Title: Identifying novel candidate genes for inborn errors of thymic stromal cells that cause severe congenital T-cell lymphopaenia
Funder: The Academy of Medical Sciences

Abstract: General Aim: To identify novel molecular pathologies underlying thymic stromal cell defects in patients with congenital T-cell deficiency. Background: Thymic stromal cells, particularly thymic epithelial cells (TEC), provide the microenvironment essential for T-cell lymphopoiesis. Inborn errors of thymic stromal cells have been suspected as the cause for rare forms of congenital, non-haematopoietic cell-intrinsic T-cell lymphopaenia. However, only a minority of these pathologies have been molecularly defined to date. We have a unique cohort of 6 patients with this rare form of congenital T-cell lymphopaenia. Known haemtopoeitic- and thymic stromal cell-intrinsic causes have been excluded, and whole genome sequencing (WGS) of their kindreds has been performed. Specific aims and methodology: 1. To identify novel genetic variants causing thymic stromal cell-prompted T-cell lymphopaenia To facilitate the identification of candidate variants, we will develop a searchable platform to allow referencing of disease-segregating variants identified by WGS to existing RNA-seq, ChIP-seq and proteomic datasets generated from human and murine thymic stromal cells at distinct developmental stages over the course of thymus organogenesis. 2. To establish a functional platform to probe the impact of candidate variants/genes on TEC Induced pluripotent stem cells, gene-edited to contain single candidate variants or knockout candidate genes, will be assessed for their ability to differentiate in vitro into TEC progenitors. Ultimately, this programme of research seeks to: 1. Establish diagnostic pathways for undefined congenital T-cell lymphopaenia. 2. Inform patient management, by providing the rationale for thymus transplantation, and genetic counselling. 3. Identify novel genes/pathways important for thymic stromal cell biology.

Lay abstract: To defend against infections, we require an immune system made from different types of white blood cell. Amongst these, T-cells are of critical importance. As well as directly killing infected cells, T-cells coordinate the responses of other immune cells in the fight against invading microbes. White blood cells originate in the bone marrow but T-cells further mature and acquire their abilities to combat infections within the thymus, a specialised organ located behind the breastbone. Severe congenital T-cell deficiencies, are a rare group of genetic disorders in which T-cells fail to develop. Affected children are highly susceptible to infections, which can be life-threatening. Many T-cell deficiencies are due to problems with white blood cells themselves, so can be cured with bone marrow transplantation. However, if the underlying problem is with thymic development, a thymus transplant is required instead. We have identified a small group of patients with congenital T-cell deficiencies that bone marrow transplantation has been unable to cure. Therefore, we suspect a problem with thymic development. Initial tests have ruled out known genetic causes, so this project aims to identify new genetic causes underlying their thymic defects. This will give the patients accurate genetic diagnoses, an understanding of the risks of passing the condition on to children, and may guide treatment by making a case for thymus transplantation. This work will also help us to develop diagnostic pathways for future cases, which are likely to be increasingly identified as awareness of these conditions increases and screening programmes are introduced.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS