LFA-1, enabling increased association of PTPN22 with its binding partners at the leading edge. The failure of PTPN22-R620W molecules to be retained at the leading edge led to increased LFA-1 clustering and integrin-mediated cell adhesion. Our data define a previously uncharacterized mechanism for fine-tuning integrin signaling in T cells, as well as a paradigm of autoimmunity in humans in which disease susceptibility is underpinned by inherited phosphatase mutations that perturb integrin function.

A Bayesian cluster analysis method for single-molecule localization microscopy data

Cell function is regulated by the spatiotemporal organization of the signaling machinery, and a key facet of this is molecular clustering. Here, we present a protocol for the analysis of clustering in data generated by 2D single-molecule localization microscopy (SMLM)—for example, photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM). Three features of such data can cause standard cluster analysis approaches to be ineffective: (i) the data take the form of a list of points rather than a pixel array; (ii) there is a non-negligible unclustered background density of points that must be accounted for; and (iii) each localization has an associated uncertainty in regard to its position. These issues are overcome using a Bayesian, model-based approach. Many possible cluster configurations are proposed and scored against a generative model, which assumes Gaussian clusters overlaid on a completely spatially random (CSR) background, before every point is scrambled by its localization precision. We present the process of generating simulated and experimental data that are suitable to our algorithm, the analysis itself, and the extraction and interpretation of key cluster descriptors such as the number of clusters, cluster radii and the number of localizations per cluster. Variations in these descriptors can be interpreted as arising from changes in the organization of the cellular nanoarchitecture. The protocol requires no specific programming ability, and the processing time for one data set, typically containing 30 regions of interest, is ∼18 h; user input takes ∼1 h.

The Nanoscale Organization of Signaling Domains at the Plasma Membrane

In this chapter, we present an overview of the role of the nanoscale organization of signaling domains in regulating key cellular processes. In particular, we illustrate the importance of protein and lipid nanodomains as triggers and mediators of cell signaling. As particular examples, we summarize the state of the art of understanding the role of nanodomains in the mounting of an immune response, cellular adhesion, intercellular communication, and cell proliferation. Thus, this chapter underlines the essential role the nanoscale organization of key signaling proteins and lipid domains. We will also see how nanodomains play an important role in the lifecycle of many pathogens relevant to human disease and therefore illustrate how these structures may become future therapeutic targets.

3D Bayesian cluster analysis of super-resolution data reveals LAT recruitment to the T cell synapse

Single-molecule localisation microscopy (SMLM) allows the localisation of fluorophores with a precision of 10–30 nm, revealing the cell’s nanoscale architecture at the molecular level. Recently, SMLM has been extended to 3D, providing a unique insight into cellular machinery. Although cluster analysis techniques have been developed for 2D SMLM data sets, few have been applied to 3D. This lack of quantification tools can be explained by the relative novelty of imaging techniques such as interferometric photo-activated localisation microscopy (iPALM). Also, existing methods that could be extended to 3D SMLM are usually subject to user defined analysis parameters, which remains a major drawback. Here, we present a new open source cluster analysis method for 3D SMLM data, free of user definable parameters, relying on a model-based Bayesian approach which takes full account of the individual localisation precisions in all three dimensions. The accuracy and reliability of the method is validated using simulated data sets. This tool is then deployed on novel experimental data as a proof of concept, illustrating the recruitment of LAT to the T-cell immunological synapse in data acquired by iPALM providing ~10 nm isotropic resolution.

Protein clustering and spatial organization in T-cells

T-cell protein microclusters have until recently been investigable only as microscale entities with their composition and structure being discerned by biochemistry or diffraction-limited light microscopy. With the advent of super resolution microscopy comes the ability to interrogate the structure and function of these clusters at the single molecule level by producing highly accurate pointillist maps of single molecule locations at ~20nm resolution. Analysis tools have also been developed to provide rich descriptors of the pointillist data, allowing us to pose questions about the nanoscale organization which governs the local and cell wide responses required of a migratory T-cell.

LYP/PTPN22 IS A NEGATIVE REGULATOR OF INTEGRIN MEDIATED T CELL ADHESION AND MIGRATION; THE DISEASE ASSOCIATED PTPN22 ALLELIC VARIANT IS A LOSS OF FUNCTION MUTANT THAT PERTURBS T CELL MIGRATION

Background and objectives A critical step in leucocyte adhesion and migration is the activation of integrins such as LFA-1. Engagement by its counterligand ICAM-1 leads to a cascade of signalling events that permit cell spreading, cytoskeletal rearrangement, cell migration and proliferation. Among intermediates that regulate integrin activation are src kinases such as Lck. The protein tyrosine phosphatase Lyp, which negatively regulates src kinases, has received much attention in recent years following reports of a strong association between a missense single nucleotide polymorphism in the gene (PTPN22) and autoimmune diseases such as rheumatoid arthritis, lupus and type I diabetes. While much work has focused on the regulatory effects of Lyp on Lck activation during antigen T cell receptor signalling, no clear consensus has emerged as to whether the disease associated mutant is a gain or a loss-of-function phosphatase. We set out to examine how Lyp regulates integrin mediated function and to explore the phenotype of T cells expressing the autoimmune disease associated LypR620W mutant. Materials and methods We used confocal microscopy to study the subcellular localisation of LFA-1, Lyp and its substrates ZAP-70 and Vav in primary human T cell blasts. Integrin mediated adhesion and migration were determined by culturing T cell blasts on Fc-ICAM coated plates. Images were captured by time–lapse microscopy every 15 s for 20 min in total, and mean speeds of each T cell calculated for single tracked cells. Lyp knockdown was performed using specific siRNA. Lyp overexpression was undertaken by transfecting HSB2 cells, which express very low levels of Lyp, with wild type Lyp620R or mutant Lyp620W, and adhesion and migration studied as above. Results Lyp is expressed at the leading edge of T cells migrating on ICAM, and co-localises and co-immunoprecipitates with ZAP-70 and Vav. In contrast, phospho-ZAP-70 is expressed in discrete zones behind the leading edge. Knockdown of Lyp enhances migratory responses, while overexpresison of wild type Lyp in HSB2 cells leads to a dramatic reduction in migration. In contrast, expression of the disease associated LypR620W mutant fails to negatively regulate migratory responses. Conclusions We show for the first time that Lyp is a negative regulator of integrin mediated T cell adhesion and migration, being expressed at the leading edge of migrating cells and serving to de-phosphorylate substrates that function to stabilise the LFA-1hi/talin complex. Importantly, the expression of the disease associated Lyp mutant is associated with failure to regulate migratory responses.